10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
16 if version_info >= (2, 6, 0):
17 def swig_import_helper():
18 from os.path
import dirname
22 fp, pathname, description = imp.find_module(
'_IMP_atom', [dirname(__file__)])
28 _mod = imp.load_module(
'_IMP_atom', fp, pathname, description)
32 _IMP_atom = swig_import_helper()
33 del swig_import_helper
38 _swig_property = property
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44 if (name ==
"thisown"):
45 return self.this.own(value)
47 if type(value).__name__ ==
'SwigPyObject':
48 self.__dict__[name] = value
50 method = class_type.__swig_setmethods__.get(name,
None)
52 return method(self, value)
54 object.__setattr__(self, name, value)
56 raise AttributeError(
"You cannot add attributes to %s" % self)
59 def _swig_setattr(self, class_type, name, value):
60 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
63 def _swig_getattr_nondynamic(self, class_type, name, static=1):
64 if (name ==
"thisown"):
65 return self.this.own()
66 method = class_type.__swig_getmethods__.get(name,
None)
70 return object.__getattr__(self, name)
72 raise AttributeError(name)
74 def _swig_getattr(self, class_type, name):
75 return _swig_getattr_nondynamic(self, class_type, name, 0)
80 strthis =
"proxy of " + self.this.__repr__()
83 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
88 except AttributeError:
95 def _swig_setattr_nondynamic_method(set):
96 def set_attr(self, name, value):
97 if (name ==
"thisown"):
98 return self.this.own(value)
99 if hasattr(self, name)
or (name ==
"this"):
100 set(self, name, value)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
110 weakref_proxy =
lambda x: x
113 class IMP_ATOM_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_ATOM_SwigPyIterator class"""
115 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
117 def __init__(self, *args, **kwargs):
118 raise AttributeError(
"No constructor defined - class is abstract")
119 __repr__ = _swig_repr
120 __swig_destroy__ = _IMP_atom.delete_IMP_ATOM_SwigPyIterator
121 __del__ =
lambda self:
None
124 """value(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
125 return _IMP_atom.IMP_ATOM_SwigPyIterator_value(self)
130 incr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
131 incr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
133 return _IMP_atom.IMP_ATOM_SwigPyIterator_incr(self, n)
138 decr(IMP_ATOM_SwigPyIterator self, size_t n=1) -> IMP_ATOM_SwigPyIterator
139 decr(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator
141 return _IMP_atom.IMP_ATOM_SwigPyIterator_decr(self, n)
144 def distance(self, x):
145 """distance(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t"""
146 return _IMP_atom.IMP_ATOM_SwigPyIterator_distance(self, x)
150 """equal(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
151 return _IMP_atom.IMP_ATOM_SwigPyIterator_equal(self, x)
155 """copy(IMP_ATOM_SwigPyIterator self) -> IMP_ATOM_SwigPyIterator"""
156 return _IMP_atom.IMP_ATOM_SwigPyIterator_copy(self)
160 """next(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
161 return _IMP_atom.IMP_ATOM_SwigPyIterator_next(self)
165 """__next__(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
166 return _IMP_atom.IMP_ATOM_SwigPyIterator___next__(self)
170 """previous(IMP_ATOM_SwigPyIterator self) -> PyObject *"""
171 return _IMP_atom.IMP_ATOM_SwigPyIterator_previous(self)
174 def advance(self, n):
175 """advance(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
176 return _IMP_atom.IMP_ATOM_SwigPyIterator_advance(self, n)
180 """__eq__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
181 return _IMP_atom.IMP_ATOM_SwigPyIterator___eq__(self, x)
185 """__ne__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> bool"""
186 return _IMP_atom.IMP_ATOM_SwigPyIterator___ne__(self, x)
189 def __iadd__(self, n):
190 """__iadd__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
191 return _IMP_atom.IMP_ATOM_SwigPyIterator___iadd__(self, n)
194 def __isub__(self, n):
195 """__isub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
196 return _IMP_atom.IMP_ATOM_SwigPyIterator___isub__(self, n)
199 def __add__(self, n):
200 """__add__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator"""
201 return _IMP_atom.IMP_ATOM_SwigPyIterator___add__(self, n)
204 def __sub__(self, *args):
206 __sub__(IMP_ATOM_SwigPyIterator self, ptrdiff_t n) -> IMP_ATOM_SwigPyIterator
207 __sub__(IMP_ATOM_SwigPyIterator self, IMP_ATOM_SwigPyIterator x) -> ptrdiff_t
209 return _IMP_atom.IMP_ATOM_SwigPyIterator___sub__(self, *args)
213 IMP_ATOM_SwigPyIterator_swigregister = _IMP_atom.IMP_ATOM_SwigPyIterator_swigregister
214 IMP_ATOM_SwigPyIterator_swigregister(IMP_ATOM_SwigPyIterator)
223 _IMP_atom.IMP_DEBUG_swigconstant(_IMP_atom)
224 IMP_DEBUG = _IMP_atom.IMP_DEBUG
226 _IMP_atom.IMP_RELEASE_swigconstant(_IMP_atom)
227 IMP_RELEASE = _IMP_atom.IMP_RELEASE
229 _IMP_atom.IMP_SILENT_swigconstant(_IMP_atom)
230 IMP_SILENT = _IMP_atom.IMP_SILENT
232 _IMP_atom.IMP_PROGRESS_swigconstant(_IMP_atom)
233 IMP_PROGRESS = _IMP_atom.IMP_PROGRESS
235 _IMP_atom.IMP_TERSE_swigconstant(_IMP_atom)
236 IMP_TERSE = _IMP_atom.IMP_TERSE
238 _IMP_atom.IMP_VERBOSE_swigconstant(_IMP_atom)
239 IMP_VERBOSE = _IMP_atom.IMP_VERBOSE
241 _IMP_atom.IMP_MEMORY_swigconstant(_IMP_atom)
242 IMP_MEMORY = _IMP_atom.IMP_MEMORY
244 _IMP_atom.IMP_NONE_swigconstant(_IMP_atom)
245 IMP_NONE = _IMP_atom.IMP_NONE
247 _IMP_atom.IMP_USAGE_swigconstant(_IMP_atom)
248 IMP_USAGE = _IMP_atom.IMP_USAGE
250 _IMP_atom.IMP_INTERNAL_swigconstant(_IMP_atom)
251 IMP_INTERNAL = _IMP_atom.IMP_INTERNAL
253 _IMP_atom.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_atom)
254 IMP_KERNEL_HAS_LOG4CXX = _IMP_atom.IMP_KERNEL_HAS_LOG4CXX
256 _IMP_atom.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_atom)
257 IMP_COMPILER_HAS_AUTO = _IMP_atom.IMP_COMPILER_HAS_AUTO
259 _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_atom)
260 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_atom.IMP_COMPILER_HAS_DEBUG_VECTOR
262 _IMP_atom.IMP_COMPILER_HAS_UNIQUE_PTR_swigconstant(_IMP_atom)
263 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_atom.IMP_COMPILER_HAS_UNIQUE_PTR
265 _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
266 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_atom.IMP_KERNEL_HAS_BOOST_RANDOM
268 _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_atom)
269 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_atom.IMP_KERNEL_HAS_GPERFTOOLS
271 _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_atom)
272 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
274 _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_atom)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_atom.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
277 _IMP_atom.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_atom)
278 IMPKERNEL_SHOW_WARNINGS = _IMP_atom.IMPKERNEL_SHOW_WARNINGS
281 class _DirectorObjects(object):
282 """@internal Simple class to keep references to director objects
283 to prevent premature deletion."""
286 def register(self, obj):
287 """Take a reference to a director object; will only work for
288 refcounted C++ classes"""
289 if hasattr(obj,
'get_ref_count'):
290 self._objects.append(obj)
292 """Only drop our reference and allow cleanup by Python if no other
293 Python references exist (we hold 3 references: one in self._objects,
294 one in x, and one in the argument list for getrefcount) *and* no
295 other C++ references exist (the Python object always holds one)"""
296 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
297 or x.get_ref_count() > 1]
301 def get_object_count(self):
302 """Get number of director objects (useful for testing only)"""
303 return len(self._objects)
304 _director_objects = _DirectorObjects()
306 class _ostream(object):
307 """Proxy of C++ std::ostream class"""
308 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
310 def __init__(self, *args, **kwargs):
311 raise AttributeError(
"No constructor defined")
312 __repr__ = _swig_repr
314 def write(self, osa_buf):
315 """write(_ostream self, char const * osa_buf)"""
316 return _IMP_atom._ostream_write(self, osa_buf)
318 _ostream_swigregister = _IMP_atom._ostream_swigregister
319 _ostream_swigregister(_ostream)
322 _IMP_atom.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_atom)
323 IMP_COMPILER_HAS_OVERRIDE = _IMP_atom.IMP_COMPILER_HAS_OVERRIDE
325 _IMP_atom.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_atom)
326 IMP_COMPILER_HAS_FINAL = _IMP_atom.IMP_COMPILER_HAS_FINAL
328 _IMP_atom.IMP_HAS_NOEXCEPT_swigconstant(_IMP_atom)
329 IMP_HAS_NOEXCEPT = _IMP_atom.IMP_HAS_NOEXCEPT
332 _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
333 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_FILESYSTEM
335 _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
336 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
338 _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
339 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_atom.IMP_CGAL_HAS_BOOST_RANDOM
341 _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
342 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CGAL_HAS_BOOST_SYSTEM
344 _IMP_atom.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_atom)
345 IMPCGAL_SHOW_WARNINGS = _IMP_atom.IMPCGAL_SHOW_WARNINGS
348 _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_atom)
349 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_IMP_CGAL
351 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
352 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
354 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
355 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
357 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
358 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_RANDOM
360 _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
361 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ALGEBRA_HAS_BOOST_SYSTEM
363 _IMP_atom.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_atom)
364 IMP_ALGEBRA_HAS_CGAL = _IMP_atom.IMP_ALGEBRA_HAS_CGAL
366 _IMP_atom.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_atom)
367 IMP_ALGEBRA_HAS_ANN = _IMP_atom.IMP_ALGEBRA_HAS_ANN
369 _IMP_atom.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_atom)
370 IMPALGEBRA_SHOW_WARNINGS = _IMP_atom.IMPALGEBRA_SHOW_WARNINGS
373 _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_atom)
374 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_atom.IMP_DISPLAY_HAS_IMP_CGAL
376 _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
377 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
379 _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
380 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
382 _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
383 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_RANDOM
385 _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
386 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_atom.IMP_DISPLAY_HAS_BOOST_SYSTEM
388 _IMP_atom.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_atom)
389 IMP_DISPLAY_HAS_CGAL = _IMP_atom.IMP_DISPLAY_HAS_CGAL
391 _IMP_atom.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_atom)
392 IMPDISPLAY_SHOW_WARNINGS = _IMP_atom.IMPDISPLAY_SHOW_WARNINGS
395 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_atom)
396 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
398 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
399 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
401 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
402 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
404 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
405 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
407 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
408 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
410 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_atom)
411 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_CGAL
413 _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_atom)
414 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_atom.IMP_SCORE_FUNCTOR_HAS_HDF5
416 _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_atom)
417 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_atom.IMPSCOREFUNCTOR_SHOW_WARNINGS
420 _IMP_atom.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_atom)
421 IMP_CORE_HAS_IMP_CGAL = _IMP_atom.IMP_CORE_HAS_IMP_CGAL
423 _IMP_atom.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_atom)
424 IMP_CORE_HAS_IMP_KERNEL = _IMP_atom.IMP_CORE_HAS_IMP_KERNEL
426 _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
427 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_FILESYSTEM
429 _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
430 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
432 _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
433 IMP_CORE_HAS_BOOST_RANDOM = _IMP_atom.IMP_CORE_HAS_BOOST_RANDOM
435 _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
436 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CORE_HAS_BOOST_SYSTEM
438 _IMP_atom.IMP_CORE_HAS_CGAL_swigconstant(_IMP_atom)
439 IMP_CORE_HAS_CGAL = _IMP_atom.IMP_CORE_HAS_CGAL
441 _IMP_atom.IMP_CORE_HAS_HDF5_swigconstant(_IMP_atom)
442 IMP_CORE_HAS_HDF5 = _IMP_atom.IMP_CORE_HAS_HDF5
444 _IMP_atom.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_atom)
445 IMPCORE_SHOW_WARNINGS = _IMP_atom.IMPCORE_SHOW_WARNINGS
448 _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_atom)
449 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_atom.IMP_CONTAINER_HAS_IMP_ALGEBRA
451 _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_atom)
452 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_atom.IMP_CONTAINER_HAS_IMP_CGAL
454 _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_atom)
455 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_atom.IMP_CONTAINER_HAS_IMP_DISPLAY
457 _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_atom)
458 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_atom.IMP_CONTAINER_HAS_IMP_KERNEL
460 _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_atom)
461 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
463 _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_atom)
464 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
466 _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
467 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
469 _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
470 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_RANDOM
472 _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
473 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_atom.IMP_CONTAINER_HAS_BOOST_SYSTEM
475 _IMP_atom.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_atom)
476 IMP_CONTAINER_HAS_CGAL = _IMP_atom.IMP_CONTAINER_HAS_CGAL
478 _IMP_atom.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_atom)
479 IMP_CONTAINER_HAS_HDF5 = _IMP_atom.IMP_CONTAINER_HAS_HDF5
481 _IMP_atom.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_atom)
482 IMPCONTAINER_SHOW_WARNINGS = _IMP_atom.IMPCONTAINER_SHOW_WARNINGS
485 _IMP_atom.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_atom)
486 IMP_ATOM_HAS_IMP_CGAL = _IMP_atom.IMP_ATOM_HAS_IMP_CGAL
488 _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_atom)
489 IMP_ATOM_HAS_IMP_KERNEL = _IMP_atom.IMP_ATOM_HAS_IMP_KERNEL
491 _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_atom)
492 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_atom.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
494 _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_atom)
495 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_atom.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
497 _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_atom)
498 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_atom.IMP_ATOM_HAS_BOOST_RANDOM
500 _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_atom)
501 IMP_ATOM_HAS_BOOST_REGEX = _IMP_atom.IMP_ATOM_HAS_BOOST_REGEX
503 _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_atom)
504 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_atom.IMP_ATOM_HAS_BOOST_SYSTEM
506 _IMP_atom.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_atom)
507 IMP_ATOM_HAS_CGAL = _IMP_atom.IMP_ATOM_HAS_CGAL
509 _IMP_atom.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_atom)
510 IMP_ATOM_HAS_HDF5 = _IMP_atom.IMP_ATOM_HAS_HDF5
512 _IMP_atom.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_atom)
513 IMPATOM_SHOW_WARNINGS = _IMP_atom.IMPATOM_SHOW_WARNINGS
515 _IMP_atom.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_atom)
516 IMP_ATOM_TYPE_INDEX = _IMP_atom.IMP_ATOM_TYPE_INDEX
518 _IMP_atom.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_atom)
519 IMP_RESIDUE_TYPE_INDEX = _IMP_atom.IMP_RESIDUE_TYPE_INDEX
521 _IMP_atom.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_atom)
522 IMP_HIERARCHY_TYPE_INDEX = _IMP_atom.IMP_HIERARCHY_TYPE_INDEX
524 """Proxy of C++ IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> class"""
525 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
526 __repr__ = _swig_repr
529 """__init__(IMP::internal::BoostDigraph<(IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex)> self) -> HierarchyTree"""
530 this = _IMP_atom.new_HierarchyTree()
532 self.this.append(this)
537 """get_graph(HierarchyTree self) -> IMP::atom::HierarchyTree const &"""
538 return _IMP_atom.HierarchyTree_get_graph(self)
542 """get_vertices(HierarchyTree self) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
543 return _IMP_atom.HierarchyTree_get_vertices(self)
546 def get_vertex_name(self, i):
547 """get_vertex_name(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor i) -> Hierarchy"""
548 return _IMP_atom.HierarchyTree_get_vertex_name(self, i)
551 def get_in_neighbors(self, v):
552 """get_in_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
553 return _IMP_atom.HierarchyTree_get_in_neighbors(self, v)
556 def get_out_neighbors(self, v):
557 """get_out_neighbors(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptors"""
558 return _IMP_atom.HierarchyTree_get_out_neighbors(self, v)
563 show_graphviz(HierarchyTree self, _ostream out)
564 show_graphviz(HierarchyTree self)
566 return _IMP_atom.HierarchyTree_show_graphviz(self, *args)
569 def get_graphviz_string(self):
570 """get_graphviz_string(HierarchyTree self) -> std::string"""
571 return _IMP_atom.HierarchyTree_get_graphviz_string(self)
574 def add_edge(self, v0, v1):
575 """add_edge(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v0, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor v1)"""
576 return _IMP_atom.HierarchyTree_add_edge(self, v0, v1)
579 def add_vertex(self, l):
580 """add_vertex(HierarchyTree self, Hierarchy l) -> IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor"""
581 return _IMP_atom.HierarchyTree_add_vertex(self, l)
584 def remove_vertex(self, l):
585 """remove_vertex(HierarchyTree self, IMP::internal::BoostDigraph< IMP::atom::HierarchyTree,IMP::atom::Hierarchy,IMP::atom::ShowHierarchyTreeVertex >::VertexDescriptor l)"""
586 return _IMP_atom.HierarchyTree_remove_vertex(self, l)
588 __swig_destroy__ = _IMP_atom.delete_HierarchyTree
589 __del__ =
lambda self:
None
590 HierarchyTree_swigregister = _IMP_atom.HierarchyTree_swigregister
591 HierarchyTree_swigregister(HierarchyTree)
594 _value_types.append(
"HierarchyTree")
597 _object_types.append(
"PDBSelector")
600 def _object_cast_to_PDBSelector(o):
601 """_object_cast_to_PDBSelector(Object o) -> PDBSelector"""
602 return _IMP_atom._object_cast_to_PDBSelector(o)
605 return [Angle(x)
for x
in l]
606 _plural_types.append(
"Angles")
609 _value_types.append(
"Angle")
613 return [Atom(x)
for x
in l]
614 _plural_types.append(
"Atoms")
617 _value_types.append(
"Atom")
621 return [Bond(x)
for x
in l]
622 _plural_types.append(
"Bonds")
625 _value_types.append(
"Bond")
629 return [Bonded(x)
for x
in l]
630 _plural_types.append(
"Bondeds")
633 _value_types.append(
"Bonded")
636 def CHARMMAtomList(l=[]):
637 return [CHARMMAtom(x)
for x
in l]
638 _plural_types.append(
"CHARMMAtomList")
641 _value_types.append(
"CHARMMAtom")
645 return [Chain(x)
for x
in l]
646 _plural_types.append(
"Chains")
649 _value_types.append(
"Chain")
652 def CenterOfMasses(l=[]):
653 return [CenterOfMass(x)
for x
in l]
654 _plural_types.append(
"CenterOfMasses")
657 _value_types.append(
"CenterOfMass")
661 return [Charged(x)
for x
in l]
662 _plural_types.append(
"Chargeds")
665 _value_types.append(
"Charged")
668 def Diffusions(l=[]):
669 return [Diffusion(x)
for x
in l]
670 _plural_types.append(
"Diffusions")
673 _value_types.append(
"Diffusion")
676 def RigidBodyDiffusions(l=[]):
677 return [RigidBodyDiffusion(x)
for x
in l]
678 _plural_types.append(
"RigidBodyDiffusions")
681 _value_types.append(
"RigidBodyDiffusion")
684 def TAMDParticles(l=[]):
685 return [TAMDParticle(x)
for x
in l]
686 _plural_types.append(
"TAMDParticles")
689 _value_types.append(
"TAMDParticle")
692 def TAMDCentroids(l=[]):
693 return [TAMDCentroid(x)
for x
in l]
694 _plural_types.append(
"TAMDCentroids")
697 _value_types.append(
"TAMDCentroid")
701 return [Dihedral(x)
for x
in l]
702 _plural_types.append(
"Dihedrals")
705 _value_types.append(
"Dihedral")
709 return [Domain(x)
for x
in l]
710 _plural_types.append(
"Domains")
713 _value_types.append(
"Domain")
717 return [Fragment(x)
for x
in l]
718 _plural_types.append(
"Fragments")
721 _value_types.append(
"Fragment")
724 def Hierarchies(l=[]):
725 return [Hierarchy(x)
for x
in l]
726 _plural_types.append(
"Hierarchies")
729 _value_types.append(
"Hierarchy")
732 def LennardJonesList(l=[]):
733 return [LennardJones(x)
for x
in l]
734 _plural_types.append(
"LennardJonesList")
737 _value_types.append(
"LennardJones")
741 return [Mass(x)
for x
in l]
742 _plural_types.append(
"Masses")
745 _value_types.append(
"Mass")
748 def LinearVelocities(l=[]):
749 return [LinearVelocity(x)
for x
in l]
750 _plural_types.append(
"LinearVelocities")
753 _value_types.append(
"LinearVelocity")
756 def AngularVelocities(l=[]):
757 return [AngularVelocity(x)
for x
in l]
758 _plural_types.append(
"AngularVelocities")
761 _value_types.append(
"AngularVelocity")
765 return [Molecule(x)
for x
in l]
766 _plural_types.append(
"Molecules")
769 _value_types.append(
"Molecule")
773 return [Residue(x)
for x
in l]
774 _plural_types.append(
"Residues")
777 _value_types.append(
"Residue")
780 def Representations(l=[]):
781 return [Representation(x)
for x
in l]
782 _plural_types.append(
"Representations")
785 _value_types.append(
"Representation")
789 return [State(x)
for x
in l]
790 _plural_types.append(
"States")
793 _value_types.append(
"State")
797 return [Copy(x)
for x
in l]
798 _plural_types.append(
"Copies")
801 _value_types.append(
"Copy")
804 def SecondaryStructureResidues(l=[]):
805 return [SecondaryStructureResidue(x)
for x
in l]
806 _plural_types.append(
"SecondaryStructureResidues")
809 _value_types.append(
"SecondaryStructureResidue")
812 def StructureSources(l=[]):
813 return [StructureSource(x)
for x
in l]
814 _plural_types.append(
"StructureSources")
817 _value_types.append(
"StructureSource")
820 _object_types.append(
"Simulator")
823 def _object_cast_to_Simulator(o):
824 """_object_cast_to_Simulator(Object o) -> Simulator"""
825 return _IMP_atom._object_cast_to_Simulator(o)
827 _object_types.append(
"ATOMPDBSelector")
830 def _object_cast_to_ATOMPDBSelector(o):
831 """_object_cast_to_ATOMPDBSelector(Object o) -> ATOMPDBSelector"""
832 return _IMP_atom._object_cast_to_ATOMPDBSelector(o)
834 _object_types.append(
"AllMol2Selector")
837 def _object_cast_to_AllMol2Selector(o):
838 """_object_cast_to_AllMol2Selector(Object o) -> AllMol2Selector"""
839 return _IMP_atom._object_cast_to_AllMol2Selector(o)
841 _object_types.append(
"AllPDBSelector")
844 def _object_cast_to_AllPDBSelector(o):
845 """_object_cast_to_AllPDBSelector(Object o) -> AllPDBSelector"""
846 return _IMP_atom._object_cast_to_AllPDBSelector(o)
848 _object_types.append(
"AndPDBSelector")
851 def _object_cast_to_AndPDBSelector(o):
852 """_object_cast_to_AndPDBSelector(Object o) -> AndPDBSelector"""
853 return _IMP_atom._object_cast_to_AndPDBSelector(o)
855 _object_types.append(
"XorPDBSelector")
858 def _object_cast_to_XorPDBSelector(o):
859 """_object_cast_to_XorPDBSelector(Object o) -> XorPDBSelector"""
860 return _IMP_atom._object_cast_to_XorPDBSelector(o)
862 _object_types.append(
"ResidueTypePDBSelector")
865 def _object_cast_to_ResidueTypePDBSelector(o):
866 """_object_cast_to_ResidueTypePDBSelector(Object o) -> ResidueTypePDBSelector"""
867 return _IMP_atom._object_cast_to_ResidueTypePDBSelector(o)
869 _object_types.append(
"AtomTypePDBSelector")
872 def _object_cast_to_AtomTypePDBSelector(o):
873 """_object_cast_to_AtomTypePDBSelector(Object o) -> AtomTypePDBSelector"""
874 return _IMP_atom._object_cast_to_AtomTypePDBSelector(o)
876 _object_types.append(
"AngleSingletonScore")
879 def _object_cast_to_AngleSingletonScore(o):
880 """_object_cast_to_AngleSingletonScore(Object o) -> AngleSingletonScore"""
881 return _IMP_atom._object_cast_to_AngleSingletonScore(o)
883 _object_types.append(
"BondEndpointsRefiner")
886 def _object_cast_to_BondEndpointsRefiner(o):
887 """_object_cast_to_BondEndpointsRefiner(Object o) -> BondEndpointsRefiner"""
888 return _IMP_atom._object_cast_to_BondEndpointsRefiner(o)
890 _object_types.append(
"BondPairContainer")
893 def _object_cast_to_BondPairContainer(o):
894 """_object_cast_to_BondPairContainer(Object o) -> BondPairContainer"""
895 return _IMP_atom._object_cast_to_BondPairContainer(o)
897 _object_types.append(
"BondSingletonScore")
900 def _object_cast_to_BondSingletonScore(o):
901 """_object_cast_to_BondSingletonScore(Object o) -> BondSingletonScore"""
902 return _IMP_atom._object_cast_to_BondSingletonScore(o)
904 _object_types.append(
"BondedPairFilter")
907 def _object_cast_to_BondedPairFilter(o):
908 """_object_cast_to_BondedPairFilter(Object o) -> BondedPairFilter"""
909 return _IMP_atom._object_cast_to_BondedPairFilter(o)
911 _object_types.append(
"BrownianDynamics")
914 def _object_cast_to_BrownianDynamics(o):
915 """_object_cast_to_BrownianDynamics(Object o) -> BrownianDynamics"""
916 return _IMP_atom._object_cast_to_BrownianDynamics(o)
918 _object_types.append(
"BrownianDynamicsTAMD")
921 def _object_cast_to_BrownianDynamicsTAMD(o):
922 """_object_cast_to_BrownianDynamicsTAMD(Object o) -> BrownianDynamicsTAMD"""
923 return _IMP_atom._object_cast_to_BrownianDynamicsTAMD(o)
925 _object_types.append(
"CAlphaPDBSelector")
928 def _object_cast_to_CAlphaPDBSelector(o):
929 """_object_cast_to_CAlphaPDBSelector(Object o) -> CAlphaPDBSelector"""
930 return _IMP_atom._object_cast_to_CAlphaPDBSelector(o)
932 _object_types.append(
"CBetaPDBSelector")
935 def _object_cast_to_CBetaPDBSelector(o):
936 """_object_cast_to_CBetaPDBSelector(Object o) -> CBetaPDBSelector"""
937 return _IMP_atom._object_cast_to_CBetaPDBSelector(o)
939 _object_types.append(
"BackbonePDBSelector")
942 def _object_cast_to_BackbonePDBSelector(o):
943 """_object_cast_to_BackbonePDBSelector(Object o) -> BackbonePDBSelector"""
944 return _IMP_atom._object_cast_to_BackbonePDBSelector(o)
946 _object_types.append(
"CHARMMParameters")
949 def _object_cast_to_CHARMMParameters(o):
950 """_object_cast_to_CHARMMParameters(Object o) -> CHARMMParameters"""
951 return _IMP_atom._object_cast_to_CHARMMParameters(o)
953 _object_types.append(
"CHARMMResidueTopology")
956 def _object_cast_to_CHARMMResidueTopology(o):
957 """_object_cast_to_CHARMMResidueTopology(Object o) -> CHARMMResidueTopology"""
958 return _IMP_atom._object_cast_to_CHARMMResidueTopology(o)
960 _object_types.append(
"CHARMMSegmentTopology")
963 def _object_cast_to_CHARMMSegmentTopology(o):
964 """_object_cast_to_CHARMMSegmentTopology(Object o) -> CHARMMSegmentTopology"""
965 return _IMP_atom._object_cast_to_CHARMMSegmentTopology(o)
967 _object_types.append(
"CHARMMStereochemistryRestraint")
970 def _object_cast_to_CHARMMStereochemistryRestraint(o):
971 """_object_cast_to_CHARMMStereochemistryRestraint(Object o) -> CHARMMStereochemistryRestraint"""
972 return _IMP_atom._object_cast_to_CHARMMStereochemistryRestraint(o)
974 _object_types.append(
"CHARMMTopology")
977 def _object_cast_to_CHARMMTopology(o):
978 """_object_cast_to_CHARMMTopology(Object o) -> CHARMMTopology"""
979 return _IMP_atom._object_cast_to_CHARMMTopology(o)
981 _object_types.append(
"CPDBSelector")
984 def _object_cast_to_CPDBSelector(o):
985 """_object_cast_to_CPDBSelector(Object o) -> CPDBSelector"""
986 return _IMP_atom._object_cast_to_CPDBSelector(o)
988 _object_types.append(
"ChainPDBSelector")
991 def _object_cast_to_ChainPDBSelector(o):
992 """_object_cast_to_ChainPDBSelector(Object o) -> ChainPDBSelector"""
993 return _IMP_atom._object_cast_to_ChainPDBSelector(o)
995 _object_types.append(
"CoulombPairScore")
998 def _object_cast_to_CoulombPairScore(o):
999 """_object_cast_to_CoulombPairScore(Object o) -> CoulombPairScore"""
1000 return _IMP_atom._object_cast_to_CoulombPairScore(o)
1002 _object_types.append(
"CoverBond")
1005 def _object_cast_to_CoverBond(o):
1006 """_object_cast_to_CoverBond(Object o) -> CoverBond"""
1007 return _IMP_atom._object_cast_to_CoverBond(o)
1009 _object_types.append(
"DihedralSingletonScore")
1012 def _object_cast_to_DihedralSingletonScore(o):
1013 """_object_cast_to_DihedralSingletonScore(Object o) -> DihedralSingletonScore"""
1014 return _IMP_atom._object_cast_to_DihedralSingletonScore(o)
1016 _object_types.append(
"DopePairScore")
1019 def _object_cast_to_DopePairScore(o):
1020 """_object_cast_to_DopePairScore(Object o) -> DopePairScore"""
1021 return _IMP_atom._object_cast_to_DopePairScore(o)
1023 _object_types.append(
"OrientedSoapPairScore")
1026 def _object_cast_to_OrientedSoapPairScore(o):
1027 """_object_cast_to_OrientedSoapPairScore(Object o) -> OrientedSoapPairScore"""
1028 return _IMP_atom._object_cast_to_OrientedSoapPairScore(o)
1030 _object_types.append(
"EzRestraint")
1033 def _object_cast_to_EzRestraint(o):
1034 """_object_cast_to_EzRestraint(Object o) -> EzRestraint"""
1035 return _IMP_atom._object_cast_to_EzRestraint(o)
1037 _object_types.append(
"ForceFieldParameters")
1040 def _object_cast_to_ForceFieldParameters(o):
1041 """_object_cast_to_ForceFieldParameters(Object o) -> ForceFieldParameters"""
1042 return _IMP_atom._object_cast_to_ForceFieldParameters(o)
1044 _object_types.append(
"ForceSwitch")
1047 def _object_cast_to_ForceSwitch(o):
1048 """_object_cast_to_ForceSwitch(Object o) -> ForceSwitch"""
1049 return _IMP_atom._object_cast_to_ForceSwitch(o)
1051 _object_types.append(
"HydrogenPDBSelector")
1054 def _object_cast_to_HydrogenPDBSelector(o):
1055 """_object_cast_to_HydrogenPDBSelector(Object o) -> HydrogenPDBSelector"""
1056 return _IMP_atom._object_cast_to_HydrogenPDBSelector(o)
1058 _object_types.append(
"ImproperSingletonScore")
1061 def _object_cast_to_ImproperSingletonScore(o):
1062 """_object_cast_to_ImproperSingletonScore(Object o) -> ImproperSingletonScore"""
1063 return _IMP_atom._object_cast_to_ImproperSingletonScore(o)
1065 _object_types.append(
"LennardJonesPairScore")
1068 def _object_cast_to_LennardJonesPairScore(o):
1069 """_object_cast_to_LennardJonesPairScore(Object o) -> LennardJonesPairScore"""
1070 return _IMP_atom._object_cast_to_LennardJonesPairScore(o)
1072 _object_types.append(
"Mol2Selector")
1075 def _object_cast_to_Mol2Selector(o):
1076 """_object_cast_to_Mol2Selector(Object o) -> Mol2Selector"""
1077 return _IMP_atom._object_cast_to_Mol2Selector(o)
1079 _object_types.append(
"MolecularDynamics")
1082 def _object_cast_to_MolecularDynamics(o):
1083 """_object_cast_to_MolecularDynamics(Object o) -> MolecularDynamics"""
1084 return _IMP_atom._object_cast_to_MolecularDynamics(o)
1086 _object_types.append(
"NPDBSelector")
1089 def _object_cast_to_NPDBSelector(o):
1090 """_object_cast_to_NPDBSelector(Object o) -> NPDBSelector"""
1091 return _IMP_atom._object_cast_to_NPDBSelector(o)
1093 _object_types.append(
"NonAlternativePDBSelector")
1096 def _object_cast_to_NonAlternativePDBSelector(o):
1097 """_object_cast_to_NonAlternativePDBSelector(Object o) -> NonAlternativePDBSelector"""
1098 return _IMP_atom._object_cast_to_NonAlternativePDBSelector(o)
1100 _object_types.append(
"NonHydrogenMol2Selector")
1103 def _object_cast_to_NonHydrogenMol2Selector(o):
1104 """_object_cast_to_NonHydrogenMol2Selector(Object o) -> NonHydrogenMol2Selector"""
1105 return _IMP_atom._object_cast_to_NonHydrogenMol2Selector(o)
1107 _object_types.append(
"NonWaterNonHydrogenPDBSelector")
1110 def _object_cast_to_NonWaterNonHydrogenPDBSelector(o):
1111 """_object_cast_to_NonWaterNonHydrogenPDBSelector(Object o) -> NonWaterNonHydrogenPDBSelector"""
1112 return _IMP_atom._object_cast_to_NonWaterNonHydrogenPDBSelector(o)
1114 _object_types.append(
"NonWaterPDBSelector")
1117 def _object_cast_to_NonWaterPDBSelector(o):
1118 """_object_cast_to_NonWaterPDBSelector(Object o) -> NonWaterPDBSelector"""
1119 return _IMP_atom._object_cast_to_NonWaterPDBSelector(o)
1121 _object_types.append(
"NotPDBSelector")
1124 def _object_cast_to_NotPDBSelector(o):
1125 """_object_cast_to_NotPDBSelector(Object o) -> NotPDBSelector"""
1126 return _IMP_atom._object_cast_to_NotPDBSelector(o)
1128 _object_types.append(
"OrPDBSelector")
1131 def _object_cast_to_OrPDBSelector(o):
1132 """_object_cast_to_OrPDBSelector(Object o) -> OrPDBSelector"""
1133 return _IMP_atom._object_cast_to_OrPDBSelector(o)
1135 _object_types.append(
"PPDBSelector")
1138 def _object_cast_to_PPDBSelector(o):
1139 """_object_cast_to_PPDBSelector(Object o) -> PPDBSelector"""
1140 return _IMP_atom._object_cast_to_PPDBSelector(o)
1142 _object_types.append(
"ProteinLigandAtomPairScore")
1145 def _object_cast_to_ProteinLigandAtomPairScore(o):
1146 """_object_cast_to_ProteinLigandAtomPairScore(Object o) -> ProteinLigandAtomPairScore"""
1147 return _IMP_atom._object_cast_to_ProteinLigandAtomPairScore(o)
1149 _object_types.append(
"ProteinLigandRestraint")
1152 def _object_cast_to_ProteinLigandRestraint(o):
1153 """_object_cast_to_ProteinLigandRestraint(Object o) -> ProteinLigandRestraint"""
1154 return _IMP_atom._object_cast_to_ProteinLigandRestraint(o)
1156 _object_types.append(
"SameResiduePairFilter")
1159 def _object_cast_to_SameResiduePairFilter(o):
1160 """_object_cast_to_SameResiduePairFilter(Object o) -> SameResiduePairFilter"""
1161 return _IMP_atom._object_cast_to_SameResiduePairFilter(o)
1163 _object_types.append(
"SoapPairFilter")
1166 def _object_cast_to_SoapPairFilter(o):
1167 """_object_cast_to_SoapPairFilter(Object o) -> SoapPairFilter"""
1168 return _IMP_atom._object_cast_to_SoapPairFilter(o)
1170 _object_types.append(
"SmoothingFunction")
1173 def _object_cast_to_SmoothingFunction(o):
1174 """_object_cast_to_SmoothingFunction(Object o) -> SmoothingFunction"""
1175 return _IMP_atom._object_cast_to_SmoothingFunction(o)
1177 _object_types.append(
"StereochemistryPairFilter")
1180 def _object_cast_to_StereochemistryPairFilter(o):
1181 """_object_cast_to_StereochemistryPairFilter(Object o) -> StereochemistryPairFilter"""
1182 return _IMP_atom._object_cast_to_StereochemistryPairFilter(o)
1184 _object_types.append(
"VelocityScalingOptimizerState")
1187 def _object_cast_to_VelocityScalingOptimizerState(o):
1188 """_object_cast_to_VelocityScalingOptimizerState(Object o) -> VelocityScalingOptimizerState"""
1189 return _IMP_atom._object_cast_to_VelocityScalingOptimizerState(o)
1191 _object_types.append(
"WaterPDBSelector")
1194 def _object_cast_to_WaterPDBSelector(o):
1195 """_object_cast_to_WaterPDBSelector(Object o) -> WaterPDBSelector"""
1196 return _IMP_atom._object_cast_to_WaterPDBSelector(o)
1198 _object_types.append(
"WritePDBOptimizerState")
1201 def _object_cast_to_WritePDBOptimizerState(o):
1202 """_object_cast_to_WritePDBOptimizerState(Object o) -> WritePDBOptimizerState"""
1203 return _IMP_atom._object_cast_to_WritePDBOptimizerState(o)
1206 _plural_types.append(
"AtomTypes")
1207 _value_types.append(
"AtomType")
1210 CHARMMAtomTopologies=list
1211 _plural_types.append(
"CHARMMAtomTopologies")
1212 _value_types.append(
"CHARMMAtomTopology")
1215 CHARMMBondEndpoints=list
1216 _plural_types.append(
"CHARMMBondEndpoints")
1217 _value_types.append(
"CHARMMBondEndpoint")
1220 CHARMMBondParametersList=list
1221 _plural_types.append(
"CHARMMBondParametersList")
1222 _value_types.append(
"CHARMMBondParameters")
1225 CHARMMDihedralParametersList=list
1226 _plural_types.append(
"CHARMMDihedralParametersList")
1227 _value_types.append(
"CHARMMDihedralParameters")
1230 _object_types.append(
"CHARMMIdealResidueTopology")
1233 def _object_cast_to_CHARMMIdealResidueTopology(o):
1234 """_object_cast_to_CHARMMIdealResidueTopology(Object o) -> CHARMMIdealResidueTopology"""
1235 return _IMP_atom._object_cast_to_CHARMMIdealResidueTopology(o)
1237 CHARMMInternalCoordinates=list
1238 _plural_types.append(
"CHARMMInternalCoordinates")
1239 _value_types.append(
"CHARMMInternalCoordinate")
1242 _object_types.append(
"CHARMMPatch")
1245 def _object_cast_to_CHARMMPatch(o):
1246 """_object_cast_to_CHARMMPatch(Object o) -> CHARMMPatch"""
1247 return _IMP_atom._object_cast_to_CHARMMPatch(o)
1249 _object_types.append(
"CHARMMResidueTopologyBase")
1252 def _object_cast_to_CHARMMResidueTopologyBase(o):
1253 """_object_cast_to_CHARMMResidueTopologyBase(Object o) -> CHARMMResidueTopologyBase"""
1254 return _IMP_atom._object_cast_to_CHARMMResidueTopologyBase(o)
1257 _plural_types.append(
"ResidueTypes")
1258 _value_types.append(
"ResidueType")
1262 _plural_types.append(
"Selections")
1263 _value_types.append(
"Selection")
1266 _object_types.append(
"RemoveRigidMotionOptimizerState")
1269 def _object_cast_to_RemoveRigidMotionOptimizerState(o):
1270 """_object_cast_to_RemoveRigidMotionOptimizerState(Object o) -> RemoveRigidMotionOptimizerState"""
1271 return _IMP_atom._object_cast_to_RemoveRigidMotionOptimizerState(o)
1273 _object_types.append(
"BerendsenThermostatOptimizerState")
1276 def _object_cast_to_BerendsenThermostatOptimizerState(o):
1277 """_object_cast_to_BerendsenThermostatOptimizerState(Object o) -> BerendsenThermostatOptimizerState"""
1278 return _IMP_atom._object_cast_to_BerendsenThermostatOptimizerState(o)
1280 _object_types.append(
"LangevinThermostatOptimizerState")
1283 def _object_cast_to_LangevinThermostatOptimizerState(o):
1284 """_object_cast_to_LangevinThermostatOptimizerState(Object o) -> LangevinThermostatOptimizerState"""
1285 return _IMP_atom._object_cast_to_LangevinThermostatOptimizerState(o)
1287 _object_types.append(
"SelectionGeometry")
1290 def _object_cast_to_SelectionGeometry(o):
1291 """_object_cast_to_SelectionGeometry(Object o) -> SelectionGeometry"""
1292 return _IMP_atom._object_cast_to_SelectionGeometry(o)
1294 _object_types.append(
"HierarchyGeometry")
1297 def _object_cast_to_HierarchyGeometry(o):
1298 """_object_cast_to_HierarchyGeometry(Object o) -> HierarchyGeometry"""
1299 return _IMP_atom._object_cast_to_HierarchyGeometry(o)
1301 _object_types.append(
"HierarchiesGeometry")
1304 def _object_cast_to_HierarchiesGeometry(o):
1305 """_object_cast_to_HierarchiesGeometry(Object o) -> HierarchiesGeometry"""
1306 return _IMP_atom._object_cast_to_HierarchiesGeometry(o)
1308 _object_types.append(
"BondGeometry")
1311 def _object_cast_to_BondGeometry(o):
1312 """_object_cast_to_BondGeometry(Object o) -> BondGeometry"""
1313 return _IMP_atom._object_cast_to_BondGeometry(o)
1315 _object_types.append(
"BondsGeometry")
1318 def _object_cast_to_BondsGeometry(o):
1319 """_object_cast_to_BondsGeometry(Object o) -> BondsGeometry"""
1320 return _IMP_atom._object_cast_to_BondsGeometry(o)
1322 _object_types.append(
"CAAngleRestraint")
1325 def _object_cast_to_CAAngleRestraint(o):
1326 """_object_cast_to_CAAngleRestraint(Object o) -> CAAngleRestraint"""
1327 return _IMP_atom._object_cast_to_CAAngleRestraint(o)
1329 _object_types.append(
"CADihedralRestraint")
1332 def _object_cast_to_CADihedralRestraint(o):
1333 """_object_cast_to_CADihedralRestraint(Object o) -> CADihedralRestraint"""
1334 return _IMP_atom._object_cast_to_CADihedralRestraint(o)
1336 CHARMMDihedrals=list
1337 _plural_types.append(
"CHARMMDihedrals")
1338 _value_types.append(
"CHARMMDihedral")
1342 _plural_types.append(
"CHARMMBonds")
1343 _value_types.append(
"CHARMMBond")
1347 _plural_types.append(
"CHARMMAngles")
1348 _value_types.append(
"CHARMMAngle")
1351 """Proxy of C++ IMP::atom::Bond class"""
1352 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1354 def __init__(self, *args):
1356 __init__(IMP::atom::Bond self) -> Bond
1357 __init__(IMP::atom::Bond self, Model m, ParticleIndex id) -> Bond
1358 __init__(IMP::atom::Bond self, _ParticleAdaptor d) -> Bond
1360 this = _IMP_atom.new_Bond(*args)
1362 self.this.append(this)
1366 def show(self, *args):
1368 show(Bond self, _ostream out)
1371 return _IMP_atom.Bond_show(self, *args)
1374 def get_is_setup(*args):
1376 get_is_setup(_ParticleAdaptor p) -> bool
1377 get_is_setup(Model m, ParticleIndex pi) -> bool
1379 return _IMP_atom.Bond_get_is_setup(*args)
1381 get_is_setup = staticmethod(get_is_setup)
1382 UNKNOWN = _IMP_atom.Bond_UNKNOWN
1383 NONBIOLOGICAL = _IMP_atom.Bond_NONBIOLOGICAL
1384 SINGLE = _IMP_atom.Bond_SINGLE
1385 DOUBLE = _IMP_atom.Bond_DOUBLE
1386 TRIPLE = _IMP_atom.Bond_TRIPLE
1387 HYDROGEN = _IMP_atom.Bond_HYDROGEN
1388 SALT = _IMP_atom.Bond_SALT
1389 PEPTIDE = _IMP_atom.Bond_PEPTIDE
1390 AMIDE = _IMP_atom.Bond_AMIDE
1391 AROMATIC = _IMP_atom.Bond_AROMATIC
1393 def get_bonded(self, i):
1394 """get_bonded(Bond self, unsigned int i) -> Bonded"""
1395 return _IMP_atom.Bond_get_bonded(self, i)
1399 """get_type(Bond self) -> IMP::Int"""
1400 return _IMP_atom.Bond_get_type(self)
1403 def set_type(self, t):
1404 """set_type(Bond self, IMP::Int t)"""
1405 return _IMP_atom.Bond_set_type(self, t)
1409 """get_order(Bond self) -> IMP::Int"""
1410 return _IMP_atom.Bond_get_order(self)
1413 def set_order(self, t):
1414 """set_order(Bond self, IMP::Int t)"""
1415 return _IMP_atom.Bond_set_order(self, t)
1418 def get_length(self):
1419 """get_length(Bond self) -> IMP::Float"""
1420 return _IMP_atom.Bond_get_length(self)
1423 def set_length(self, t):
1424 """set_length(Bond self, IMP::Float t)"""
1425 return _IMP_atom.Bond_set_length(self, t)
1428 def get_stiffness(self):
1429 """get_stiffness(Bond self) -> IMP::Float"""
1430 return _IMP_atom.Bond_get_stiffness(self)
1433 def set_stiffness(self, t):
1434 """set_stiffness(Bond self, IMP::Float t)"""
1435 return _IMP_atom.Bond_set_stiffness(self, t)
1438 def get_length_key():
1439 """get_length_key() -> FloatKey"""
1440 return _IMP_atom.Bond_get_length_key()
1442 get_length_key = staticmethod(get_length_key)
1444 def add_attribute(self, *args):
1446 add_attribute(Bond self, FloatKey k, IMP::Float v, bool opt)
1447 add_attribute(Bond self, FloatKey a0, IMP::Float a1)
1448 add_attribute(Bond self, IntKey a0, IMP::Int a1)
1449 add_attribute(Bond self, StringKey a0, IMP::String a1)
1450 add_attribute(Bond self, ParticleIndexKey a0, Particle a1)
1451 add_attribute(Bond self, ObjectKey a0, Object a1)
1453 return _IMP_atom.Bond_add_attribute(self, *args)
1456 def get_value(self, *args):
1458 get_value(Bond self, FloatKey a0) -> IMP::Float
1459 get_value(Bond self, IntKey a0) -> IMP::Int
1460 get_value(Bond self, StringKey a0) -> IMP::String
1461 get_value(Bond self, ParticleIndexKey a0) -> Particle
1462 get_value(Bond self, ObjectKey a0) -> Object
1464 return _IMP_atom.Bond_get_value(self, *args)
1467 def set_value(self, *args):
1469 set_value(Bond self, FloatKey a0, IMP::Float a1)
1470 set_value(Bond self, IntKey a0, IMP::Int a1)
1471 set_value(Bond self, StringKey a0, IMP::String a1)
1472 set_value(Bond self, ParticleIndexKey a0, Particle a1)
1473 set_value(Bond self, ObjectKey a0, Object a1)
1475 return _IMP_atom.Bond_set_value(self, *args)
1478 def remove_attribute(self, *args):
1480 remove_attribute(Bond self, FloatKey a0)
1481 remove_attribute(Bond self, IntKey a0)
1482 remove_attribute(Bond self, StringKey a0)
1483 remove_attribute(Bond self, ParticleIndexKey a0)
1484 remove_attribute(Bond self, ObjectKey a0)
1486 return _IMP_atom.Bond_remove_attribute(self, *args)
1489 def has_attribute(self, *args):
1491 has_attribute(Bond self, FloatKey a0) -> bool
1492 has_attribute(Bond self, IntKey a0) -> bool
1493 has_attribute(Bond self, StringKey a0) -> bool
1494 has_attribute(Bond self, ParticleIndexKey a0) -> bool
1495 has_attribute(Bond self, ObjectKey a0) -> bool
1497 return _IMP_atom.Bond_has_attribute(self, *args)
1500 def get_derivative(self, a0):
1501 """get_derivative(Bond self, FloatKey a0) -> double"""
1502 return _IMP_atom.Bond_get_derivative(self, a0)
1506 """get_name(Bond self) -> std::string"""
1507 return _IMP_atom.Bond_get_name(self)
1510 def clear_caches(self):
1511 """clear_caches(Bond self)"""
1512 return _IMP_atom.Bond_clear_caches(self)
1515 def set_name(self, a0):
1516 """set_name(Bond self, std::string a0)"""
1517 return _IMP_atom.Bond_set_name(self, a0)
1521 """set_check_level(Bond self, IMP::CheckLevel a0)"""
1522 return _IMP_atom.Bond_set_check_level(self, a0)
1525 def add_to_derivative(self, a0, a1, a2):
1526 """add_to_derivative(Bond self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1527 return _IMP_atom.Bond_add_to_derivative(self, a0, a1, a2)
1530 def set_is_optimized(self, a0, a1):
1531 """set_is_optimized(Bond self, FloatKey a0, bool a1)"""
1532 return _IMP_atom.Bond_set_is_optimized(self, a0, a1)
1535 def get_is_optimized(self, a0):
1536 """get_is_optimized(Bond self, FloatKey a0) -> bool"""
1537 return _IMP_atom.Bond_get_is_optimized(self, a0)
1541 """get_check_level(Bond self) -> IMP::CheckLevel"""
1542 return _IMP_atom.Bond_get_check_level(self)
1545 def __eq__(self, *args):
1547 __eq__(Bond self, Bond o) -> bool
1548 __eq__(Bond self, Particle d) -> bool
1550 return _IMP_atom.Bond___eq__(self, *args)
1553 def __ne__(self, *args):
1555 __ne__(Bond self, Bond o) -> bool
1556 __ne__(Bond self, Particle d) -> bool
1558 return _IMP_atom.Bond___ne__(self, *args)
1561 def __le__(self, *args):
1563 __le__(Bond self, Bond o) -> bool
1564 __le__(Bond self, Particle d) -> bool
1566 return _IMP_atom.Bond___le__(self, *args)
1569 def __lt__(self, *args):
1571 __lt__(Bond self, Bond o) -> bool
1572 __lt__(Bond self, Particle d) -> bool
1574 return _IMP_atom.Bond___lt__(self, *args)
1577 def __ge__(self, *args):
1579 __ge__(Bond self, Bond o) -> bool
1580 __ge__(Bond self, Particle d) -> bool
1582 return _IMP_atom.Bond___ge__(self, *args)
1585 def __gt__(self, *args):
1587 __gt__(Bond self, Bond o) -> bool
1588 __gt__(Bond self, Particle d) -> bool
1590 return _IMP_atom.Bond___gt__(self, *args)
1594 """__hash__(Bond self) -> std::size_t"""
1595 return _IMP_atom.Bond___hash__(self)
1599 """__str__(Bond self) -> std::string"""
1600 return _IMP_atom.Bond___str__(self)
1604 """__repr__(Bond self) -> std::string"""
1605 return _IMP_atom.Bond___repr__(self)
1607 __swig_destroy__ = _IMP_atom.delete_Bond
1608 __del__ =
lambda self:
None
1609 Bond_swigregister = _IMP_atom.Bond_swigregister
1610 Bond_swigregister(Bond)
1612 def Bond_get_is_setup(*args):
1614 get_is_setup(_ParticleAdaptor p) -> bool
1615 Bond_get_is_setup(Model m, ParticleIndex pi) -> bool
1617 return _IMP_atom.Bond_get_is_setup(*args)
1619 def Bond_get_length_key():
1620 """Bond_get_length_key() -> FloatKey"""
1621 return _IMP_atom.Bond_get_length_key()
1624 """Proxy of C++ IMP::atom::Bonded class"""
1625 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1627 def __init__(self, *args):
1629 __init__(IMP::atom::Bonded self) -> Bonded
1630 __init__(IMP::atom::Bonded self, Model m, ParticleIndex id) -> Bonded
1631 __init__(IMP::atom::Bonded self, _ParticleAdaptor d) -> Bonded
1633 this = _IMP_atom.new_Bonded(*args)
1635 self.this.append(this)
1639 def show(self, *args):
1641 show(Bonded self, _ostream out)
1644 return _IMP_atom.Bonded_show(self, *args)
1647 def setup_particle(*args):
1649 setup_particle(Model m, ParticleIndex pi) -> Bonded
1650 setup_particle(_ParticleAdaptor decorator) -> Bonded
1652 return _IMP_atom.Bonded_setup_particle(*args)
1654 setup_particle = staticmethod(setup_particle)
1656 def get_is_setup(*args):
1658 get_is_setup(_ParticleAdaptor p) -> bool
1659 get_is_setup(Model m, ParticleIndex pi) -> bool
1661 return _IMP_atom.Bonded_get_is_setup(*args)
1663 get_is_setup = staticmethod(get_is_setup)
1665 def get_number_of_bonds(self):
1666 """get_number_of_bonds(Bonded self) -> unsigned int"""
1667 return _IMP_atom.Bonded_get_number_of_bonds(self)
1670 def get_bond_indexes(self):
1671 """get_bond_indexes(Bonded self) -> IMP::ParticleIndexes"""
1672 return _IMP_atom.Bonded_get_bond_indexes(self)
1676 """get_bond(Bonded self, unsigned int i) -> Bond"""
1677 return _IMP_atom.Bonded_get_bond(self, i)
1680 def get_bonded(self, i):
1681 """get_bonded(Bonded self, unsigned int i) -> Bonded"""
1682 return _IMP_atom.Bonded_get_bonded(self, i)
1685 def add_attribute(self, *args):
1687 add_attribute(Bonded self, FloatKey k, IMP::Float v, bool opt)
1688 add_attribute(Bonded self, FloatKey a0, IMP::Float a1)
1689 add_attribute(Bonded self, IntKey a0, IMP::Int a1)
1690 add_attribute(Bonded self, StringKey a0, IMP::String a1)
1691 add_attribute(Bonded self, ParticleIndexKey a0, Particle a1)
1692 add_attribute(Bonded self, ObjectKey a0, Object a1)
1694 return _IMP_atom.Bonded_add_attribute(self, *args)
1697 def get_value(self, *args):
1699 get_value(Bonded self, FloatKey a0) -> IMP::Float
1700 get_value(Bonded self, IntKey a0) -> IMP::Int
1701 get_value(Bonded self, StringKey a0) -> IMP::String
1702 get_value(Bonded self, ParticleIndexKey a0) -> Particle
1703 get_value(Bonded self, ObjectKey a0) -> Object
1705 return _IMP_atom.Bonded_get_value(self, *args)
1708 def set_value(self, *args):
1710 set_value(Bonded self, FloatKey a0, IMP::Float a1)
1711 set_value(Bonded self, IntKey a0, IMP::Int a1)
1712 set_value(Bonded self, StringKey a0, IMP::String a1)
1713 set_value(Bonded self, ParticleIndexKey a0, Particle a1)
1714 set_value(Bonded self, ObjectKey a0, Object a1)
1716 return _IMP_atom.Bonded_set_value(self, *args)
1719 def remove_attribute(self, *args):
1721 remove_attribute(Bonded self, FloatKey a0)
1722 remove_attribute(Bonded self, IntKey a0)
1723 remove_attribute(Bonded self, StringKey a0)
1724 remove_attribute(Bonded self, ParticleIndexKey a0)
1725 remove_attribute(Bonded self, ObjectKey a0)
1727 return _IMP_atom.Bonded_remove_attribute(self, *args)
1730 def has_attribute(self, *args):
1732 has_attribute(Bonded self, FloatKey a0) -> bool
1733 has_attribute(Bonded self, IntKey a0) -> bool
1734 has_attribute(Bonded self, StringKey a0) -> bool
1735 has_attribute(Bonded self, ParticleIndexKey a0) -> bool
1736 has_attribute(Bonded self, ObjectKey a0) -> bool
1738 return _IMP_atom.Bonded_has_attribute(self, *args)
1741 def get_derivative(self, a0):
1742 """get_derivative(Bonded self, FloatKey a0) -> double"""
1743 return _IMP_atom.Bonded_get_derivative(self, a0)
1747 """get_name(Bonded self) -> std::string"""
1748 return _IMP_atom.Bonded_get_name(self)
1751 def clear_caches(self):
1752 """clear_caches(Bonded self)"""
1753 return _IMP_atom.Bonded_clear_caches(self)
1756 def set_name(self, a0):
1757 """set_name(Bonded self, std::string a0)"""
1758 return _IMP_atom.Bonded_set_name(self, a0)
1762 """set_check_level(Bonded self, IMP::CheckLevel a0)"""
1763 return _IMP_atom.Bonded_set_check_level(self, a0)
1766 def add_to_derivative(self, a0, a1, a2):
1767 """add_to_derivative(Bonded self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1768 return _IMP_atom.Bonded_add_to_derivative(self, a0, a1, a2)
1771 def set_is_optimized(self, a0, a1):
1772 """set_is_optimized(Bonded self, FloatKey a0, bool a1)"""
1773 return _IMP_atom.Bonded_set_is_optimized(self, a0, a1)
1776 def get_is_optimized(self, a0):
1777 """get_is_optimized(Bonded self, FloatKey a0) -> bool"""
1778 return _IMP_atom.Bonded_get_is_optimized(self, a0)
1782 """get_check_level(Bonded self) -> IMP::CheckLevel"""
1783 return _IMP_atom.Bonded_get_check_level(self)
1786 def __eq__(self, *args):
1788 __eq__(Bonded self, Bonded o) -> bool
1789 __eq__(Bonded self, Particle d) -> bool
1791 return _IMP_atom.Bonded___eq__(self, *args)
1794 def __ne__(self, *args):
1796 __ne__(Bonded self, Bonded o) -> bool
1797 __ne__(Bonded self, Particle d) -> bool
1799 return _IMP_atom.Bonded___ne__(self, *args)
1802 def __le__(self, *args):
1804 __le__(Bonded self, Bonded o) -> bool
1805 __le__(Bonded self, Particle d) -> bool
1807 return _IMP_atom.Bonded___le__(self, *args)
1810 def __lt__(self, *args):
1812 __lt__(Bonded self, Bonded o) -> bool
1813 __lt__(Bonded self, Particle d) -> bool
1815 return _IMP_atom.Bonded___lt__(self, *args)
1818 def __ge__(self, *args):
1820 __ge__(Bonded self, Bonded o) -> bool
1821 __ge__(Bonded self, Particle d) -> bool
1823 return _IMP_atom.Bonded___ge__(self, *args)
1826 def __gt__(self, *args):
1828 __gt__(Bonded self, Bonded o) -> bool
1829 __gt__(Bonded self, Particle d) -> bool
1831 return _IMP_atom.Bonded___gt__(self, *args)
1835 """__hash__(Bonded self) -> std::size_t"""
1836 return _IMP_atom.Bonded___hash__(self)
1840 """__str__(Bonded self) -> std::string"""
1841 return _IMP_atom.Bonded___str__(self)
1845 """__repr__(Bonded self) -> std::string"""
1846 return _IMP_atom.Bonded___repr__(self)
1848 __swig_destroy__ = _IMP_atom.delete_Bonded
1849 __del__ =
lambda self:
None
1850 Bonded_swigregister = _IMP_atom.Bonded_swigregister
1851 Bonded_swigregister(Bonded)
1853 def Bonded_setup_particle(*args):
1855 setup_particle(Model m, ParticleIndex pi) -> Bonded
1856 Bonded_setup_particle(_ParticleAdaptor decorator) -> Bonded
1858 return _IMP_atom.Bonded_setup_particle(*args)
1860 def Bonded_get_is_setup(*args):
1862 get_is_setup(_ParticleAdaptor p) -> bool
1863 Bonded_get_is_setup(Model m, ParticleIndex pi) -> bool
1865 return _IMP_atom.Bonded_get_is_setup(*args)
1870 create_custom_bond(Bonded a, Bonded b, IMP::Float length, IMP::Float stiffness=-1) -> Bond
1871 create_custom_bond(Bonded a, Bonded b, IMP::Float length) -> Bond
1873 return _IMP_atom.create_custom_bond(a, b, length, stiffness)
1877 create_bond(Bonded a, Bonded b, IMP::Int t) -> Bond
1878 create_bond(Bonded a, Bonded b, Bond o) -> Bond
1880 return _IMP_atom.create_bond(*args)
1883 """destroy_bond(Bond b)"""
1884 return _IMP_atom.destroy_bond(b)
1887 """get_bond(Bonded a, Bonded b) -> Bond"""
1888 return _IMP_atom.get_bond(a, b)
1890 """Proxy of C++ IMP::atom::BondGeometry class"""
1891 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1893 def __init__(self, *args):
1895 __init__(IMP::atom::BondGeometry self, Particle p) -> BondGeometry
1896 __init__(IMP::atom::BondGeometry self, Bond d) -> BondGeometry
1898 this = _IMP_atom.new_BondGeometry(*args)
1900 self.this.append(this)
1904 def get_version_info(self):
1905 """get_version_info(BondGeometry self) -> VersionInfo"""
1906 return _IMP_atom.BondGeometry_get_version_info(self)
1910 """__str__(BondGeometry self) -> std::string"""
1911 return _IMP_atom.BondGeometry___str__(self)
1915 """__repr__(BondGeometry self) -> std::string"""
1916 return _IMP_atom.BondGeometry___repr__(self)
1921 return _object_cast_to_BondGeometry(o)
1923 BondGeometry_swigregister = _IMP_atom.BondGeometry_swigregister
1924 BondGeometry_swigregister(BondGeometry)
1927 """Proxy of C++ IMP::atom::BondsGeometry class"""
1928 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1930 def __init__(self, sc):
1931 """__init__(IMP::atom::BondsGeometry self, SingletonContainer sc) -> BondsGeometry"""
1932 this = _IMP_atom.new_BondsGeometry(sc)
1934 self.this.append(this)
1938 def get_version_info(self):
1939 """get_version_info(BondsGeometry self) -> VersionInfo"""
1940 return _IMP_atom.BondsGeometry_get_version_info(self)
1944 """__str__(BondsGeometry self) -> std::string"""
1945 return _IMP_atom.BondsGeometry___str__(self)
1949 """__repr__(BondsGeometry self) -> std::string"""
1950 return _IMP_atom.BondsGeometry___repr__(self)
1955 return _object_cast_to_BondsGeometry(o)
1957 BondsGeometry_swigregister = _IMP_atom.BondsGeometry_swigregister
1958 BondsGeometry_swigregister(BondsGeometry)
1961 """Proxy of C++ IMP::atom::Hierarchy class"""
1962 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1964 def __init__(self, *args):
1966 __init__(IMP::atom::Hierarchy self, Model m, ParticleIndex pi) -> Hierarchy
1967 __init__(IMP::atom::Hierarchy self, _ParticleAdaptor pi) -> Hierarchy
1968 __init__(IMP::atom::Hierarchy self) -> Hierarchy
1969 __init__(IMP::atom::Hierarchy self, Hierarchy h) -> Hierarchy
1971 this = _IMP_atom.new_Hierarchy(*args)
1973 self.this.append(this)
1977 def setup_particle(*args):
1979 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
1980 setup_particle(Particle p) -> Hierarchy
1981 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
1982 setup_particle(Model m, ParticleIndex pi) -> Hierarchy
1984 return _IMP_atom.Hierarchy_setup_particle(*args)
1986 setup_particle = staticmethod(setup_particle)
1988 def get_is_setup(*args):
1990 get_is_setup(Particle p) -> bool
1991 get_is_setup(Model m, ParticleIndex p) -> bool
1993 return _IMP_atom.Hierarchy_get_is_setup(*args)
1995 get_is_setup = staticmethod(get_is_setup)
1997 def get_is_valid(self, print_info=False):
1999 get_is_valid(Hierarchy self, bool print_info=False) -> bool
2000 get_is_valid(Hierarchy self) -> bool
2002 return _IMP_atom.Hierarchy_get_is_valid(self, print_info)
2005 def add_child(self, o):
2006 """add_child(Hierarchy self, Hierarchy o)"""
2007 return _IMP_atom.Hierarchy_add_child(self, o)
2010 def get_child(self, i):
2011 """get_child(Hierarchy self, unsigned int i) -> Hierarchy"""
2012 return _IMP_atom.Hierarchy_get_child(self, i)
2015 def get_children(self):
2016 """get_children(Hierarchy self) -> IMP::atom::Hierarchies"""
2017 return _IMP_atom.Hierarchy_get_children(self)
2020 def get_parent(self):
2021 """get_parent(Hierarchy self) -> Hierarchy"""
2022 return _IMP_atom.Hierarchy_get_parent(self)
2025 def get_as_atom(self):
2026 """get_as_atom(Hierarchy self) -> Atom"""
2027 return _IMP_atom.Hierarchy_get_as_atom(self)
2030 def get_as_residue(self):
2031 """get_as_residue(Hierarchy self) -> Residue"""
2032 return _IMP_atom.Hierarchy_get_as_residue(self)
2035 def get_as_chain(self):
2036 """get_as_chain(Hierarchy self) -> Chain"""
2037 return _IMP_atom.Hierarchy_get_as_chain(self)
2040 def get_as_molecule(self):
2041 """get_as_molecule(Hierarchy self) -> Molecule"""
2042 return _IMP_atom.Hierarchy_get_as_molecule(self)
2045 def get_as_domain(self):
2046 """get_as_domain(Hierarchy self) -> Domain"""
2047 return _IMP_atom.Hierarchy_get_as_domain(self)
2050 def get_as_fragment(self):
2051 """get_as_fragment(Hierarchy self) -> Fragment"""
2052 return _IMP_atom.Hierarchy_get_as_fragment(self)
2055 def get_as_xyz(self):
2056 """get_as_xyz(Hierarchy self) -> XYZ"""
2057 return _IMP_atom.Hierarchy_get_as_xyz(self)
2060 def get_as_xyzr(self):
2061 """get_as_xyzr(Hierarchy self) -> XYZR"""
2062 return _IMP_atom.Hierarchy_get_as_xyzr(self)
2065 def get_as_mass(self):
2066 """get_as_mass(Hierarchy self) -> Mass"""
2067 return _IMP_atom.Hierarchy_get_as_mass(self)
2070 def get_as_state(self):
2071 """get_as_state(Hierarchy self) -> State"""
2072 return _IMP_atom.Hierarchy_get_as_state(self)
2076 """get_traits() -> HierarchyTraits"""
2077 return _IMP_atom.Hierarchy_get_traits()
2079 get_traits = staticmethod(get_traits)
2081 def show(self, *args):
2083 show(Hierarchy self, _ostream out, std::string delimiter)
2084 show(Hierarchy self, _ostream out)
2085 show(Hierarchy self)
2087 return _IMP_atom.Hierarchy_show(self, *args)
2090 def add_attribute(self, *args):
2092 add_attribute(Hierarchy self, FloatKey k, IMP::Float v, bool opt)
2093 add_attribute(Hierarchy self, FloatKey a0, IMP::Float a1)
2094 add_attribute(Hierarchy self, IntKey a0, IMP::Int a1)
2095 add_attribute(Hierarchy self, StringKey a0, IMP::String a1)
2096 add_attribute(Hierarchy self, ParticleIndexKey a0, Particle a1)
2097 add_attribute(Hierarchy self, ObjectKey a0, Object a1)
2099 return _IMP_atom.Hierarchy_add_attribute(self, *args)
2102 def get_value(self, *args):
2104 get_value(Hierarchy self, FloatKey a0) -> IMP::Float
2105 get_value(Hierarchy self, IntKey a0) -> IMP::Int
2106 get_value(Hierarchy self, StringKey a0) -> IMP::String
2107 get_value(Hierarchy self, ParticleIndexKey a0) -> Particle
2108 get_value(Hierarchy self, ObjectKey a0) -> Object
2110 return _IMP_atom.Hierarchy_get_value(self, *args)
2113 def set_value(self, *args):
2115 set_value(Hierarchy self, FloatKey a0, IMP::Float a1)
2116 set_value(Hierarchy self, IntKey a0, IMP::Int a1)
2117 set_value(Hierarchy self, StringKey a0, IMP::String a1)
2118 set_value(Hierarchy self, ParticleIndexKey a0, Particle a1)
2119 set_value(Hierarchy self, ObjectKey a0, Object a1)
2121 return _IMP_atom.Hierarchy_set_value(self, *args)
2124 def remove_attribute(self, *args):
2126 remove_attribute(Hierarchy self, FloatKey a0)
2127 remove_attribute(Hierarchy self, IntKey a0)
2128 remove_attribute(Hierarchy self, StringKey a0)
2129 remove_attribute(Hierarchy self, ParticleIndexKey a0)
2130 remove_attribute(Hierarchy self, ObjectKey a0)
2132 return _IMP_atom.Hierarchy_remove_attribute(self, *args)
2135 def has_attribute(self, *args):
2137 has_attribute(Hierarchy self, FloatKey a0) -> bool
2138 has_attribute(Hierarchy self, IntKey a0) -> bool
2139 has_attribute(Hierarchy self, StringKey a0) -> bool
2140 has_attribute(Hierarchy self, ParticleIndexKey a0) -> bool
2141 has_attribute(Hierarchy self, ObjectKey a0) -> bool
2143 return _IMP_atom.Hierarchy_has_attribute(self, *args)
2146 def get_derivative(self, a0):
2147 """get_derivative(Hierarchy self, FloatKey a0) -> double"""
2148 return _IMP_atom.Hierarchy_get_derivative(self, a0)
2152 """get_name(Hierarchy self) -> std::string"""
2153 return _IMP_atom.Hierarchy_get_name(self)
2156 def clear_caches(self):
2157 """clear_caches(Hierarchy self)"""
2158 return _IMP_atom.Hierarchy_clear_caches(self)
2161 def set_name(self, a0):
2162 """set_name(Hierarchy self, std::string a0)"""
2163 return _IMP_atom.Hierarchy_set_name(self, a0)
2167 """set_check_level(Hierarchy self, IMP::CheckLevel a0)"""
2168 return _IMP_atom.Hierarchy_set_check_level(self, a0)
2171 def add_to_derivative(self, a0, a1, a2):
2172 """add_to_derivative(Hierarchy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2173 return _IMP_atom.Hierarchy_add_to_derivative(self, a0, a1, a2)
2176 def set_is_optimized(self, a0, a1):
2177 """set_is_optimized(Hierarchy self, FloatKey a0, bool a1)"""
2178 return _IMP_atom.Hierarchy_set_is_optimized(self, a0, a1)
2181 def get_is_optimized(self, a0):
2182 """get_is_optimized(Hierarchy self, FloatKey a0) -> bool"""
2183 return _IMP_atom.Hierarchy_get_is_optimized(self, a0)
2187 """get_check_level(Hierarchy self) -> IMP::CheckLevel"""
2188 return _IMP_atom.Hierarchy_get_check_level(self)
2191 def __eq__(self, *args):
2193 __eq__(Hierarchy self, Hierarchy o) -> bool
2194 __eq__(Hierarchy self, Particle d) -> bool
2196 return _IMP_atom.Hierarchy___eq__(self, *args)
2199 def __ne__(self, *args):
2201 __ne__(Hierarchy self, Hierarchy o) -> bool
2202 __ne__(Hierarchy self, Particle d) -> bool
2204 return _IMP_atom.Hierarchy___ne__(self, *args)
2207 def __le__(self, *args):
2209 __le__(Hierarchy self, Hierarchy o) -> bool
2210 __le__(Hierarchy self, Particle d) -> bool
2212 return _IMP_atom.Hierarchy___le__(self, *args)
2215 def __lt__(self, *args):
2217 __lt__(Hierarchy self, Hierarchy o) -> bool
2218 __lt__(Hierarchy self, Particle d) -> bool
2220 return _IMP_atom.Hierarchy___lt__(self, *args)
2223 def __ge__(self, *args):
2225 __ge__(Hierarchy self, Hierarchy o) -> bool
2226 __ge__(Hierarchy self, Particle d) -> bool
2228 return _IMP_atom.Hierarchy___ge__(self, *args)
2231 def __gt__(self, *args):
2233 __gt__(Hierarchy self, Hierarchy o) -> bool
2234 __gt__(Hierarchy self, Particle d) -> bool
2236 return _IMP_atom.Hierarchy___gt__(self, *args)
2240 """__hash__(Hierarchy self) -> std::size_t"""
2241 return _IMP_atom.Hierarchy___hash__(self)
2245 """__str__(Hierarchy self) -> std::string"""
2246 return _IMP_atom.Hierarchy___str__(self)
2250 """__repr__(Hierarchy self) -> std::string"""
2251 return _IMP_atom.Hierarchy___repr__(self)
2253 __swig_destroy__ = _IMP_atom.delete_Hierarchy
2254 __del__ =
lambda self:
None
2255 Hierarchy_swigregister = _IMP_atom.Hierarchy_swigregister
2256 Hierarchy_swigregister(Hierarchy)
2258 def Hierarchy_setup_particle(*args):
2260 setup_particle(Particle p, _ParticleIndexesAdaptor children) -> Hierarchy
2261 setup_particle(Particle p) -> Hierarchy
2262 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor children) -> Hierarchy
2263 Hierarchy_setup_particle(Model m, ParticleIndex pi) -> Hierarchy
2265 return _IMP_atom.Hierarchy_setup_particle(*args)
2267 def Hierarchy_get_is_setup(*args):
2269 get_is_setup(Particle p) -> bool
2270 Hierarchy_get_is_setup(Model m, ParticleIndex p) -> bool
2272 return _IMP_atom.Hierarchy_get_is_setup(*args)
2274 def Hierarchy_get_traits():
2275 """Hierarchy_get_traits() -> HierarchyTraits"""
2276 return _IMP_atom.Hierarchy_get_traits()
2279 _IMP_atom.ATOM_TYPE_swigconstant(_IMP_atom)
2280 ATOM_TYPE = _IMP_atom.ATOM_TYPE
2282 _IMP_atom.RESIDUE_TYPE_swigconstant(_IMP_atom)
2283 RESIDUE_TYPE = _IMP_atom.RESIDUE_TYPE
2285 _IMP_atom.CHAIN_TYPE_swigconstant(_IMP_atom)
2286 CHAIN_TYPE = _IMP_atom.CHAIN_TYPE
2288 _IMP_atom.MOLECULE_TYPE_swigconstant(_IMP_atom)
2289 MOLECULE_TYPE = _IMP_atom.MOLECULE_TYPE
2291 _IMP_atom.DOMAIN_TYPE_swigconstant(_IMP_atom)
2292 DOMAIN_TYPE = _IMP_atom.DOMAIN_TYPE
2294 _IMP_atom.FRAGMENT_TYPE_swigconstant(_IMP_atom)
2295 FRAGMENT_TYPE = _IMP_atom.FRAGMENT_TYPE
2297 _IMP_atom.XYZ_TYPE_swigconstant(_IMP_atom)
2298 XYZ_TYPE = _IMP_atom.XYZ_TYPE
2300 _IMP_atom.XYZR_TYPE_swigconstant(_IMP_atom)
2301 XYZR_TYPE = _IMP_atom.XYZR_TYPE
2303 _IMP_atom.MASS_TYPE_swigconstant(_IMP_atom)
2304 MASS_TYPE = _IMP_atom.MASS_TYPE
2306 _IMP_atom.STATE_TYPE_swigconstant(_IMP_atom)
2307 STATE_TYPE = _IMP_atom.STATE_TYPE
2309 def get_by_type(mhd, t):
2310 """get_by_type(Hierarchy mhd, IMP::atom::GetByType t) -> IMP::atom::Hierarchies"""
2311 return _IMP_atom.get_by_type(mhd, t)
2313 def create_fragment(ps):
2314 """create_fragment(IMP::atom::Hierarchies const & ps) -> Hierarchy"""
2315 return _IMP_atom.create_fragment(ps)
2317 def get_internal_bonds(mhd):
2318 """get_internal_bonds(Hierarchy mhd) -> IMP::atom::Bonds"""
2319 return _IMP_atom.get_internal_bonds(mhd)
2322 """get_root(Hierarchy h) -> Hierarchy"""
2323 return _IMP_atom.get_root(h)
2327 show(Hierarchy h, _ostream out)
2330 return _IMP_atom.show(*args)
2334 create_rigid_body(IMP::atom::Hierarchies const & h, std::string name) -> RigidBody
2335 create_rigid_body(IMP::atom::Hierarchies const & h) -> RigidBody
2336 create_rigid_body(Hierarchy h) -> RigidBody
2338 return _IMP_atom.create_rigid_body(*args)
2341 """create_compatible_rigid_body(Hierarchy h, Hierarchy reference) -> RigidBody"""
2342 return _IMP_atom.create_compatible_rigid_body(h, reference)
2344 def setup_as_rigid_body(h):
2345 """setup_as_rigid_body(Hierarchy h) -> RigidBody"""
2346 return _IMP_atom.setup_as_rigid_body(h)
2348 def get_is_heterogen(h):
2349 """get_is_heterogen(Hierarchy h) -> bool"""
2350 return _IMP_atom.get_is_heterogen(h)
2352 def create_clone(d):
2353 """create_clone(Hierarchy d) -> Hierarchy"""
2354 return _IMP_atom.create_clone(d)
2356 def create_clone_one(d):
2357 """create_clone_one(Hierarchy d) -> Hierarchy"""
2358 return _IMP_atom.create_clone_one(d)
2361 """destroy(Hierarchy d)"""
2362 return _IMP_atom.destroy(d)
2364 def get_bounding_box(h):
2365 """get_bounding_box(Hierarchy h) -> BoundingBox3D"""
2366 return _IMP_atom.get_bounding_box(h)
2368 def get_bounding_sphere(h):
2369 """get_bounding_sphere(Hierarchy h) -> Sphere3D"""
2370 return _IMP_atom.get_bounding_sphere(h)
2372 """Proxy of C++ IMP::atom::Angle class"""
2373 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2375 def __init__(self, *args):
2377 __init__(IMP::atom::Angle self) -> Angle
2378 __init__(IMP::atom::Angle self, Model m, ParticleIndex id) -> Angle
2379 __init__(IMP::atom::Angle self, _ParticleAdaptor d) -> Angle
2381 this = _IMP_atom.new_Angle(*args)
2383 self.this.append(this)
2387 def show(self, *args):
2389 show(Angle self, _ostream out)
2392 return _IMP_atom.Angle_show(self, *args)
2395 def setup_particle(*args):
2397 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2398 setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2400 return _IMP_atom.Angle_setup_particle(*args)
2402 setup_particle = staticmethod(setup_particle)
2404 def get_is_setup(*args):
2406 get_is_setup(_ParticleAdaptor p) -> bool
2407 get_is_setup(Model m, ParticleIndex pi) -> bool
2409 return _IMP_atom.Angle_get_is_setup(*args)
2411 get_is_setup = staticmethod(get_is_setup)
2413 def get_particle(self, *args):
2415 get_particle(Angle self) -> Particle
2416 get_particle(Angle self, unsigned int i) -> Particle
2418 return _IMP_atom.Angle_get_particle(self, *args)
2421 def get_ideal(self):
2422 """get_ideal(Angle self) -> IMP::Float"""
2423 return _IMP_atom.Angle_get_ideal(self)
2426 def set_ideal(self, t):
2427 """set_ideal(Angle self, IMP::Float t)"""
2428 return _IMP_atom.Angle_set_ideal(self, t)
2431 def get_stiffness(self):
2432 """get_stiffness(Angle self) -> IMP::Float"""
2433 return _IMP_atom.Angle_get_stiffness(self)
2436 def set_stiffness(self, t):
2437 """set_stiffness(Angle self, IMP::Float t)"""
2438 return _IMP_atom.Angle_set_stiffness(self, t)
2441 def get_particle_key(i):
2442 """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2443 return _IMP_atom.Angle_get_particle_key(i)
2445 get_particle_key = staticmethod(get_particle_key)
2447 def get_ideal_key():
2448 """get_ideal_key() -> FloatKey"""
2449 return _IMP_atom.Angle_get_ideal_key()
2451 get_ideal_key = staticmethod(get_ideal_key)
2453 def get_stiffness_key():
2454 """get_stiffness_key() -> FloatKey"""
2455 return _IMP_atom.Angle_get_stiffness_key()
2457 get_stiffness_key = staticmethod(get_stiffness_key)
2459 def add_attribute(self, *args):
2461 add_attribute(Angle self, FloatKey k, IMP::Float v, bool opt)
2462 add_attribute(Angle self, FloatKey a0, IMP::Float a1)
2463 add_attribute(Angle self, IntKey a0, IMP::Int a1)
2464 add_attribute(Angle self, StringKey a0, IMP::String a1)
2465 add_attribute(Angle self, ParticleIndexKey a0, Particle a1)
2466 add_attribute(Angle self, ObjectKey a0, Object a1)
2468 return _IMP_atom.Angle_add_attribute(self, *args)
2471 def get_value(self, *args):
2473 get_value(Angle self, FloatKey a0) -> IMP::Float
2474 get_value(Angle self, IntKey a0) -> IMP::Int
2475 get_value(Angle self, StringKey a0) -> IMP::String
2476 get_value(Angle self, ParticleIndexKey a0) -> Particle
2477 get_value(Angle self, ObjectKey a0) -> Object
2479 return _IMP_atom.Angle_get_value(self, *args)
2482 def set_value(self, *args):
2484 set_value(Angle self, FloatKey a0, IMP::Float a1)
2485 set_value(Angle self, IntKey a0, IMP::Int a1)
2486 set_value(Angle self, StringKey a0, IMP::String a1)
2487 set_value(Angle self, ParticleIndexKey a0, Particle a1)
2488 set_value(Angle self, ObjectKey a0, Object a1)
2490 return _IMP_atom.Angle_set_value(self, *args)
2493 def remove_attribute(self, *args):
2495 remove_attribute(Angle self, FloatKey a0)
2496 remove_attribute(Angle self, IntKey a0)
2497 remove_attribute(Angle self, StringKey a0)
2498 remove_attribute(Angle self, ParticleIndexKey a0)
2499 remove_attribute(Angle self, ObjectKey a0)
2501 return _IMP_atom.Angle_remove_attribute(self, *args)
2504 def has_attribute(self, *args):
2506 has_attribute(Angle self, FloatKey a0) -> bool
2507 has_attribute(Angle self, IntKey a0) -> bool
2508 has_attribute(Angle self, StringKey a0) -> bool
2509 has_attribute(Angle self, ParticleIndexKey a0) -> bool
2510 has_attribute(Angle self, ObjectKey a0) -> bool
2512 return _IMP_atom.Angle_has_attribute(self, *args)
2515 def get_derivative(self, a0):
2516 """get_derivative(Angle self, FloatKey a0) -> double"""
2517 return _IMP_atom.Angle_get_derivative(self, a0)
2521 """get_name(Angle self) -> std::string"""
2522 return _IMP_atom.Angle_get_name(self)
2525 def clear_caches(self):
2526 """clear_caches(Angle self)"""
2527 return _IMP_atom.Angle_clear_caches(self)
2530 def set_name(self, a0):
2531 """set_name(Angle self, std::string a0)"""
2532 return _IMP_atom.Angle_set_name(self, a0)
2536 """set_check_level(Angle self, IMP::CheckLevel a0)"""
2537 return _IMP_atom.Angle_set_check_level(self, a0)
2540 def add_to_derivative(self, a0, a1, a2):
2541 """add_to_derivative(Angle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2542 return _IMP_atom.Angle_add_to_derivative(self, a0, a1, a2)
2545 def set_is_optimized(self, a0, a1):
2546 """set_is_optimized(Angle self, FloatKey a0, bool a1)"""
2547 return _IMP_atom.Angle_set_is_optimized(self, a0, a1)
2550 def get_is_optimized(self, a0):
2551 """get_is_optimized(Angle self, FloatKey a0) -> bool"""
2552 return _IMP_atom.Angle_get_is_optimized(self, a0)
2556 """get_check_level(Angle self) -> IMP::CheckLevel"""
2557 return _IMP_atom.Angle_get_check_level(self)
2560 def __eq__(self, *args):
2562 __eq__(Angle self, Angle o) -> bool
2563 __eq__(Angle self, Particle d) -> bool
2565 return _IMP_atom.Angle___eq__(self, *args)
2568 def __ne__(self, *args):
2570 __ne__(Angle self, Angle o) -> bool
2571 __ne__(Angle self, Particle d) -> bool
2573 return _IMP_atom.Angle___ne__(self, *args)
2576 def __le__(self, *args):
2578 __le__(Angle self, Angle o) -> bool
2579 __le__(Angle self, Particle d) -> bool
2581 return _IMP_atom.Angle___le__(self, *args)
2584 def __lt__(self, *args):
2586 __lt__(Angle self, Angle o) -> bool
2587 __lt__(Angle self, Particle d) -> bool
2589 return _IMP_atom.Angle___lt__(self, *args)
2592 def __ge__(self, *args):
2594 __ge__(Angle self, Angle o) -> bool
2595 __ge__(Angle self, Particle d) -> bool
2597 return _IMP_atom.Angle___ge__(self, *args)
2600 def __gt__(self, *args):
2602 __gt__(Angle self, Angle o) -> bool
2603 __gt__(Angle self, Particle d) -> bool
2605 return _IMP_atom.Angle___gt__(self, *args)
2609 """__hash__(Angle self) -> std::size_t"""
2610 return _IMP_atom.Angle___hash__(self)
2614 """__str__(Angle self) -> std::string"""
2615 return _IMP_atom.Angle___str__(self)
2619 """__repr__(Angle self) -> std::string"""
2620 return _IMP_atom.Angle___repr__(self)
2622 __swig_destroy__ = _IMP_atom.delete_Angle
2623 __del__ =
lambda self:
None
2624 Angle_swigregister = _IMP_atom.Angle_swigregister
2625 Angle_swigregister(Angle)
2627 def Angle_setup_particle(*args):
2629 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c) -> Angle
2630 Angle_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c) -> Angle
2632 return _IMP_atom.Angle_setup_particle(*args)
2634 def Angle_get_is_setup(*args):
2636 get_is_setup(_ParticleAdaptor p) -> bool
2637 Angle_get_is_setup(Model m, ParticleIndex pi) -> bool
2639 return _IMP_atom.Angle_get_is_setup(*args)
2641 def Angle_get_particle_key(i):
2642 """Angle_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2643 return _IMP_atom.Angle_get_particle_key(i)
2645 def Angle_get_ideal_key():
2646 """Angle_get_ideal_key() -> FloatKey"""
2647 return _IMP_atom.Angle_get_ideal_key()
2649 def Angle_get_stiffness_key():
2650 """Angle_get_stiffness_key() -> FloatKey"""
2651 return _IMP_atom.Angle_get_stiffness_key()
2654 """Proxy of C++ IMP::atom::Dihedral class"""
2655 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2657 def __init__(self, *args):
2659 __init__(IMP::atom::Dihedral self) -> Dihedral
2660 __init__(IMP::atom::Dihedral self, Model m, ParticleIndex id) -> Dihedral
2661 __init__(IMP::atom::Dihedral self, _ParticleAdaptor d) -> Dihedral
2663 this = _IMP_atom.new_Dihedral(*args)
2665 self.this.append(this)
2669 def show(self, *args):
2671 show(Dihedral self, _ostream out)
2674 return _IMP_atom.Dihedral_show(self, *args)
2677 def setup_particle(*args):
2679 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2680 setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2682 return _IMP_atom.Dihedral_setup_particle(*args)
2684 setup_particle = staticmethod(setup_particle)
2686 def get_is_setup(*args):
2688 get_is_setup(_ParticleAdaptor p) -> bool
2689 get_is_setup(Model m, ParticleIndex pi) -> bool
2691 return _IMP_atom.Dihedral_get_is_setup(*args)
2693 get_is_setup = staticmethod(get_is_setup)
2695 def get_particle(self, *args):
2697 get_particle(Dihedral self) -> Particle
2698 get_particle(Dihedral self, unsigned int i) -> Particle
2700 return _IMP_atom.Dihedral_get_particle(self, *args)
2703 def get_ideal(self):
2704 """get_ideal(Dihedral self) -> IMP::Float"""
2705 return _IMP_atom.Dihedral_get_ideal(self)
2708 def set_ideal(self, t):
2709 """set_ideal(Dihedral self, IMP::Float t)"""
2710 return _IMP_atom.Dihedral_set_ideal(self, t)
2713 def get_multiplicity(self):
2714 """get_multiplicity(Dihedral self) -> IMP::Int"""
2715 return _IMP_atom.Dihedral_get_multiplicity(self)
2718 def set_multiplicity(self, t):
2719 """set_multiplicity(Dihedral self, IMP::Int t)"""
2720 return _IMP_atom.Dihedral_set_multiplicity(self, t)
2723 def get_stiffness(self):
2724 """get_stiffness(Dihedral self) -> IMP::Float"""
2725 return _IMP_atom.Dihedral_get_stiffness(self)
2728 def set_stiffness(self, t):
2729 """set_stiffness(Dihedral self, IMP::Float t)"""
2730 return _IMP_atom.Dihedral_set_stiffness(self, t)
2733 def get_particle_key(i):
2734 """get_particle_key(unsigned int i) -> ParticleIndexKey"""
2735 return _IMP_atom.Dihedral_get_particle_key(i)
2737 get_particle_key = staticmethod(get_particle_key)
2739 def get_ideal_key():
2740 """get_ideal_key() -> FloatKey"""
2741 return _IMP_atom.Dihedral_get_ideal_key()
2743 get_ideal_key = staticmethod(get_ideal_key)
2745 def get_multiplicity_key():
2746 """get_multiplicity_key() -> IntKey"""
2747 return _IMP_atom.Dihedral_get_multiplicity_key()
2749 get_multiplicity_key = staticmethod(get_multiplicity_key)
2751 def get_stiffness_key():
2752 """get_stiffness_key() -> FloatKey"""
2753 return _IMP_atom.Dihedral_get_stiffness_key()
2755 get_stiffness_key = staticmethod(get_stiffness_key)
2757 def add_attribute(self, *args):
2759 add_attribute(Dihedral self, FloatKey k, IMP::Float v, bool opt)
2760 add_attribute(Dihedral self, FloatKey a0, IMP::Float a1)
2761 add_attribute(Dihedral self, IntKey a0, IMP::Int a1)
2762 add_attribute(Dihedral self, StringKey a0, IMP::String a1)
2763 add_attribute(Dihedral self, ParticleIndexKey a0, Particle a1)
2764 add_attribute(Dihedral self, ObjectKey a0, Object a1)
2766 return _IMP_atom.Dihedral_add_attribute(self, *args)
2769 def get_value(self, *args):
2771 get_value(Dihedral self, FloatKey a0) -> IMP::Float
2772 get_value(Dihedral self, IntKey a0) -> IMP::Int
2773 get_value(Dihedral self, StringKey a0) -> IMP::String
2774 get_value(Dihedral self, ParticleIndexKey a0) -> Particle
2775 get_value(Dihedral self, ObjectKey a0) -> Object
2777 return _IMP_atom.Dihedral_get_value(self, *args)
2780 def set_value(self, *args):
2782 set_value(Dihedral self, FloatKey a0, IMP::Float a1)
2783 set_value(Dihedral self, IntKey a0, IMP::Int a1)
2784 set_value(Dihedral self, StringKey a0, IMP::String a1)
2785 set_value(Dihedral self, ParticleIndexKey a0, Particle a1)
2786 set_value(Dihedral self, ObjectKey a0, Object a1)
2788 return _IMP_atom.Dihedral_set_value(self, *args)
2791 def remove_attribute(self, *args):
2793 remove_attribute(Dihedral self, FloatKey a0)
2794 remove_attribute(Dihedral self, IntKey a0)
2795 remove_attribute(Dihedral self, StringKey a0)
2796 remove_attribute(Dihedral self, ParticleIndexKey a0)
2797 remove_attribute(Dihedral self, ObjectKey a0)
2799 return _IMP_atom.Dihedral_remove_attribute(self, *args)
2802 def has_attribute(self, *args):
2804 has_attribute(Dihedral self, FloatKey a0) -> bool
2805 has_attribute(Dihedral self, IntKey a0) -> bool
2806 has_attribute(Dihedral self, StringKey a0) -> bool
2807 has_attribute(Dihedral self, ParticleIndexKey a0) -> bool
2808 has_attribute(Dihedral self, ObjectKey a0) -> bool
2810 return _IMP_atom.Dihedral_has_attribute(self, *args)
2813 def get_derivative(self, a0):
2814 """get_derivative(Dihedral self, FloatKey a0) -> double"""
2815 return _IMP_atom.Dihedral_get_derivative(self, a0)
2819 """get_name(Dihedral self) -> std::string"""
2820 return _IMP_atom.Dihedral_get_name(self)
2823 def clear_caches(self):
2824 """clear_caches(Dihedral self)"""
2825 return _IMP_atom.Dihedral_clear_caches(self)
2828 def set_name(self, a0):
2829 """set_name(Dihedral self, std::string a0)"""
2830 return _IMP_atom.Dihedral_set_name(self, a0)
2834 """set_check_level(Dihedral self, IMP::CheckLevel a0)"""
2835 return _IMP_atom.Dihedral_set_check_level(self, a0)
2838 def add_to_derivative(self, a0, a1, a2):
2839 """add_to_derivative(Dihedral self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2840 return _IMP_atom.Dihedral_add_to_derivative(self, a0, a1, a2)
2843 def set_is_optimized(self, a0, a1):
2844 """set_is_optimized(Dihedral self, FloatKey a0, bool a1)"""
2845 return _IMP_atom.Dihedral_set_is_optimized(self, a0, a1)
2848 def get_is_optimized(self, a0):
2849 """get_is_optimized(Dihedral self, FloatKey a0) -> bool"""
2850 return _IMP_atom.Dihedral_get_is_optimized(self, a0)
2854 """get_check_level(Dihedral self) -> IMP::CheckLevel"""
2855 return _IMP_atom.Dihedral_get_check_level(self)
2858 def __eq__(self, *args):
2860 __eq__(Dihedral self, Dihedral o) -> bool
2861 __eq__(Dihedral self, Particle d) -> bool
2863 return _IMP_atom.Dihedral___eq__(self, *args)
2866 def __ne__(self, *args):
2868 __ne__(Dihedral self, Dihedral o) -> bool
2869 __ne__(Dihedral self, Particle d) -> bool
2871 return _IMP_atom.Dihedral___ne__(self, *args)
2874 def __le__(self, *args):
2876 __le__(Dihedral self, Dihedral o) -> bool
2877 __le__(Dihedral self, Particle d) -> bool
2879 return _IMP_atom.Dihedral___le__(self, *args)
2882 def __lt__(self, *args):
2884 __lt__(Dihedral self, Dihedral o) -> bool
2885 __lt__(Dihedral self, Particle d) -> bool
2887 return _IMP_atom.Dihedral___lt__(self, *args)
2890 def __ge__(self, *args):
2892 __ge__(Dihedral self, Dihedral o) -> bool
2893 __ge__(Dihedral self, Particle d) -> bool
2895 return _IMP_atom.Dihedral___ge__(self, *args)
2898 def __gt__(self, *args):
2900 __gt__(Dihedral self, Dihedral o) -> bool
2901 __gt__(Dihedral self, Particle d) -> bool
2903 return _IMP_atom.Dihedral___gt__(self, *args)
2907 """__hash__(Dihedral self) -> std::size_t"""
2908 return _IMP_atom.Dihedral___hash__(self)
2912 """__str__(Dihedral self) -> std::string"""
2913 return _IMP_atom.Dihedral___str__(self)
2917 """__repr__(Dihedral self) -> std::string"""
2918 return _IMP_atom.Dihedral___repr__(self)
2920 __swig_destroy__ = _IMP_atom.delete_Dihedral
2921 __del__ =
lambda self:
None
2922 Dihedral_swigregister = _IMP_atom.Dihedral_swigregister
2923 Dihedral_swigregister(Dihedral)
2925 def Dihedral_setup_particle(*args):
2927 setup_particle(Model m, ParticleIndex pi, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2928 Dihedral_setup_particle(_ParticleAdaptor decorator, XYZ a, XYZ b, XYZ c, XYZ d) -> Dihedral
2930 return _IMP_atom.Dihedral_setup_particle(*args)
2932 def Dihedral_get_is_setup(*args):
2934 get_is_setup(_ParticleAdaptor p) -> bool
2935 Dihedral_get_is_setup(Model m, ParticleIndex pi) -> bool
2937 return _IMP_atom.Dihedral_get_is_setup(*args)
2939 def Dihedral_get_particle_key(i):
2940 """Dihedral_get_particle_key(unsigned int i) -> ParticleIndexKey"""
2941 return _IMP_atom.Dihedral_get_particle_key(i)
2943 def Dihedral_get_ideal_key():
2944 """Dihedral_get_ideal_key() -> FloatKey"""
2945 return _IMP_atom.Dihedral_get_ideal_key()
2947 def Dihedral_get_multiplicity_key():
2948 """Dihedral_get_multiplicity_key() -> IntKey"""
2949 return _IMP_atom.Dihedral_get_multiplicity_key()
2951 def Dihedral_get_stiffness_key():
2952 """Dihedral_get_stiffness_key() -> FloatKey"""
2953 return _IMP_atom.Dihedral_get_stiffness_key()
2956 """Proxy of C++ IMP::atom::SmoothingFunction class"""
2957 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2959 def __init__(self, *args, **kwargs):
2960 raise AttributeError(
"No constructor defined - class is abstract")
2962 def __call__(self, *args):
2964 __call__(SmoothingFunction self, double score, double distance) -> double
2965 __call__(SmoothingFunction self, double score, double deriv, double distance) -> IMP::DerivativePair
2967 return _IMP_atom.SmoothingFunction___call__(self, *args)
2969 __swig_destroy__ = _IMP_atom.delete_SmoothingFunction
2970 __del__ =
lambda self:
None
2973 """__str__(SmoothingFunction self) -> std::string"""
2974 return _IMP_atom.SmoothingFunction___str__(self)
2978 """__repr__(SmoothingFunction self) -> std::string"""
2979 return _IMP_atom.SmoothingFunction___repr__(self)
2984 return _object_cast_to_SmoothingFunction(o)
2986 SmoothingFunction_swigregister = _IMP_atom.SmoothingFunction_swigregister
2987 SmoothingFunction_swigregister(SmoothingFunction)
2989 class ForceSwitch(SmoothingFunction):
2990 """Proxy of C++ IMP::atom::ForceSwitch class"""
2991 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2993 def __init__(self, min_distance, max_distance):
2994 """__init__(IMP::atom::ForceSwitch self, double min_distance, double max_distance) -> ForceSwitch"""
2995 this = _IMP_atom.new_ForceSwitch(min_distance, max_distance)
2997 self.this.append(this)
3001 def __call__(self, *args):
3003 __call__(ForceSwitch self, double score, double distance) -> double
3004 __call__(ForceSwitch self, double score, double deriv, double distance) -> IMP::DerivativePair
3006 return _IMP_atom.ForceSwitch___call__(self, *args)
3009 def get_version_info(self):
3010 """get_version_info(ForceSwitch self) -> VersionInfo"""
3011 return _IMP_atom.ForceSwitch_get_version_info(self)
3015 """__str__(ForceSwitch self) -> std::string"""
3016 return _IMP_atom.ForceSwitch___str__(self)
3020 """__repr__(ForceSwitch self) -> std::string"""
3021 return _IMP_atom.ForceSwitch___repr__(self)
3026 return _object_cast_to_ForceSwitch(o)
3028 ForceSwitch_swigregister = _IMP_atom.ForceSwitch_swigregister
3029 ForceSwitch_swigregister(ForceSwitch)
3032 """Proxy of C++ IMP::atom::AngleSingletonScore class"""
3033 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3035 def __init__(self, f):
3036 """__init__(IMP::atom::AngleSingletonScore self, UnaryFunction f) -> AngleSingletonScore"""
3037 this = _IMP_atom.new_AngleSingletonScore(f)
3039 self.this.append(this)
3043 def do_get_inputs(self, m, pis):
3044 """do_get_inputs(AngleSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3045 return _IMP_atom.AngleSingletonScore_do_get_inputs(self, m, pis)
3048 def get_version_info(self):
3049 """get_version_info(AngleSingletonScore self) -> VersionInfo"""
3050 return _IMP_atom.AngleSingletonScore_get_version_info(self)
3054 """__str__(AngleSingletonScore self) -> std::string"""
3055 return _IMP_atom.AngleSingletonScore___str__(self)
3059 """__repr__(AngleSingletonScore self) -> std::string"""
3060 return _IMP_atom.AngleSingletonScore___repr__(self)
3065 return _object_cast_to_AngleSingletonScore(o)
3067 AngleSingletonScore_swigregister = _IMP_atom.AngleSingletonScore_swigregister
3068 AngleSingletonScore_swigregister(AngleSingletonScore)
3071 """Proxy of C++ IMP::atom::BondEndpointsRefiner class"""
3072 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3075 """__init__(IMP::atom::BondEndpointsRefiner self) -> BondEndpointsRefiner"""
3076 this = _IMP_atom.new_BondEndpointsRefiner()
3078 self.this.append(this)
3082 def do_get_inputs(self, m, pis):
3083 """do_get_inputs(BondEndpointsRefiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3084 return _IMP_atom.BondEndpointsRefiner_do_get_inputs(self, m, pis)
3087 def get_version_info(self):
3088 """get_version_info(BondEndpointsRefiner self) -> VersionInfo"""
3089 return _IMP_atom.BondEndpointsRefiner_get_version_info(self)
3093 """__str__(BondEndpointsRefiner self) -> std::string"""
3094 return _IMP_atom.BondEndpointsRefiner___str__(self)
3098 """__repr__(BondEndpointsRefiner self) -> std::string"""
3099 return _IMP_atom.BondEndpointsRefiner___repr__(self)
3104 return _object_cast_to_BondEndpointsRefiner(o)
3106 BondEndpointsRefiner_swigregister = _IMP_atom.BondEndpointsRefiner_swigregister
3107 BondEndpointsRefiner_swigregister(BondEndpointsRefiner)
3110 """Proxy of C++ IMP::atom::BondPairContainer class"""
3111 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3113 def __init__(self, sc):
3114 """__init__(IMP::atom::BondPairContainer self, SingletonContainer sc) -> BondPairContainer"""
3115 this = _IMP_atom.new_BondPairContainer(sc)
3117 self.this.append(this)
3121 def do_get_inputs(self):
3122 """do_get_inputs(BondPairContainer self) -> IMP::ModelObjectsTemp"""
3123 return _IMP_atom.BondPairContainer_do_get_inputs(self)
3126 def do_apply(self, sm):
3127 """do_apply(BondPairContainer self, PairModifier sm)"""
3128 return _IMP_atom.BondPairContainer_do_apply(self, sm)
3131 def get_version_info(self):
3132 """get_version_info(BondPairContainer self) -> VersionInfo"""
3133 return _IMP_atom.BondPairContainer_get_version_info(self)
3137 """__str__(BondPairContainer self) -> std::string"""
3138 return _IMP_atom.BondPairContainer___str__(self)
3142 """__repr__(BondPairContainer self) -> std::string"""
3143 return _IMP_atom.BondPairContainer___repr__(self)
3148 return _object_cast_to_BondPairContainer(o)
3150 BondPairContainer_swigregister = _IMP_atom.BondPairContainer_swigregister
3151 BondPairContainer_swigregister(BondPairContainer)
3154 """Proxy of C++ IMP::atom::BondSingletonScore class"""
3155 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3157 def __init__(self, f):
3158 """__init__(IMP::atom::BondSingletonScore self, UnaryFunction f) -> BondSingletonScore"""
3159 this = _IMP_atom.new_BondSingletonScore(f)
3161 self.this.append(this)
3165 def get_unary_function(self):
3166 """get_unary_function(BondSingletonScore self) -> UnaryFunction"""
3167 return _IMP_atom.BondSingletonScore_get_unary_function(self)
3170 def do_get_inputs(self, m, pis):
3171 """do_get_inputs(BondSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3172 return _IMP_atom.BondSingletonScore_do_get_inputs(self, m, pis)
3175 def get_version_info(self):
3176 """get_version_info(BondSingletonScore self) -> VersionInfo"""
3177 return _IMP_atom.BondSingletonScore_get_version_info(self)
3181 """__str__(BondSingletonScore self) -> std::string"""
3182 return _IMP_atom.BondSingletonScore___str__(self)
3186 """__repr__(BondSingletonScore self) -> std::string"""
3187 return _IMP_atom.BondSingletonScore___repr__(self)
3192 return _object_cast_to_BondSingletonScore(o)
3194 BondSingletonScore_swigregister = _IMP_atom.BondSingletonScore_swigregister
3195 BondSingletonScore_swigregister(BondSingletonScore)
3198 """Proxy of C++ IMP::atom::DihedralSingletonScore class"""
3199 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3202 """__init__(IMP::atom::DihedralSingletonScore self) -> DihedralSingletonScore"""
3203 this = _IMP_atom.new_DihedralSingletonScore()
3205 self.this.append(this)
3209 def do_get_inputs(self, m, pis):
3210 """do_get_inputs(DihedralSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3211 return _IMP_atom.DihedralSingletonScore_do_get_inputs(self, m, pis)
3214 def get_version_info(self):
3215 """get_version_info(DihedralSingletonScore self) -> VersionInfo"""
3216 return _IMP_atom.DihedralSingletonScore_get_version_info(self)
3220 """__str__(DihedralSingletonScore self) -> std::string"""
3221 return _IMP_atom.DihedralSingletonScore___str__(self)
3225 """__repr__(DihedralSingletonScore self) -> std::string"""
3226 return _IMP_atom.DihedralSingletonScore___repr__(self)
3231 return _object_cast_to_DihedralSingletonScore(o)
3233 DihedralSingletonScore_swigregister = _IMP_atom.DihedralSingletonScore_swigregister
3234 DihedralSingletonScore_swigregister(DihedralSingletonScore)
3237 """Proxy of C++ IMP::atom::ImproperSingletonScore class"""
3238 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3240 def __init__(self, f):
3241 """__init__(IMP::atom::ImproperSingletonScore self, UnaryFunction f) -> ImproperSingletonScore"""
3242 this = _IMP_atom.new_ImproperSingletonScore(f)
3244 self.this.append(this)
3248 def do_get_inputs(self, m, pis):
3249 """do_get_inputs(ImproperSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3250 return _IMP_atom.ImproperSingletonScore_do_get_inputs(self, m, pis)
3253 def get_version_info(self):
3254 """get_version_info(ImproperSingletonScore self) -> VersionInfo"""
3255 return _IMP_atom.ImproperSingletonScore_get_version_info(self)
3259 """__str__(ImproperSingletonScore self) -> std::string"""
3260 return _IMP_atom.ImproperSingletonScore___str__(self)
3264 """__repr__(ImproperSingletonScore self) -> std::string"""
3265 return _IMP_atom.ImproperSingletonScore___repr__(self)
3270 return _object_cast_to_ImproperSingletonScore(o)
3272 ImproperSingletonScore_swigregister = _IMP_atom.ImproperSingletonScore_swigregister
3273 ImproperSingletonScore_swigregister(ImproperSingletonScore)
3276 """Proxy of C++ IMP::atom::CenterOfMass class"""
3277 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3279 def get_constraint(self):
3280 """get_constraint(CenterOfMass self) -> Constraint"""
3281 return _IMP_atom.CenterOfMass_get_constraint(self)
3285 """get_mass(CenterOfMass self) -> IMP::Float"""
3286 return _IMP_atom.CenterOfMass_get_mass(self)
3289 def get_coordinate(self, i):
3290 """get_coordinate(CenterOfMass self, int i) -> IMP::Float"""
3291 return _IMP_atom.CenterOfMass_get_coordinate(self, i)
3294 def get_coordinates(self):
3295 """get_coordinates(CenterOfMass self) -> Vector3D"""
3296 return _IMP_atom.CenterOfMass_get_coordinates(self)
3299 def __init__(self, *args):
3301 __init__(IMP::atom::CenterOfMass self) -> CenterOfMass
3302 __init__(IMP::atom::CenterOfMass self, Model m, ParticleIndex id) -> CenterOfMass
3303 __init__(IMP::atom::CenterOfMass self, _ParticleAdaptor d) -> CenterOfMass
3305 this = _IMP_atom.new_CenterOfMass(*args)
3307 self.this.append(this)
3311 def show(self, *args):
3313 show(CenterOfMass self, _ostream out)
3314 show(CenterOfMass self)
3316 return _IMP_atom.CenterOfMass_show(self, *args)
3319 def setup_particle(*args):
3321 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3322 setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3323 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3324 setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3326 return _IMP_atom.CenterOfMass_setup_particle(*args)
3328 setup_particle = staticmethod(setup_particle)
3330 def get_is_setup(*args):
3332 get_is_setup(_ParticleAdaptor p) -> bool
3333 get_is_setup(Model m, ParticleIndex pi) -> bool
3335 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3337 get_is_setup = staticmethod(get_is_setup)
3339 def add_attribute(self, *args):
3341 add_attribute(CenterOfMass self, FloatKey k, IMP::Float v, bool opt)
3342 add_attribute(CenterOfMass self, FloatKey a0, IMP::Float a1)
3343 add_attribute(CenterOfMass self, IntKey a0, IMP::Int a1)
3344 add_attribute(CenterOfMass self, StringKey a0, IMP::String a1)
3345 add_attribute(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3346 add_attribute(CenterOfMass self, ObjectKey a0, Object a1)
3348 return _IMP_atom.CenterOfMass_add_attribute(self, *args)
3351 def get_value(self, *args):
3353 get_value(CenterOfMass self, FloatKey a0) -> IMP::Float
3354 get_value(CenterOfMass self, IntKey a0) -> IMP::Int
3355 get_value(CenterOfMass self, StringKey a0) -> IMP::String
3356 get_value(CenterOfMass self, ParticleIndexKey a0) -> Particle
3357 get_value(CenterOfMass self, ObjectKey a0) -> Object
3359 return _IMP_atom.CenterOfMass_get_value(self, *args)
3362 def set_value(self, *args):
3364 set_value(CenterOfMass self, FloatKey a0, IMP::Float a1)
3365 set_value(CenterOfMass self, IntKey a0, IMP::Int a1)
3366 set_value(CenterOfMass self, StringKey a0, IMP::String a1)
3367 set_value(CenterOfMass self, ParticleIndexKey a0, Particle a1)
3368 set_value(CenterOfMass self, ObjectKey a0, Object a1)
3370 return _IMP_atom.CenterOfMass_set_value(self, *args)
3373 def remove_attribute(self, *args):
3375 remove_attribute(CenterOfMass self, FloatKey a0)
3376 remove_attribute(CenterOfMass self, IntKey a0)
3377 remove_attribute(CenterOfMass self, StringKey a0)
3378 remove_attribute(CenterOfMass self, ParticleIndexKey a0)
3379 remove_attribute(CenterOfMass self, ObjectKey a0)
3381 return _IMP_atom.CenterOfMass_remove_attribute(self, *args)
3384 def has_attribute(self, *args):
3386 has_attribute(CenterOfMass self, FloatKey a0) -> bool
3387 has_attribute(CenterOfMass self, IntKey a0) -> bool
3388 has_attribute(CenterOfMass self, StringKey a0) -> bool
3389 has_attribute(CenterOfMass self, ParticleIndexKey a0) -> bool
3390 has_attribute(CenterOfMass self, ObjectKey a0) -> bool
3392 return _IMP_atom.CenterOfMass_has_attribute(self, *args)
3395 def get_derivative(self, a0):
3396 """get_derivative(CenterOfMass self, FloatKey a0) -> double"""
3397 return _IMP_atom.CenterOfMass_get_derivative(self, a0)
3401 """get_name(CenterOfMass self) -> std::string"""
3402 return _IMP_atom.CenterOfMass_get_name(self)
3405 def clear_caches(self):
3406 """clear_caches(CenterOfMass self)"""
3407 return _IMP_atom.CenterOfMass_clear_caches(self)
3410 def set_name(self, a0):
3411 """set_name(CenterOfMass self, std::string a0)"""
3412 return _IMP_atom.CenterOfMass_set_name(self, a0)
3416 """set_check_level(CenterOfMass self, IMP::CheckLevel a0)"""
3417 return _IMP_atom.CenterOfMass_set_check_level(self, a0)
3420 def add_to_derivative(self, a0, a1, a2):
3421 """add_to_derivative(CenterOfMass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3422 return _IMP_atom.CenterOfMass_add_to_derivative(self, a0, a1, a2)
3425 def set_is_optimized(self, a0, a1):
3426 """set_is_optimized(CenterOfMass self, FloatKey a0, bool a1)"""
3427 return _IMP_atom.CenterOfMass_set_is_optimized(self, a0, a1)
3430 def get_is_optimized(self, a0):
3431 """get_is_optimized(CenterOfMass self, FloatKey a0) -> bool"""
3432 return _IMP_atom.CenterOfMass_get_is_optimized(self, a0)
3436 """get_check_level(CenterOfMass self) -> IMP::CheckLevel"""
3437 return _IMP_atom.CenterOfMass_get_check_level(self)
3440 def __eq__(self, *args):
3442 __eq__(CenterOfMass self, CenterOfMass o) -> bool
3443 __eq__(CenterOfMass self, Particle d) -> bool
3445 return _IMP_atom.CenterOfMass___eq__(self, *args)
3448 def __ne__(self, *args):
3450 __ne__(CenterOfMass self, CenterOfMass o) -> bool
3451 __ne__(CenterOfMass self, Particle d) -> bool
3453 return _IMP_atom.CenterOfMass___ne__(self, *args)
3456 def __le__(self, *args):
3458 __le__(CenterOfMass self, CenterOfMass o) -> bool
3459 __le__(CenterOfMass self, Particle d) -> bool
3461 return _IMP_atom.CenterOfMass___le__(self, *args)
3464 def __lt__(self, *args):
3466 __lt__(CenterOfMass self, CenterOfMass o) -> bool
3467 __lt__(CenterOfMass self, Particle d) -> bool
3469 return _IMP_atom.CenterOfMass___lt__(self, *args)
3472 def __ge__(self, *args):
3474 __ge__(CenterOfMass self, CenterOfMass o) -> bool
3475 __ge__(CenterOfMass self, Particle d) -> bool
3477 return _IMP_atom.CenterOfMass___ge__(self, *args)
3480 def __gt__(self, *args):
3482 __gt__(CenterOfMass self, CenterOfMass o) -> bool
3483 __gt__(CenterOfMass self, Particle d) -> bool
3485 return _IMP_atom.CenterOfMass___gt__(self, *args)
3489 """__hash__(CenterOfMass self) -> std::size_t"""
3490 return _IMP_atom.CenterOfMass___hash__(self)
3494 """__str__(CenterOfMass self) -> std::string"""
3495 return _IMP_atom.CenterOfMass___str__(self)
3499 """__repr__(CenterOfMass self) -> std::string"""
3500 return _IMP_atom.CenterOfMass___repr__(self)
3502 __swig_destroy__ = _IMP_atom.delete_CenterOfMass
3503 __del__ =
lambda self:
None
3504 CenterOfMass_swigregister = _IMP_atom.CenterOfMass_swigregister
3505 CenterOfMass_swigregister(CenterOfMass)
3507 def CenterOfMass_setup_particle(*args):
3509 setup_particle(Model m, ParticleIndex pi, _ParticleIndexesAdaptor members) -> CenterOfMass
3510 setup_particle(_ParticleAdaptor decorator, _ParticleIndexesAdaptor members) -> CenterOfMass
3511 setup_particle(Model m, ParticleIndex pi, Refiner refiner) -> CenterOfMass
3512 CenterOfMass_setup_particle(_ParticleAdaptor decorator, Refiner refiner) -> CenterOfMass
3514 return _IMP_atom.CenterOfMass_setup_particle(*args)
3516 def CenterOfMass_get_is_setup(*args):
3518 get_is_setup(_ParticleAdaptor p) -> bool
3519 CenterOfMass_get_is_setup(Model m, ParticleIndex pi) -> bool
3521 return _IMP_atom.CenterOfMass_get_is_setup(*args)
3524 """Proxy of C++ IMP::atom::CoverBond class"""
3525 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3528 """__init__(IMP::atom::CoverBond self) -> CoverBond"""
3529 this = _IMP_atom.new_CoverBond()
3531 self.this.append(this)
3535 def do_get_inputs(self, m, pis):
3536 """do_get_inputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3537 return _IMP_atom.CoverBond_do_get_inputs(self, m, pis)
3540 def do_get_outputs(self, m, pis):
3541 """do_get_outputs(CoverBond self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3542 return _IMP_atom.CoverBond_do_get_outputs(self, m, pis)
3545 def get_version_info(self):
3546 """get_version_info(CoverBond self) -> VersionInfo"""
3547 return _IMP_atom.CoverBond_get_version_info(self)
3551 """__str__(CoverBond self) -> std::string"""
3552 return _IMP_atom.CoverBond___str__(self)
3556 """__repr__(CoverBond self) -> std::string"""
3557 return _IMP_atom.CoverBond___repr__(self)
3562 return _object_cast_to_CoverBond(o)
3564 CoverBond_swigregister = _IMP_atom.CoverBond_swigregister
3565 CoverBond_swigregister(CoverBond)
3568 """Proxy of C++ IMP::atom::Simulator class"""
3569 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3571 def __init__(self, *args):
3573 __init__(IMP::atom::Simulator self, Model m, std::string name, double wave_factor=1.0) -> Simulator
3574 __init__(IMP::atom::Simulator self, Model m, std::string name) -> Simulator
3575 __init__(IMP::atom::Simulator self, Model m) -> Simulator
3577 if self.__class__ == Simulator:
3581 this = _IMP_atom.new_Simulator(_self, *args)
3583 self.this.append(this)
3587 if self.__class__ != Simulator:
3588 _director_objects.register(self)
3593 def simulate(self, time_in_fs):
3594 """simulate(Simulator self, double time_in_fs) -> double"""
3595 return _IMP_atom.Simulator_simulate(self, time_in_fs)
3598 def simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3600 simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3601 simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3602 simulate_wave(Simulator self, double time_in_fs) -> double
3604 return _IMP_atom.Simulator_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3607 def get_temperature(self):
3608 """get_temperature(Simulator self) -> double"""
3609 return _IMP_atom.Simulator_get_temperature(self)
3612 def set_temperature(self, d):
3613 """set_temperature(Simulator self, double d)"""
3614 return _IMP_atom.Simulator_set_temperature(self, d)
3617 def set_maximum_time_step(self, ts):
3618 """set_maximum_time_step(Simulator self, double ts)"""
3619 return _IMP_atom.Simulator_set_maximum_time_step(self, ts)
3622 def get_maximum_time_step(self):
3623 """get_maximum_time_step(Simulator self) -> double"""
3624 return _IMP_atom.Simulator_get_maximum_time_step(self)
3627 def get_last_time_step(self):
3628 """get_last_time_step(Simulator self) -> double"""
3629 return _IMP_atom.Simulator_get_last_time_step(self)
3632 def set_time_step(self, ts):
3633 """set_time_step(Simulator self, double ts)"""
3634 return _IMP_atom.Simulator_set_time_step(self, ts)
3638 """get_kt(Simulator self) -> double"""
3639 return _IMP_atom.Simulator_get_kt(self)
3642 def get_current_time(self):
3643 """get_current_time(Simulator self) -> double"""
3644 return _IMP_atom.Simulator_get_current_time(self)
3647 def set_current_time(self, ct):
3648 """set_current_time(Simulator self, double ct)"""
3649 return _IMP_atom.Simulator_set_current_time(self, ct)
3652 def get_simulation_particles(self):
3653 """get_simulation_particles(Simulator self) -> IMP::ParticlesTemp"""
3654 return _IMP_atom.Simulator_get_simulation_particles(self)
3657 def get_simulation_particle_indexes(self):
3658 """get_simulation_particle_indexes(Simulator self) -> IMP::ParticleIndexes"""
3659 return _IMP_atom.Simulator_get_simulation_particle_indexes(self)
3662 def remove_particle(self, d):
3663 """remove_particle(Simulator self, Particle d)"""
3664 return _IMP_atom.Simulator_remove_particle(self, d)
3667 def remove_particles(self, d):
3668 """remove_particles(Simulator self, IMP::Particles const & d)"""
3669 return _IMP_atom.Simulator_remove_particles(self, d)
3672 def set_particles(self, ps):
3673 """set_particles(Simulator self, IMP::Particles const & ps)"""
3674 return _IMP_atom.Simulator_set_particles(self, ps)
3677 def set_particles_order(self, objs):
3678 """set_particles_order(Simulator self, IMP::Particles const & objs)"""
3679 return _IMP_atom.Simulator_set_particles_order(self, objs)
3683 """add_particle(Simulator self, Particle obj) -> unsigned int"""
3684 return _IMP_atom.Simulator_add_particle(self, obj)
3688 """add_particles(Simulator self, IMP::Particles const & objs)"""
3689 return _IMP_atom.Simulator_add_particles(self, objs)
3692 def clear_particles(self):
3693 """clear_particles(Simulator self)"""
3694 return _IMP_atom.Simulator_clear_particles(self)
3697 def get_number_of_particles(self):
3698 """get_number_of_particles(Simulator self) -> unsigned int"""
3699 return _IMP_atom.Simulator_get_number_of_particles(self)
3702 def get_has_particles(self):
3703 """get_has_particles(Simulator self) -> bool"""
3704 return _IMP_atom.Simulator_get_has_particles(self)
3707 def get_particle(self, i):
3708 """get_particle(Simulator self, unsigned int i) -> Particle"""
3709 return _IMP_atom.Simulator_get_particle(self, i)
3713 """get_particles(Simulator self) -> IMP::Particles"""
3714 return _IMP_atom.Simulator_get_particles(self)
3717 def reserve_particles(self, sz):
3718 """reserve_particles(Simulator self, unsigned int sz)"""
3719 return _IMP_atom.Simulator_reserve_particles(self, sz)
3722 def do_optimize(self, max_steps):
3723 """do_optimize(Simulator self, unsigned int max_steps) -> IMP::Float"""
3724 return _IMP_atom.Simulator_do_optimize(self, max_steps)
3727 def setup(self, arg0):
3728 """setup(Simulator self, IMP::ParticleIndexes const & arg0)"""
3729 return _IMP_atom.Simulator_setup(self, arg0)
3732 def do_step(self, sc, dt):
3733 """do_step(Simulator self, IMP::ParticleIndexes const & sc, double dt) -> double"""
3734 return _IMP_atom.Simulator_do_step(self, sc, dt)
3737 def get_is_simulation_particle(self, p):
3738 """get_is_simulation_particle(Simulator self, ParticleIndex p) -> bool"""
3739 return _IMP_atom.Simulator_get_is_simulation_particle(self, p)
3742 def do_simulate(self, time):
3743 """do_simulate(Simulator self, double time) -> double"""
3744 return _IMP_atom.Simulator_do_simulate(self, time)
3747 def do_simulate_wave(self, time_in_fs, max_time_step_factor=10.0, base=1.5):
3749 do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0, double base=1.5) -> double
3750 do_simulate_wave(Simulator self, double time_in_fs, double max_time_step_factor=10.0) -> double
3751 do_simulate_wave(Simulator self, double time_in_fs) -> double
3753 return _IMP_atom.Simulator_do_simulate_wave(self, time_in_fs, max_time_step_factor, base)
3757 """__str__(Simulator self) -> std::string"""
3758 return _IMP_atom.Simulator___str__(self)
3762 """__repr__(Simulator self) -> std::string"""
3763 return _IMP_atom.Simulator___repr__(self)
3768 return _object_cast_to_Simulator(o)
3771 def get_type_name(self):
3772 return self.__class__.__name__
3773 def do_show(self, out):
3775 def get_version_info(self):
3776 if"IMP::atom" ==
"IMP":
3777 return VersionInfo(self.__module__,
3778 __import__(self.__module__).get_module_version())
3781 __import__(self.__module__).get_module_version())
3784 return _object_cast_to_Simulator(o)
3786 __swig_destroy__ = _IMP_atom.delete_Simulator
3787 __del__ =
lambda self:
None
3788 def __disown__(self):
3790 _IMP_atom.disown_Simulator(self)
3791 return weakref_proxy(self)
3793 def do_destroy(self):
3794 """do_destroy(Simulator self)"""
3795 return _IMP_atom.Simulator_do_destroy(self)
3798 def handle_set_has_required_score_states(self, arg0):
3799 """handle_set_has_required_score_states(Simulator self, bool arg0)"""
3800 return _IMP_atom.Simulator_handle_set_has_required_score_states(self, arg0)
3803 def do_get_inputs(self):
3804 """do_get_inputs(Simulator self) -> IMP::ModelObjectsTemp"""
3805 return _IMP_atom.Simulator_do_get_inputs(self)
3808 def do_get_outputs(self):
3809 """do_get_outputs(Simulator self) -> IMP::ModelObjectsTemp"""
3810 return _IMP_atom.Simulator_do_get_outputs(self)
3813 def do_get_interactions(self):
3814 """do_get_interactions(Simulator self) -> IMP::ModelObjectsTemps"""
3815 return _IMP_atom.Simulator_do_get_interactions(self)
3817 Simulator_swigregister = _IMP_atom.Simulator_swigregister
3818 Simulator_swigregister(Simulator)
3821 def get_energy_in_femto_joules(energy_in_kcal_per_mol):
3822 """get_energy_in_femto_joules(double energy_in_kcal_per_mol) -> double"""
3823 return _IMP_atom.get_energy_in_femto_joules(energy_in_kcal_per_mol)
3825 def get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom):
3826 """get_force_in_femto_newtons(double force_in_kcal_per_mol_per_angstrom) -> double"""
3827 return _IMP_atom.get_force_in_femto_newtons(force_in_kcal_per_mol_per_angstrom)
3829 def get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square):
3830 """get_spring_constant_in_femto_newtons_per_angstrom(double k_in_kcal_per_mol_per_angstrom_square) -> double"""
3831 return _IMP_atom.get_spring_constant_in_femto_newtons_per_angstrom(k_in_kcal_per_mol_per_angstrom_square)
3833 _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE_swigconstant(_IMP_atom)
3834 IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE = _IMP_atom.IMP_ATOM_DEFAULT_BD_RANDOM_POOL_SIZE
3835 class BrownianDynamics(Simulator):
3836 """Proxy of C++ IMP::atom::BrownianDynamics class"""
3837 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3839 def __init__(self, *args):
3841 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0, unsigned int random_pool_size=500) -> BrownianDynamics
3842 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamics
3843 __init__(IMP::atom::BrownianDynamics self, Model m, std::string name) -> BrownianDynamics
3844 __init__(IMP::atom::BrownianDynamics self, Model m) -> BrownianDynamics
3846 this = _IMP_atom.new_BrownianDynamics(*args)
3848 self.this.append(this)
3852 def set_maximum_move(self, ms):
3853 """set_maximum_move(BrownianDynamics self, double ms)"""
3854 return _IMP_atom.BrownianDynamics_set_maximum_move(self, ms)
3857 def set_use_stochastic_runge_kutta(self, tf):
3858 """set_use_stochastic_runge_kutta(BrownianDynamics self, bool tf)"""
3859 return _IMP_atom.BrownianDynamics_set_use_stochastic_runge_kutta(self, tf)
3862 def get_version_info(self):
3863 """get_version_info(BrownianDynamics self) -> VersionInfo"""
3864 return _IMP_atom.BrownianDynamics_get_version_info(self)
3868 """__str__(BrownianDynamics self) -> std::string"""
3869 return _IMP_atom.BrownianDynamics___str__(self)
3873 """__repr__(BrownianDynamics self) -> std::string"""
3874 return _IMP_atom.BrownianDynamics___repr__(self)
3879 return _object_cast_to_BrownianDynamics(o)
3881 BrownianDynamics_swigregister = _IMP_atom.BrownianDynamics_swigregister
3882 BrownianDynamics_swigregister(BrownianDynamics)
3886 """get_maximum_time_step_estimate(BrownianDynamics bd) -> double"""
3887 return _IMP_atom.get_maximum_time_step_estimate(bd)
3889 def get_harmonic_sigma(D, f):
3890 """get_harmonic_sigma(double D, double f) -> double"""
3891 return _IMP_atom.get_harmonic_sigma(D, f)
3892 class BrownianDynamicsTAMD(BrownianDynamics):
3893 """Proxy of C++ IMP::atom::BrownianDynamicsTAMD class"""
3894 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3896 def __init__(self, *args):
3898 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMD
3899 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m, std::string name) -> BrownianDynamicsTAMD
3900 __init__(IMP::atom::BrownianDynamicsTAMD self, Model m) -> BrownianDynamicsTAMD
3902 this = _IMP_atom.new_BrownianDynamicsTAMD(*args)
3904 self.this.append(this)
3909 """__str__(BrownianDynamicsTAMD self) -> std::string"""
3910 return _IMP_atom.BrownianDynamicsTAMD___str__(self)
3914 """__repr__(BrownianDynamicsTAMD self) -> std::string"""
3915 return _IMP_atom.BrownianDynamicsTAMD___repr__(self)
3920 return _object_cast_to_BrownianDynamicsTAMD(o)
3922 __swig_destroy__ = _IMP_atom.delete_BrownianDynamicsTAMD
3923 __del__ =
lambda self:
None
3924 BrownianDynamicsTAMD_swigregister = _IMP_atom.BrownianDynamicsTAMD_swigregister
3925 BrownianDynamicsTAMD_swigregister(BrownianDynamicsTAMD)
3928 """Proxy of C++ IMP::atom::Diffusion class"""
3929 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3931 def __init__(self, *args):
3933 __init__(IMP::atom::Diffusion self) -> Diffusion
3934 __init__(IMP::atom::Diffusion self, Model m, ParticleIndex id) -> Diffusion
3935 __init__(IMP::atom::Diffusion self, _ParticleAdaptor d) -> Diffusion
3937 this = _IMP_atom.new_Diffusion(*args)
3939 self.this.append(this)
3943 def show(self, *args):
3945 show(Diffusion self, _ostream out)
3946 show(Diffusion self)
3948 return _IMP_atom.Diffusion_show(self, *args)
3951 def setup_particle(*args):
3953 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
3954 setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
3955 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
3956 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
3957 setup_particle(Model m, ParticleIndex pi) -> Diffusion
3958 setup_particle(_ParticleAdaptor decorator) -> Diffusion
3960 return _IMP_atom.Diffusion_setup_particle(*args)
3962 setup_particle = staticmethod(setup_particle)
3964 def get_is_setup(*args):
3966 get_is_setup(_ParticleAdaptor p) -> bool
3967 get_is_setup(Model m, ParticleIndex p) -> bool
3969 return _IMP_atom.Diffusion_get_is_setup(*args)
3971 get_is_setup = staticmethod(get_is_setup)
3973 def set_diffusion_coefficient(self, d):
3974 """set_diffusion_coefficient(Diffusion self, double d)"""
3975 return _IMP_atom.Diffusion_set_diffusion_coefficient(self, d)
3979 """get_diffusion_coefficient(Diffusion self) -> double"""
3980 return _IMP_atom.Diffusion_get_diffusion_coefficient(self)
3983 def get_diffusion_coefficient_key():
3984 """get_diffusion_coefficient_key() -> FloatKey"""
3985 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
3987 get_diffusion_coefficient_key = staticmethod(get_diffusion_coefficient_key)
3989 def add_attribute(self, *args):
3991 add_attribute(Diffusion self, FloatKey k, IMP::Float v, bool opt)
3992 add_attribute(Diffusion self, FloatKey a0, IMP::Float a1)
3993 add_attribute(Diffusion self, IntKey a0, IMP::Int a1)
3994 add_attribute(Diffusion self, StringKey a0, IMP::String a1)
3995 add_attribute(Diffusion self, ParticleIndexKey a0, Particle a1)
3996 add_attribute(Diffusion self, ObjectKey a0, Object a1)
3998 return _IMP_atom.Diffusion_add_attribute(self, *args)
4001 def get_value(self, *args):
4003 get_value(Diffusion self, FloatKey a0) -> IMP::Float
4004 get_value(Diffusion self, IntKey a0) -> IMP::Int
4005 get_value(Diffusion self, StringKey a0) -> IMP::String
4006 get_value(Diffusion self, ParticleIndexKey a0) -> Particle
4007 get_value(Diffusion self, ObjectKey a0) -> Object
4009 return _IMP_atom.Diffusion_get_value(self, *args)
4012 def set_value(self, *args):
4014 set_value(Diffusion self, FloatKey a0, IMP::Float a1)
4015 set_value(Diffusion self, IntKey a0, IMP::Int a1)
4016 set_value(Diffusion self, StringKey a0, IMP::String a1)
4017 set_value(Diffusion self, ParticleIndexKey a0, Particle a1)
4018 set_value(Diffusion self, ObjectKey a0, Object a1)
4020 return _IMP_atom.Diffusion_set_value(self, *args)
4023 def remove_attribute(self, *args):
4025 remove_attribute(Diffusion self, FloatKey a0)
4026 remove_attribute(Diffusion self, IntKey a0)
4027 remove_attribute(Diffusion self, StringKey a0)
4028 remove_attribute(Diffusion self, ParticleIndexKey a0)
4029 remove_attribute(Diffusion self, ObjectKey a0)
4031 return _IMP_atom.Diffusion_remove_attribute(self, *args)
4034 def has_attribute(self, *args):
4036 has_attribute(Diffusion self, FloatKey a0) -> bool
4037 has_attribute(Diffusion self, IntKey a0) -> bool
4038 has_attribute(Diffusion self, StringKey a0) -> bool
4039 has_attribute(Diffusion self, ParticleIndexKey a0) -> bool
4040 has_attribute(Diffusion self, ObjectKey a0) -> bool
4042 return _IMP_atom.Diffusion_has_attribute(self, *args)
4045 def get_derivative(self, a0):
4046 """get_derivative(Diffusion self, FloatKey a0) -> double"""
4047 return _IMP_atom.Diffusion_get_derivative(self, a0)
4051 """get_name(Diffusion self) -> std::string"""
4052 return _IMP_atom.Diffusion_get_name(self)
4055 def clear_caches(self):
4056 """clear_caches(Diffusion self)"""
4057 return _IMP_atom.Diffusion_clear_caches(self)
4060 def set_name(self, a0):
4061 """set_name(Diffusion self, std::string a0)"""
4062 return _IMP_atom.Diffusion_set_name(self, a0)
4066 """set_check_level(Diffusion self, IMP::CheckLevel a0)"""
4067 return _IMP_atom.Diffusion_set_check_level(self, a0)
4070 def add_to_derivative(self, a0, a1, a2):
4071 """add_to_derivative(Diffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4072 return _IMP_atom.Diffusion_add_to_derivative(self, a0, a1, a2)
4075 def set_is_optimized(self, a0, a1):
4076 """set_is_optimized(Diffusion self, FloatKey a0, bool a1)"""
4077 return _IMP_atom.Diffusion_set_is_optimized(self, a0, a1)
4080 def get_is_optimized(self, a0):
4081 """get_is_optimized(Diffusion self, FloatKey a0) -> bool"""
4082 return _IMP_atom.Diffusion_get_is_optimized(self, a0)
4086 """get_check_level(Diffusion self) -> IMP::CheckLevel"""
4087 return _IMP_atom.Diffusion_get_check_level(self)
4090 def __eq__(self, *args):
4092 __eq__(Diffusion self, Diffusion o) -> bool
4093 __eq__(Diffusion self, Particle d) -> bool
4095 return _IMP_atom.Diffusion___eq__(self, *args)
4098 def __ne__(self, *args):
4100 __ne__(Diffusion self, Diffusion o) -> bool
4101 __ne__(Diffusion self, Particle d) -> bool
4103 return _IMP_atom.Diffusion___ne__(self, *args)
4106 def __le__(self, *args):
4108 __le__(Diffusion self, Diffusion o) -> bool
4109 __le__(Diffusion self, Particle d) -> bool
4111 return _IMP_atom.Diffusion___le__(self, *args)
4114 def __lt__(self, *args):
4116 __lt__(Diffusion self, Diffusion o) -> bool
4117 __lt__(Diffusion self, Particle d) -> bool
4119 return _IMP_atom.Diffusion___lt__(self, *args)
4122 def __ge__(self, *args):
4124 __ge__(Diffusion self, Diffusion o) -> bool
4125 __ge__(Diffusion self, Particle d) -> bool
4127 return _IMP_atom.Diffusion___ge__(self, *args)
4130 def __gt__(self, *args):
4132 __gt__(Diffusion self, Diffusion o) -> bool
4133 __gt__(Diffusion self, Particle d) -> bool
4135 return _IMP_atom.Diffusion___gt__(self, *args)
4139 """__hash__(Diffusion self) -> std::size_t"""
4140 return _IMP_atom.Diffusion___hash__(self)
4144 """__str__(Diffusion self) -> std::string"""
4145 return _IMP_atom.Diffusion___str__(self)
4149 """__repr__(Diffusion self) -> std::string"""
4150 return _IMP_atom.Diffusion___repr__(self)
4152 __swig_destroy__ = _IMP_atom.delete_Diffusion
4153 __del__ =
lambda self:
None
4154 Diffusion_swigregister = _IMP_atom.Diffusion_swigregister
4155 Diffusion_swigregister(Diffusion)
4157 def Diffusion_setup_particle(*args):
4159 setup_particle(Model m, ParticleIndex pi, IMP::Float D) -> Diffusion
4160 setup_particle(_ParticleAdaptor decorator, IMP::Float D) -> Diffusion
4161 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float D) -> Diffusion
4162 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float D) -> Diffusion
4163 setup_particle(Model m, ParticleIndex pi) -> Diffusion
4164 Diffusion_setup_particle(_ParticleAdaptor decorator) -> Diffusion
4166 return _IMP_atom.Diffusion_setup_particle(*args)
4168 def Diffusion_get_is_setup(*args):
4170 get_is_setup(_ParticleAdaptor p) -> bool
4171 Diffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4173 return _IMP_atom.Diffusion_get_is_setup(*args)
4175 def Diffusion_get_diffusion_coefficient_key():
4176 """Diffusion_get_diffusion_coefficient_key() -> FloatKey"""
4177 return _IMP_atom.Diffusion_get_diffusion_coefficient_key()
4180 def get_diffusion_coefficient_from_cm2_per_second(din):
4181 """get_diffusion_coefficient_from_cm2_per_second(double din) -> double"""
4182 return _IMP_atom.get_diffusion_coefficient_from_cm2_per_second(din)
4183 class RigidBodyDiffusion(Diffusion):
4184 """Proxy of C++ IMP::atom::RigidBodyDiffusion class"""
4185 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4187 def __init__(self, *args):
4189 __init__(IMP::atom::RigidBodyDiffusion self) -> RigidBodyDiffusion
4190 __init__(IMP::atom::RigidBodyDiffusion self, Model m, ParticleIndex id) -> RigidBodyDiffusion
4191 __init__(IMP::atom::RigidBodyDiffusion self, _ParticleAdaptor d) -> RigidBodyDiffusion
4193 this = _IMP_atom.new_RigidBodyDiffusion(*args)
4195 self.this.append(this)
4199 def show(self, *args):
4201 show(RigidBodyDiffusion self, _ostream out)
4202 show(RigidBodyDiffusion self)
4204 return _IMP_atom.RigidBodyDiffusion_show(self, *args)
4207 def setup_particle(*args):
4209 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4210 setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4212 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4214 setup_particle = staticmethod(setup_particle)
4217 """get_rotational_diffusion_coefficient(RigidBodyDiffusion self) -> double"""
4218 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient(self)
4221 def set_rotational_diffusion_coefficient(self, d):
4222 """set_rotational_diffusion_coefficient(RigidBodyDiffusion self, double d)"""
4223 return _IMP_atom.RigidBodyDiffusion_set_rotational_diffusion_coefficient(self, d)
4226 def get_is_setup(*args):
4228 get_is_setup(_ParticleAdaptor p) -> bool
4229 get_is_setup(Model m, ParticleIndex p) -> bool
4231 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4233 get_is_setup = staticmethod(get_is_setup)
4235 def get_rotational_diffusion_coefficient_key():
4236 """get_rotational_diffusion_coefficient_key() -> FloatKey"""
4237 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4239 get_rotational_diffusion_coefficient_key = staticmethod(get_rotational_diffusion_coefficient_key)
4241 def add_attribute(self, *args):
4243 add_attribute(RigidBodyDiffusion self, FloatKey k, IMP::Float v, bool opt)
4244 add_attribute(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4245 add_attribute(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4246 add_attribute(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4247 add_attribute(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4248 add_attribute(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4250 return _IMP_atom.RigidBodyDiffusion_add_attribute(self, *args)
4253 def get_value(self, *args):
4255 get_value(RigidBodyDiffusion self, FloatKey a0) -> IMP::Float
4256 get_value(RigidBodyDiffusion self, IntKey a0) -> IMP::Int
4257 get_value(RigidBodyDiffusion self, StringKey a0) -> IMP::String
4258 get_value(RigidBodyDiffusion self, ParticleIndexKey a0) -> Particle
4259 get_value(RigidBodyDiffusion self, ObjectKey a0) -> Object
4261 return _IMP_atom.RigidBodyDiffusion_get_value(self, *args)
4264 def set_value(self, *args):
4266 set_value(RigidBodyDiffusion self, FloatKey a0, IMP::Float a1)
4267 set_value(RigidBodyDiffusion self, IntKey a0, IMP::Int a1)
4268 set_value(RigidBodyDiffusion self, StringKey a0, IMP::String a1)
4269 set_value(RigidBodyDiffusion self, ParticleIndexKey a0, Particle a1)
4270 set_value(RigidBodyDiffusion self, ObjectKey a0, Object a1)
4272 return _IMP_atom.RigidBodyDiffusion_set_value(self, *args)
4275 def remove_attribute(self, *args):
4277 remove_attribute(RigidBodyDiffusion self, FloatKey a0)
4278 remove_attribute(RigidBodyDiffusion self, IntKey a0)
4279 remove_attribute(RigidBodyDiffusion self, StringKey a0)
4280 remove_attribute(RigidBodyDiffusion self, ParticleIndexKey a0)
4281 remove_attribute(RigidBodyDiffusion self, ObjectKey a0)
4283 return _IMP_atom.RigidBodyDiffusion_remove_attribute(self, *args)
4286 def has_attribute(self, *args):
4288 has_attribute(RigidBodyDiffusion self, FloatKey a0) -> bool
4289 has_attribute(RigidBodyDiffusion self, IntKey a0) -> bool
4290 has_attribute(RigidBodyDiffusion self, StringKey a0) -> bool
4291 has_attribute(RigidBodyDiffusion self, ParticleIndexKey a0) -> bool
4292 has_attribute(RigidBodyDiffusion self, ObjectKey a0) -> bool
4294 return _IMP_atom.RigidBodyDiffusion_has_attribute(self, *args)
4297 def get_derivative(self, a0):
4298 """get_derivative(RigidBodyDiffusion self, FloatKey a0) -> double"""
4299 return _IMP_atom.RigidBodyDiffusion_get_derivative(self, a0)
4303 """get_name(RigidBodyDiffusion self) -> std::string"""
4304 return _IMP_atom.RigidBodyDiffusion_get_name(self)
4307 def clear_caches(self):
4308 """clear_caches(RigidBodyDiffusion self)"""
4309 return _IMP_atom.RigidBodyDiffusion_clear_caches(self)
4312 def set_name(self, a0):
4313 """set_name(RigidBodyDiffusion self, std::string a0)"""
4314 return _IMP_atom.RigidBodyDiffusion_set_name(self, a0)
4318 """set_check_level(RigidBodyDiffusion self, IMP::CheckLevel a0)"""
4319 return _IMP_atom.RigidBodyDiffusion_set_check_level(self, a0)
4322 def add_to_derivative(self, a0, a1, a2):
4323 """add_to_derivative(RigidBodyDiffusion self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4324 return _IMP_atom.RigidBodyDiffusion_add_to_derivative(self, a0, a1, a2)
4327 def set_is_optimized(self, a0, a1):
4328 """set_is_optimized(RigidBodyDiffusion self, FloatKey a0, bool a1)"""
4329 return _IMP_atom.RigidBodyDiffusion_set_is_optimized(self, a0, a1)
4332 def get_is_optimized(self, a0):
4333 """get_is_optimized(RigidBodyDiffusion self, FloatKey a0) -> bool"""
4334 return _IMP_atom.RigidBodyDiffusion_get_is_optimized(self, a0)
4338 """get_check_level(RigidBodyDiffusion self) -> IMP::CheckLevel"""
4339 return _IMP_atom.RigidBodyDiffusion_get_check_level(self)
4342 def __eq__(self, *args):
4344 __eq__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4345 __eq__(RigidBodyDiffusion self, Particle d) -> bool
4347 return _IMP_atom.RigidBodyDiffusion___eq__(self, *args)
4350 def __ne__(self, *args):
4352 __ne__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4353 __ne__(RigidBodyDiffusion self, Particle d) -> bool
4355 return _IMP_atom.RigidBodyDiffusion___ne__(self, *args)
4358 def __le__(self, *args):
4360 __le__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4361 __le__(RigidBodyDiffusion self, Particle d) -> bool
4363 return _IMP_atom.RigidBodyDiffusion___le__(self, *args)
4366 def __lt__(self, *args):
4368 __lt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4369 __lt__(RigidBodyDiffusion self, Particle d) -> bool
4371 return _IMP_atom.RigidBodyDiffusion___lt__(self, *args)
4374 def __ge__(self, *args):
4376 __ge__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4377 __ge__(RigidBodyDiffusion self, Particle d) -> bool
4379 return _IMP_atom.RigidBodyDiffusion___ge__(self, *args)
4382 def __gt__(self, *args):
4384 __gt__(RigidBodyDiffusion self, RigidBodyDiffusion o) -> bool
4385 __gt__(RigidBodyDiffusion self, Particle d) -> bool
4387 return _IMP_atom.RigidBodyDiffusion___gt__(self, *args)
4391 """__hash__(RigidBodyDiffusion self) -> std::size_t"""
4392 return _IMP_atom.RigidBodyDiffusion___hash__(self)
4396 """__str__(RigidBodyDiffusion self) -> std::string"""
4397 return _IMP_atom.RigidBodyDiffusion___str__(self)
4401 """__repr__(RigidBodyDiffusion self) -> std::string"""
4402 return _IMP_atom.RigidBodyDiffusion___repr__(self)
4404 __swig_destroy__ = _IMP_atom.delete_RigidBodyDiffusion
4405 __del__ =
lambda self:
None
4406 RigidBodyDiffusion_swigregister = _IMP_atom.RigidBodyDiffusion_swigregister
4407 RigidBodyDiffusion_swigregister(RigidBodyDiffusion)
4409 def RigidBodyDiffusion_setup_particle(*args):
4411 setup_particle(Model m, ParticleIndex pi) -> RigidBodyDiffusion
4412 RigidBodyDiffusion_setup_particle(_ParticleAdaptor decorator) -> RigidBodyDiffusion
4414 return _IMP_atom.RigidBodyDiffusion_setup_particle(*args)
4416 def RigidBodyDiffusion_get_is_setup(*args):
4418 get_is_setup(_ParticleAdaptor p) -> bool
4419 RigidBodyDiffusion_get_is_setup(Model m, ParticleIndex p) -> bool
4421 return _IMP_atom.RigidBodyDiffusion_get_is_setup(*args)
4423 def RigidBodyDiffusion_get_rotational_diffusion_coefficient_key():
4424 """RigidBodyDiffusion_get_rotational_diffusion_coefficient_key() -> FloatKey"""
4425 return _IMP_atom.RigidBodyDiffusion_get_rotational_diffusion_coefficient_key()
4428 """Proxy of C++ IMP::atom::TAMDParticle class"""
4429 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4431 def __init__(self, *args):
4433 __init__(IMP::atom::TAMDParticle self) -> TAMDParticle
4434 __init__(IMP::atom::TAMDParticle self, Model m, ParticleIndex id) -> TAMDParticle
4435 __init__(IMP::atom::TAMDParticle self, _ParticleAdaptor d) -> TAMDParticle
4437 this = _IMP_atom.new_TAMDParticle(*args)
4439 self.this.append(this)
4443 def show(self, *args):
4445 show(TAMDParticle self, _ostream out)
4446 show(TAMDParticle self)
4448 return _IMP_atom.TAMDParticle_show(self, *args)
4451 def setup_particle(*args):
4453 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4454 setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4455 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4456 setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4458 return _IMP_atom.TAMDParticle_setup_particle(*args)
4460 setup_particle = staticmethod(setup_particle)
4462 def get_is_setup(*args):
4464 get_is_setup(_ParticleAdaptor p) -> bool
4465 get_is_setup(Model m, ParticleIndex p) -> bool
4467 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4469 get_is_setup = staticmethod(get_is_setup)
4471 def get_reference_particle_index(self):
4472 """get_reference_particle_index(TAMDParticle self) -> ParticleIndex"""
4473 return _IMP_atom.TAMDParticle_get_reference_particle_index(self)
4476 def set_temperature_scale_factor(self, tsf):
4477 """set_temperature_scale_factor(TAMDParticle self, float tsf)"""
4478 return _IMP_atom.TAMDParticle_set_temperature_scale_factor(self, tsf)
4481 def get_temperature_scale_factor(self):
4482 """get_temperature_scale_factor(TAMDParticle self) -> double"""
4483 return _IMP_atom.TAMDParticle_get_temperature_scale_factor(self)
4486 def set_friction_scale_factor(self, tsf):
4487 """set_friction_scale_factor(TAMDParticle self, float tsf)"""
4488 return _IMP_atom.TAMDParticle_set_friction_scale_factor(self, tsf)
4491 def get_friction_scale_factor(self):
4492 """get_friction_scale_factor(TAMDParticle self) -> double"""
4493 return _IMP_atom.TAMDParticle_get_friction_scale_factor(self)
4496 def update_coordinates_from_ref(self):
4497 """update_coordinates_from_ref(TAMDParticle self)"""
4498 return _IMP_atom.TAMDParticle_update_coordinates_from_ref(self)
4501 def get_temperature_scale_factor_key():
4502 """get_temperature_scale_factor_key() -> FloatKey"""
4503 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4505 get_temperature_scale_factor_key = staticmethod(get_temperature_scale_factor_key)
4507 def get_friction_scale_factor_key():
4508 """get_friction_scale_factor_key() -> FloatKey"""
4509 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4511 get_friction_scale_factor_key = staticmethod(get_friction_scale_factor_key)
4513 def get_reference_particle_index_key():
4514 """get_reference_particle_index_key() -> ParticleIndexKey"""
4515 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4517 get_reference_particle_index_key = staticmethod(get_reference_particle_index_key)
4519 def add_attribute(self, *args):
4521 add_attribute(TAMDParticle self, FloatKey k, IMP::Float v, bool opt)
4522 add_attribute(TAMDParticle self, FloatKey a0, IMP::Float a1)
4523 add_attribute(TAMDParticle self, IntKey a0, IMP::Int a1)
4524 add_attribute(TAMDParticle self, StringKey a0, IMP::String a1)
4525 add_attribute(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4526 add_attribute(TAMDParticle self, ObjectKey a0, Object a1)
4528 return _IMP_atom.TAMDParticle_add_attribute(self, *args)
4531 def get_value(self, *args):
4533 get_value(TAMDParticle self, FloatKey a0) -> IMP::Float
4534 get_value(TAMDParticle self, IntKey a0) -> IMP::Int
4535 get_value(TAMDParticle self, StringKey a0) -> IMP::String
4536 get_value(TAMDParticle self, ParticleIndexKey a0) -> Particle
4537 get_value(TAMDParticle self, ObjectKey a0) -> Object
4539 return _IMP_atom.TAMDParticle_get_value(self, *args)
4542 def set_value(self, *args):
4544 set_value(TAMDParticle self, FloatKey a0, IMP::Float a1)
4545 set_value(TAMDParticle self, IntKey a0, IMP::Int a1)
4546 set_value(TAMDParticle self, StringKey a0, IMP::String a1)
4547 set_value(TAMDParticle self, ParticleIndexKey a0, Particle a1)
4548 set_value(TAMDParticle self, ObjectKey a0, Object a1)
4550 return _IMP_atom.TAMDParticle_set_value(self, *args)
4553 def remove_attribute(self, *args):
4555 remove_attribute(TAMDParticle self, FloatKey a0)
4556 remove_attribute(TAMDParticle self, IntKey a0)
4557 remove_attribute(TAMDParticle self, StringKey a0)
4558 remove_attribute(TAMDParticle self, ParticleIndexKey a0)
4559 remove_attribute(TAMDParticle self, ObjectKey a0)
4561 return _IMP_atom.TAMDParticle_remove_attribute(self, *args)
4564 def has_attribute(self, *args):
4566 has_attribute(TAMDParticle self, FloatKey a0) -> bool
4567 has_attribute(TAMDParticle self, IntKey a0) -> bool
4568 has_attribute(TAMDParticle self, StringKey a0) -> bool
4569 has_attribute(TAMDParticle self, ParticleIndexKey a0) -> bool
4570 has_attribute(TAMDParticle self, ObjectKey a0) -> bool
4572 return _IMP_atom.TAMDParticle_has_attribute(self, *args)
4575 def get_derivative(self, a0):
4576 """get_derivative(TAMDParticle self, FloatKey a0) -> double"""
4577 return _IMP_atom.TAMDParticle_get_derivative(self, a0)
4581 """get_name(TAMDParticle self) -> std::string"""
4582 return _IMP_atom.TAMDParticle_get_name(self)
4585 def clear_caches(self):
4586 """clear_caches(TAMDParticle self)"""
4587 return _IMP_atom.TAMDParticle_clear_caches(self)
4590 def set_name(self, a0):
4591 """set_name(TAMDParticle self, std::string a0)"""
4592 return _IMP_atom.TAMDParticle_set_name(self, a0)
4596 """set_check_level(TAMDParticle self, IMP::CheckLevel a0)"""
4597 return _IMP_atom.TAMDParticle_set_check_level(self, a0)
4600 def add_to_derivative(self, a0, a1, a2):
4601 """add_to_derivative(TAMDParticle self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4602 return _IMP_atom.TAMDParticle_add_to_derivative(self, a0, a1, a2)
4605 def set_is_optimized(self, a0, a1):
4606 """set_is_optimized(TAMDParticle self, FloatKey a0, bool a1)"""
4607 return _IMP_atom.TAMDParticle_set_is_optimized(self, a0, a1)
4610 def get_is_optimized(self, a0):
4611 """get_is_optimized(TAMDParticle self, FloatKey a0) -> bool"""
4612 return _IMP_atom.TAMDParticle_get_is_optimized(self, a0)
4616 """get_check_level(TAMDParticle self) -> IMP::CheckLevel"""
4617 return _IMP_atom.TAMDParticle_get_check_level(self)
4620 def __eq__(self, *args):
4622 __eq__(TAMDParticle self, TAMDParticle o) -> bool
4623 __eq__(TAMDParticle self, Particle d) -> bool
4625 return _IMP_atom.TAMDParticle___eq__(self, *args)
4628 def __ne__(self, *args):
4630 __ne__(TAMDParticle self, TAMDParticle o) -> bool
4631 __ne__(TAMDParticle self, Particle d) -> bool
4633 return _IMP_atom.TAMDParticle___ne__(self, *args)
4636 def __le__(self, *args):
4638 __le__(TAMDParticle self, TAMDParticle o) -> bool
4639 __le__(TAMDParticle self, Particle d) -> bool
4641 return _IMP_atom.TAMDParticle___le__(self, *args)
4644 def __lt__(self, *args):
4646 __lt__(TAMDParticle self, TAMDParticle o) -> bool
4647 __lt__(TAMDParticle self, Particle d) -> bool
4649 return _IMP_atom.TAMDParticle___lt__(self, *args)
4652 def __ge__(self, *args):
4654 __ge__(TAMDParticle self, TAMDParticle o) -> bool
4655 __ge__(TAMDParticle self, Particle d) -> bool
4657 return _IMP_atom.TAMDParticle___ge__(self, *args)
4660 def __gt__(self, *args):
4662 __gt__(TAMDParticle self, TAMDParticle o) -> bool
4663 __gt__(TAMDParticle self, Particle d) -> bool
4665 return _IMP_atom.TAMDParticle___gt__(self, *args)
4669 """__hash__(TAMDParticle self) -> std::size_t"""
4670 return _IMP_atom.TAMDParticle___hash__(self)
4674 """__str__(TAMDParticle self) -> std::string"""
4675 return _IMP_atom.TAMDParticle___str__(self)
4679 """__repr__(TAMDParticle self) -> std::string"""
4680 return _IMP_atom.TAMDParticle___repr__(self)
4682 __swig_destroy__ = _IMP_atom.delete_TAMDParticle
4683 __del__ =
lambda self:
None
4684 TAMDParticle_swigregister = _IMP_atom.TAMDParticle_swigregister
4685 TAMDParticle_swigregister(TAMDParticle)
4687 def TAMDParticle_setup_particle(*args):
4689 setup_particle(Model m, ParticleIndex pi, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4690 setup_particle(_ParticleAdaptor decorator, ParticleIndex pi_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4691 setup_particle(Model m, ParticleIndex pi, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4692 TAMDParticle_setup_particle(_ParticleAdaptor decorator, Particle p_ref, IMP::Float tsf, IMP::Float fsf) -> TAMDParticle
4694 return _IMP_atom.TAMDParticle_setup_particle(*args)
4696 def TAMDParticle_get_is_setup(*args):
4698 get_is_setup(_ParticleAdaptor p) -> bool
4699 TAMDParticle_get_is_setup(Model m, ParticleIndex p) -> bool
4701 return _IMP_atom.TAMDParticle_get_is_setup(*args)
4703 def TAMDParticle_get_temperature_scale_factor_key():
4704 """TAMDParticle_get_temperature_scale_factor_key() -> FloatKey"""
4705 return _IMP_atom.TAMDParticle_get_temperature_scale_factor_key()
4707 def TAMDParticle_get_friction_scale_factor_key():
4708 """TAMDParticle_get_friction_scale_factor_key() -> FloatKey"""
4709 return _IMP_atom.TAMDParticle_get_friction_scale_factor_key()
4711 def TAMDParticle_get_reference_particle_index_key():
4712 """TAMDParticle_get_reference_particle_index_key() -> ParticleIndexKey"""
4713 return _IMP_atom.TAMDParticle_get_reference_particle_index_key()
4715 class Chain(Hierarchy):
4716 """Proxy of C++ IMP::atom::Chain class"""
4717 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4719 def __init__(self, *args):
4721 __init__(IMP::atom::Chain self) -> Chain
4722 __init__(IMP::atom::Chain self, Model m, ParticleIndex id) -> Chain
4723 __init__(IMP::atom::Chain self, _ParticleAdaptor d) -> Chain
4725 this = _IMP_atom.new_Chain(*args)
4727 self.this.append(this)
4731 def show(self, *args):
4733 show(Chain self, _ostream out)
4736 return _IMP_atom.Chain_show(self, *args)
4739 def setup_particle(*args):
4741 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4742 setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4743 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4744 setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4745 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4746 setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4748 return _IMP_atom.Chain_setup_particle(*args)
4750 setup_particle = staticmethod(setup_particle)
4752 def get_is_setup(*args):
4754 get_is_setup(_ParticleAdaptor p) -> bool
4755 get_is_setup(Model m, ParticleIndex pi) -> bool
4757 return _IMP_atom.Chain_get_is_setup(*args)
4759 get_is_setup = staticmethod(get_is_setup)
4762 """get_id(Chain self) -> std::string"""
4763 return _IMP_atom.Chain_get_id(self)
4766 def set_id(self, c):
4767 """set_id(Chain self, std::string c)"""
4768 return _IMP_atom.Chain_set_id(self, c)
4772 """get_id_key() -> StringKey"""
4773 return _IMP_atom.Chain_get_id_key()
4775 get_id_key = staticmethod(get_id_key)
4777 def add_attribute(self, *args):
4779 add_attribute(Chain self, FloatKey k, IMP::Float v, bool opt)
4780 add_attribute(Chain self, FloatKey a0, IMP::Float a1)
4781 add_attribute(Chain self, IntKey a0, IMP::Int a1)
4782 add_attribute(Chain self, StringKey a0, IMP::String a1)
4783 add_attribute(Chain self, ParticleIndexKey a0, Particle a1)
4784 add_attribute(Chain self, ObjectKey a0, Object a1)
4786 return _IMP_atom.Chain_add_attribute(self, *args)
4789 def get_value(self, *args):
4791 get_value(Chain self, FloatKey a0) -> IMP::Float
4792 get_value(Chain self, IntKey a0) -> IMP::Int
4793 get_value(Chain self, StringKey a0) -> IMP::String
4794 get_value(Chain self, ParticleIndexKey a0) -> Particle
4795 get_value(Chain self, ObjectKey a0) -> Object
4797 return _IMP_atom.Chain_get_value(self, *args)
4800 def set_value(self, *args):
4802 set_value(Chain self, FloatKey a0, IMP::Float a1)
4803 set_value(Chain self, IntKey a0, IMP::Int a1)
4804 set_value(Chain self, StringKey a0, IMP::String a1)
4805 set_value(Chain self, ParticleIndexKey a0, Particle a1)
4806 set_value(Chain self, ObjectKey a0, Object a1)
4808 return _IMP_atom.Chain_set_value(self, *args)
4811 def remove_attribute(self, *args):
4813 remove_attribute(Chain self, FloatKey a0)
4814 remove_attribute(Chain self, IntKey a0)
4815 remove_attribute(Chain self, StringKey a0)
4816 remove_attribute(Chain self, ParticleIndexKey a0)
4817 remove_attribute(Chain self, ObjectKey a0)
4819 return _IMP_atom.Chain_remove_attribute(self, *args)
4822 def has_attribute(self, *args):
4824 has_attribute(Chain self, FloatKey a0) -> bool
4825 has_attribute(Chain self, IntKey a0) -> bool
4826 has_attribute(Chain self, StringKey a0) -> bool
4827 has_attribute(Chain self, ParticleIndexKey a0) -> bool
4828 has_attribute(Chain self, ObjectKey a0) -> bool
4830 return _IMP_atom.Chain_has_attribute(self, *args)
4833 def get_derivative(self, a0):
4834 """get_derivative(Chain self, FloatKey a0) -> double"""
4835 return _IMP_atom.Chain_get_derivative(self, a0)
4839 """get_name(Chain self) -> std::string"""
4840 return _IMP_atom.Chain_get_name(self)
4843 def clear_caches(self):
4844 """clear_caches(Chain self)"""
4845 return _IMP_atom.Chain_clear_caches(self)
4848 def set_name(self, a0):
4849 """set_name(Chain self, std::string a0)"""
4850 return _IMP_atom.Chain_set_name(self, a0)
4854 """set_check_level(Chain self, IMP::CheckLevel a0)"""
4855 return _IMP_atom.Chain_set_check_level(self, a0)
4858 def add_to_derivative(self, a0, a1, a2):
4859 """add_to_derivative(Chain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4860 return _IMP_atom.Chain_add_to_derivative(self, a0, a1, a2)
4863 def set_is_optimized(self, a0, a1):
4864 """set_is_optimized(Chain self, FloatKey a0, bool a1)"""
4865 return _IMP_atom.Chain_set_is_optimized(self, a0, a1)
4868 def get_is_optimized(self, a0):
4869 """get_is_optimized(Chain self, FloatKey a0) -> bool"""
4870 return _IMP_atom.Chain_get_is_optimized(self, a0)
4874 """get_check_level(Chain self) -> IMP::CheckLevel"""
4875 return _IMP_atom.Chain_get_check_level(self)
4878 def __eq__(self, *args):
4880 __eq__(Chain self, Chain o) -> bool
4881 __eq__(Chain self, Particle d) -> bool
4883 return _IMP_atom.Chain___eq__(self, *args)
4886 def __ne__(self, *args):
4888 __ne__(Chain self, Chain o) -> bool
4889 __ne__(Chain self, Particle d) -> bool
4891 return _IMP_atom.Chain___ne__(self, *args)
4894 def __le__(self, *args):
4896 __le__(Chain self, Chain o) -> bool
4897 __le__(Chain self, Particle d) -> bool
4899 return _IMP_atom.Chain___le__(self, *args)
4902 def __lt__(self, *args):
4904 __lt__(Chain self, Chain o) -> bool
4905 __lt__(Chain self, Particle d) -> bool
4907 return _IMP_atom.Chain___lt__(self, *args)
4910 def __ge__(self, *args):
4912 __ge__(Chain self, Chain o) -> bool
4913 __ge__(Chain self, Particle d) -> bool
4915 return _IMP_atom.Chain___ge__(self, *args)
4918 def __gt__(self, *args):
4920 __gt__(Chain self, Chain o) -> bool
4921 __gt__(Chain self, Particle d) -> bool
4923 return _IMP_atom.Chain___gt__(self, *args)
4927 """__hash__(Chain self) -> std::size_t"""
4928 return _IMP_atom.Chain___hash__(self)
4932 """__str__(Chain self) -> std::string"""
4933 return _IMP_atom.Chain___str__(self)
4937 """__repr__(Chain self) -> std::string"""
4938 return _IMP_atom.Chain___repr__(self)
4940 __swig_destroy__ = _IMP_atom.delete_Chain
4941 __del__ =
lambda self:
None
4942 Chain_swigregister = _IMP_atom.Chain_swigregister
4943 Chain_swigregister(Chain)
4945 def Chain_setup_particle(*args):
4947 setup_particle(Model m, ParticleIndex pi, std::string id) -> Chain
4948 setup_particle(_ParticleAdaptor decorator, std::string id) -> Chain
4949 setup_particle(Model m, ParticleIndex pi, char id) -> Chain
4950 setup_particle(_ParticleAdaptor decorator, char id) -> Chain
4951 setup_particle(Model m, ParticleIndex pi, Chain other) -> Chain
4952 Chain_setup_particle(_ParticleAdaptor decorator, Chain other) -> Chain
4954 return _IMP_atom.Chain_setup_particle(*args)
4956 def Chain_get_is_setup(*args):
4958 get_is_setup(_ParticleAdaptor p) -> bool
4959 Chain_get_is_setup(Model m, ParticleIndex pi) -> bool
4961 return _IMP_atom.Chain_get_is_setup(*args)
4963 def Chain_get_id_key():
4964 """Chain_get_id_key() -> StringKey"""
4965 return _IMP_atom.Chain_get_id_key()
4969 """get_chain(Hierarchy h) -> Chain"""
4970 return _IMP_atom.get_chain(h)
4973 """get_chain_id(Hierarchy h) -> std::string"""
4974 return _IMP_atom.get_chain_id(h)
4976 """Proxy of C++ IMP::atom::Charged class"""
4977 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4979 def __init__(self, *args):
4981 __init__(IMP::atom::Charged self) -> Charged
4982 __init__(IMP::atom::Charged self, Model m, ParticleIndex id) -> Charged
4983 __init__(IMP::atom::Charged self, _ParticleAdaptor d) -> Charged
4985 this = _IMP_atom.new_Charged(*args)
4987 self.this.append(this)
4991 def show(self, *args):
4993 show(Charged self, _ostream out)
4996 return _IMP_atom.Charged_show(self, *args)
4999 def setup_particle(*args):
5001 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
5002 setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
5003 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
5004 setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5006 return _IMP_atom.Charged_setup_particle(*args)
5008 setup_particle = staticmethod(setup_particle)
5010 def get_charge(self):
5011 """get_charge(Charged self) -> IMP::Float"""
5012 return _IMP_atom.Charged_get_charge(self)
5015 def set_charge(self, t):
5016 """set_charge(Charged self, IMP::Float t)"""
5017 return _IMP_atom.Charged_set_charge(self, t)
5020 def get_is_setup(*args):
5022 get_is_setup(_ParticleAdaptor p) -> bool
5023 get_is_setup(Model m, ParticleIndex pi) -> bool
5025 return _IMP_atom.Charged_get_is_setup(*args)
5027 get_is_setup = staticmethod(get_is_setup)
5029 def get_charge_key():
5030 """get_charge_key() -> FloatKey"""
5031 return _IMP_atom.Charged_get_charge_key()
5033 get_charge_key = staticmethod(get_charge_key)
5035 def add_attribute(self, *args):
5037 add_attribute(Charged self, FloatKey k, IMP::Float v, bool opt)
5038 add_attribute(Charged self, FloatKey a0, IMP::Float a1)
5039 add_attribute(Charged self, IntKey a0, IMP::Int a1)
5040 add_attribute(Charged self, StringKey a0, IMP::String a1)
5041 add_attribute(Charged self, ParticleIndexKey a0, Particle a1)
5042 add_attribute(Charged self, ObjectKey a0, Object a1)
5044 return _IMP_atom.Charged_add_attribute(self, *args)
5047 def get_value(self, *args):
5049 get_value(Charged self, FloatKey a0) -> IMP::Float
5050 get_value(Charged self, IntKey a0) -> IMP::Int
5051 get_value(Charged self, StringKey a0) -> IMP::String
5052 get_value(Charged self, ParticleIndexKey a0) -> Particle
5053 get_value(Charged self, ObjectKey a0) -> Object
5055 return _IMP_atom.Charged_get_value(self, *args)
5058 def set_value(self, *args):
5060 set_value(Charged self, FloatKey a0, IMP::Float a1)
5061 set_value(Charged self, IntKey a0, IMP::Int a1)
5062 set_value(Charged self, StringKey a0, IMP::String a1)
5063 set_value(Charged self, ParticleIndexKey a0, Particle a1)
5064 set_value(Charged self, ObjectKey a0, Object a1)
5066 return _IMP_atom.Charged_set_value(self, *args)
5069 def remove_attribute(self, *args):
5071 remove_attribute(Charged self, FloatKey a0)
5072 remove_attribute(Charged self, IntKey a0)
5073 remove_attribute(Charged self, StringKey a0)
5074 remove_attribute(Charged self, ParticleIndexKey a0)
5075 remove_attribute(Charged self, ObjectKey a0)
5077 return _IMP_atom.Charged_remove_attribute(self, *args)
5080 def has_attribute(self, *args):
5082 has_attribute(Charged self, FloatKey a0) -> bool
5083 has_attribute(Charged self, IntKey a0) -> bool
5084 has_attribute(Charged self, StringKey a0) -> bool
5085 has_attribute(Charged self, ParticleIndexKey a0) -> bool
5086 has_attribute(Charged self, ObjectKey a0) -> bool
5088 return _IMP_atom.Charged_has_attribute(self, *args)
5091 def get_derivative(self, a0):
5092 """get_derivative(Charged self, FloatKey a0) -> double"""
5093 return _IMP_atom.Charged_get_derivative(self, a0)
5097 """get_name(Charged self) -> std::string"""
5098 return _IMP_atom.Charged_get_name(self)
5101 def clear_caches(self):
5102 """clear_caches(Charged self)"""
5103 return _IMP_atom.Charged_clear_caches(self)
5106 def set_name(self, a0):
5107 """set_name(Charged self, std::string a0)"""
5108 return _IMP_atom.Charged_set_name(self, a0)
5112 """set_check_level(Charged self, IMP::CheckLevel a0)"""
5113 return _IMP_atom.Charged_set_check_level(self, a0)
5116 def add_to_derivative(self, a0, a1, a2):
5117 """add_to_derivative(Charged self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5118 return _IMP_atom.Charged_add_to_derivative(self, a0, a1, a2)
5121 def set_is_optimized(self, a0, a1):
5122 """set_is_optimized(Charged self, FloatKey a0, bool a1)"""
5123 return _IMP_atom.Charged_set_is_optimized(self, a0, a1)
5126 def get_is_optimized(self, a0):
5127 """get_is_optimized(Charged self, FloatKey a0) -> bool"""
5128 return _IMP_atom.Charged_get_is_optimized(self, a0)
5132 """get_check_level(Charged self) -> IMP::CheckLevel"""
5133 return _IMP_atom.Charged_get_check_level(self)
5136 def __eq__(self, *args):
5138 __eq__(Charged self, Charged o) -> bool
5139 __eq__(Charged self, Particle d) -> bool
5141 return _IMP_atom.Charged___eq__(self, *args)
5144 def __ne__(self, *args):
5146 __ne__(Charged self, Charged o) -> bool
5147 __ne__(Charged self, Particle d) -> bool
5149 return _IMP_atom.Charged___ne__(self, *args)
5152 def __le__(self, *args):
5154 __le__(Charged self, Charged o) -> bool
5155 __le__(Charged self, Particle d) -> bool
5157 return _IMP_atom.Charged___le__(self, *args)
5160 def __lt__(self, *args):
5162 __lt__(Charged self, Charged o) -> bool
5163 __lt__(Charged self, Particle d) -> bool
5165 return _IMP_atom.Charged___lt__(self, *args)
5168 def __ge__(self, *args):
5170 __ge__(Charged self, Charged o) -> bool
5171 __ge__(Charged self, Particle d) -> bool
5173 return _IMP_atom.Charged___ge__(self, *args)
5176 def __gt__(self, *args):
5178 __gt__(Charged self, Charged o) -> bool
5179 __gt__(Charged self, Particle d) -> bool
5181 return _IMP_atom.Charged___gt__(self, *args)
5185 """__hash__(Charged self) -> std::size_t"""
5186 return _IMP_atom.Charged___hash__(self)
5190 """__str__(Charged self) -> std::string"""
5191 return _IMP_atom.Charged___str__(self)
5195 """__repr__(Charged self) -> std::string"""
5196 return _IMP_atom.Charged___repr__(self)
5198 __swig_destroy__ = _IMP_atom.delete_Charged
5199 __del__ =
lambda self:
None
5200 Charged_swigregister = _IMP_atom.Charged_swigregister
5201 Charged_swigregister(Charged)
5203 def Charged_setup_particle(*args):
5205 setup_particle(Model m, ParticleIndex pi, IMP::Float charge) -> Charged
5206 setup_particle(_ParticleAdaptor decorator, IMP::Float charge) -> Charged
5207 setup_particle(Model m, ParticleIndex pi, Vector3D v, IMP::Float charge) -> Charged
5208 Charged_setup_particle(_ParticleAdaptor decorator, Vector3D v, IMP::Float charge) -> Charged
5210 return _IMP_atom.Charged_setup_particle(*args)
5212 def Charged_get_is_setup(*args):
5214 get_is_setup(_ParticleAdaptor p) -> bool
5215 Charged_get_is_setup(Model m, ParticleIndex pi) -> bool
5217 return _IMP_atom.Charged_get_is_setup(*args)
5219 def Charged_get_charge_key():
5220 """Charged_get_charge_key() -> FloatKey"""
5221 return _IMP_atom.Charged_get_charge_key()
5224 """Proxy of C++ IMP::atom::CoulombPairScore class"""
5225 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5227 def __init__(self, f):
5228 """__init__(IMP::atom::CoulombPairScore self, SmoothingFunction f) -> CoulombPairScore"""
5229 this = _IMP_atom.new_CoulombPairScore(f)
5231 self.this.append(this)
5235 def set_relative_dielectric(self, relative_dielectric):
5236 """set_relative_dielectric(CoulombPairScore self, double relative_dielectric)"""
5237 return _IMP_atom.CoulombPairScore_set_relative_dielectric(self, relative_dielectric)
5240 def get_relative_dielectric(self):
5241 """get_relative_dielectric(CoulombPairScore self) -> double"""
5242 return _IMP_atom.CoulombPairScore_get_relative_dielectric(self)
5245 def do_get_inputs(self, m, pis):
5246 """do_get_inputs(CoulombPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5247 return _IMP_atom.CoulombPairScore_do_get_inputs(self, m, pis)
5250 def get_version_info(self):
5251 """get_version_info(CoulombPairScore self) -> VersionInfo"""
5252 return _IMP_atom.CoulombPairScore_get_version_info(self)
5256 """__str__(CoulombPairScore self) -> std::string"""
5257 return _IMP_atom.CoulombPairScore___str__(self)
5261 """__repr__(CoulombPairScore self) -> std::string"""
5262 return _IMP_atom.CoulombPairScore___repr__(self)
5267 return _object_cast_to_CoulombPairScore(o)
5269 CoulombPairScore_swigregister = _IMP_atom.CoulombPairScore_swigregister
5270 CoulombPairScore_swigregister(CoulombPairScore)
5272 class Domain(Hierarchy):
5273 """Proxy of C++ IMP::atom::Domain class"""
5274 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5276 def set_index_range(self, ir):
5277 """set_index_range(Domain self, IMP::IntRange ir)"""
5278 return _IMP_atom.Domain_set_index_range(self, ir)
5281 def get_index_range(self):
5282 """get_index_range(Domain self) -> IMP::IntRange"""
5283 return _IMP_atom.Domain_get_index_range(self)
5286 def __init__(self, *args):
5288 __init__(IMP::atom::Domain self) -> Domain
5289 __init__(IMP::atom::Domain self, Model m, ParticleIndex id) -> Domain
5290 __init__(IMP::atom::Domain self, _ParticleAdaptor d) -> Domain
5292 this = _IMP_atom.new_Domain(*args)
5294 self.this.append(this)
5298 def get_is_setup(*args):
5300 get_is_setup(Model m, ParticleIndex pi) -> bool
5301 get_is_setup(_ParticleAdaptor p) -> bool
5303 return _IMP_atom.Domain_get_is_setup(*args)
5305 get_is_setup = staticmethod(get_is_setup)
5307 def show(self, *args):
5309 show(Domain self, _ostream out)
5312 return _IMP_atom.Domain_show(self, *args)
5315 def setup_particle(*args):
5317 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5318 setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5319 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5320 setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5322 return _IMP_atom.Domain_setup_particle(*args)
5324 setup_particle = staticmethod(setup_particle)
5326 def add_attribute(self, *args):
5328 add_attribute(Domain self, FloatKey k, IMP::Float v, bool opt)
5329 add_attribute(Domain self, FloatKey a0, IMP::Float a1)
5330 add_attribute(Domain self, IntKey a0, IMP::Int a1)
5331 add_attribute(Domain self, StringKey a0, IMP::String a1)
5332 add_attribute(Domain self, ParticleIndexKey a0, Particle a1)
5333 add_attribute(Domain self, ObjectKey a0, Object a1)
5335 return _IMP_atom.Domain_add_attribute(self, *args)
5338 def get_value(self, *args):
5340 get_value(Domain self, FloatKey a0) -> IMP::Float
5341 get_value(Domain self, IntKey a0) -> IMP::Int
5342 get_value(Domain self, StringKey a0) -> IMP::String
5343 get_value(Domain self, ParticleIndexKey a0) -> Particle
5344 get_value(Domain self, ObjectKey a0) -> Object
5346 return _IMP_atom.Domain_get_value(self, *args)
5349 def set_value(self, *args):
5351 set_value(Domain self, FloatKey a0, IMP::Float a1)
5352 set_value(Domain self, IntKey a0, IMP::Int a1)
5353 set_value(Domain self, StringKey a0, IMP::String a1)
5354 set_value(Domain self, ParticleIndexKey a0, Particle a1)
5355 set_value(Domain self, ObjectKey a0, Object a1)
5357 return _IMP_atom.Domain_set_value(self, *args)
5360 def remove_attribute(self, *args):
5362 remove_attribute(Domain self, FloatKey a0)
5363 remove_attribute(Domain self, IntKey a0)
5364 remove_attribute(Domain self, StringKey a0)
5365 remove_attribute(Domain self, ParticleIndexKey a0)
5366 remove_attribute(Domain self, ObjectKey a0)
5368 return _IMP_atom.Domain_remove_attribute(self, *args)
5371 def has_attribute(self, *args):
5373 has_attribute(Domain self, FloatKey a0) -> bool
5374 has_attribute(Domain self, IntKey a0) -> bool
5375 has_attribute(Domain self, StringKey a0) -> bool
5376 has_attribute(Domain self, ParticleIndexKey a0) -> bool
5377 has_attribute(Domain self, ObjectKey a0) -> bool
5379 return _IMP_atom.Domain_has_attribute(self, *args)
5382 def get_derivative(self, a0):
5383 """get_derivative(Domain self, FloatKey a0) -> double"""
5384 return _IMP_atom.Domain_get_derivative(self, a0)
5388 """get_name(Domain self) -> std::string"""
5389 return _IMP_atom.Domain_get_name(self)
5392 def clear_caches(self):
5393 """clear_caches(Domain self)"""
5394 return _IMP_atom.Domain_clear_caches(self)
5397 def set_name(self, a0):
5398 """set_name(Domain self, std::string a0)"""
5399 return _IMP_atom.Domain_set_name(self, a0)
5403 """set_check_level(Domain self, IMP::CheckLevel a0)"""
5404 return _IMP_atom.Domain_set_check_level(self, a0)
5407 def add_to_derivative(self, a0, a1, a2):
5408 """add_to_derivative(Domain self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5409 return _IMP_atom.Domain_add_to_derivative(self, a0, a1, a2)
5412 def set_is_optimized(self, a0, a1):
5413 """set_is_optimized(Domain self, FloatKey a0, bool a1)"""
5414 return _IMP_atom.Domain_set_is_optimized(self, a0, a1)
5417 def get_is_optimized(self, a0):
5418 """get_is_optimized(Domain self, FloatKey a0) -> bool"""
5419 return _IMP_atom.Domain_get_is_optimized(self, a0)
5423 """get_check_level(Domain self) -> IMP::CheckLevel"""
5424 return _IMP_atom.Domain_get_check_level(self)
5427 def __eq__(self, *args):
5429 __eq__(Domain self, Domain o) -> bool
5430 __eq__(Domain self, Particle d) -> bool
5432 return _IMP_atom.Domain___eq__(self, *args)
5435 def __ne__(self, *args):
5437 __ne__(Domain self, Domain o) -> bool
5438 __ne__(Domain self, Particle d) -> bool
5440 return _IMP_atom.Domain___ne__(self, *args)
5443 def __le__(self, *args):
5445 __le__(Domain self, Domain o) -> bool
5446 __le__(Domain self, Particle d) -> bool
5448 return _IMP_atom.Domain___le__(self, *args)
5451 def __lt__(self, *args):
5453 __lt__(Domain self, Domain o) -> bool
5454 __lt__(Domain self, Particle d) -> bool
5456 return _IMP_atom.Domain___lt__(self, *args)
5459 def __ge__(self, *args):
5461 __ge__(Domain self, Domain o) -> bool
5462 __ge__(Domain self, Particle d) -> bool
5464 return _IMP_atom.Domain___ge__(self, *args)
5467 def __gt__(self, *args):
5469 __gt__(Domain self, Domain o) -> bool
5470 __gt__(Domain self, Particle d) -> bool
5472 return _IMP_atom.Domain___gt__(self, *args)
5476 """__hash__(Domain self) -> std::size_t"""
5477 return _IMP_atom.Domain___hash__(self)
5481 """__str__(Domain self) -> std::string"""
5482 return _IMP_atom.Domain___str__(self)
5486 """__repr__(Domain self) -> std::string"""
5487 return _IMP_atom.Domain___repr__(self)
5489 __swig_destroy__ = _IMP_atom.delete_Domain
5490 __del__ =
lambda self:
None
5491 Domain_swigregister = _IMP_atom.Domain_swigregister
5492 Domain_swigregister(Domain)
5494 def Domain_get_is_setup(*args):
5496 get_is_setup(Model m, ParticleIndex pi) -> bool
5497 Domain_get_is_setup(_ParticleAdaptor p) -> bool
5499 return _IMP_atom.Domain_get_is_setup(*args)
5501 def Domain_setup_particle(*args):
5503 setup_particle(Model m, ParticleIndex pi, Domain other) -> Domain
5504 setup_particle(_ParticleAdaptor decorator, Domain other) -> Domain
5505 setup_particle(Model m, ParticleIndex pi, IMP::IntRange residues) -> Domain
5506 Domain_setup_particle(_ParticleAdaptor decorator, IMP::IntRange residues) -> Domain
5508 return _IMP_atom.Domain_setup_particle(*args)
5511 """Proxy of C++ IMP::atom::LennardJones class"""
5512 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5514 def __init__(self, *args):
5516 __init__(IMP::atom::LennardJones self) -> LennardJones
5517 __init__(IMP::atom::LennardJones self, Model m, ParticleIndex id) -> LennardJones
5518 __init__(IMP::atom::LennardJones self, _ParticleAdaptor d) -> LennardJones
5520 this = _IMP_atom.new_LennardJones(*args)
5522 self.this.append(this)
5526 def show(self, *args):
5528 show(LennardJones self, _ostream out)
5529 show(LennardJones self)
5531 return _IMP_atom.LennardJones_show(self, *args)
5534 def setup_particle(*args):
5536 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5537 setup_particle(_ParticleAdaptor decorator) -> LennardJones
5538 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5539 setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5541 return _IMP_atom.LennardJones_setup_particle(*args)
5543 setup_particle = staticmethod(setup_particle)
5545 def get_well_depth(self):
5546 """get_well_depth(LennardJones self) -> IMP::Float"""
5547 return _IMP_atom.LennardJones_get_well_depth(self)
5550 def set_well_depth(self, well_depth):
5551 """set_well_depth(LennardJones self, IMP::Float well_depth)"""
5552 return _IMP_atom.LennardJones_set_well_depth(self, well_depth)
5555 def get_is_setup(*args):
5557 get_is_setup(_ParticleAdaptor p) -> bool
5558 get_is_setup(Model m, ParticleIndex pi) -> bool
5560 return _IMP_atom.LennardJones_get_is_setup(*args)
5562 get_is_setup = staticmethod(get_is_setup)
5564 def get_well_depth_key():
5565 """get_well_depth_key() -> FloatKey"""
5566 return _IMP_atom.LennardJones_get_well_depth_key()
5568 get_well_depth_key = staticmethod(get_well_depth_key)
5570 def add_attribute(self, *args):
5572 add_attribute(LennardJones self, FloatKey k, IMP::Float v, bool opt)
5573 add_attribute(LennardJones self, FloatKey a0, IMP::Float a1)
5574 add_attribute(LennardJones self, IntKey a0, IMP::Int a1)
5575 add_attribute(LennardJones self, StringKey a0, IMP::String a1)
5576 add_attribute(LennardJones self, ParticleIndexKey a0, Particle a1)
5577 add_attribute(LennardJones self, ObjectKey a0, Object a1)
5579 return _IMP_atom.LennardJones_add_attribute(self, *args)
5582 def get_value(self, *args):
5584 get_value(LennardJones self, FloatKey a0) -> IMP::Float
5585 get_value(LennardJones self, IntKey a0) -> IMP::Int
5586 get_value(LennardJones self, StringKey a0) -> IMP::String
5587 get_value(LennardJones self, ParticleIndexKey a0) -> Particle
5588 get_value(LennardJones self, ObjectKey a0) -> Object
5590 return _IMP_atom.LennardJones_get_value(self, *args)
5593 def set_value(self, *args):
5595 set_value(LennardJones self, FloatKey a0, IMP::Float a1)
5596 set_value(LennardJones self, IntKey a0, IMP::Int a1)
5597 set_value(LennardJones self, StringKey a0, IMP::String a1)
5598 set_value(LennardJones self, ParticleIndexKey a0, Particle a1)
5599 set_value(LennardJones self, ObjectKey a0, Object a1)
5601 return _IMP_atom.LennardJones_set_value(self, *args)
5604 def remove_attribute(self, *args):
5606 remove_attribute(LennardJones self, FloatKey a0)
5607 remove_attribute(LennardJones self, IntKey a0)
5608 remove_attribute(LennardJones self, StringKey a0)
5609 remove_attribute(LennardJones self, ParticleIndexKey a0)
5610 remove_attribute(LennardJones self, ObjectKey a0)
5612 return _IMP_atom.LennardJones_remove_attribute(self, *args)
5615 def has_attribute(self, *args):
5617 has_attribute(LennardJones self, FloatKey a0) -> bool
5618 has_attribute(LennardJones self, IntKey a0) -> bool
5619 has_attribute(LennardJones self, StringKey a0) -> bool
5620 has_attribute(LennardJones self, ParticleIndexKey a0) -> bool
5621 has_attribute(LennardJones self, ObjectKey a0) -> bool
5623 return _IMP_atom.LennardJones_has_attribute(self, *args)
5626 def get_derivative(self, a0):
5627 """get_derivative(LennardJones self, FloatKey a0) -> double"""
5628 return _IMP_atom.LennardJones_get_derivative(self, a0)
5632 """get_name(LennardJones self) -> std::string"""
5633 return _IMP_atom.LennardJones_get_name(self)
5636 def clear_caches(self):
5637 """clear_caches(LennardJones self)"""
5638 return _IMP_atom.LennardJones_clear_caches(self)
5641 def set_name(self, a0):
5642 """set_name(LennardJones self, std::string a0)"""
5643 return _IMP_atom.LennardJones_set_name(self, a0)
5647 """set_check_level(LennardJones self, IMP::CheckLevel a0)"""
5648 return _IMP_atom.LennardJones_set_check_level(self, a0)
5651 def add_to_derivative(self, a0, a1, a2):
5652 """add_to_derivative(LennardJones self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5653 return _IMP_atom.LennardJones_add_to_derivative(self, a0, a1, a2)
5656 def set_is_optimized(self, a0, a1):
5657 """set_is_optimized(LennardJones self, FloatKey a0, bool a1)"""
5658 return _IMP_atom.LennardJones_set_is_optimized(self, a0, a1)
5661 def get_is_optimized(self, a0):
5662 """get_is_optimized(LennardJones self, FloatKey a0) -> bool"""
5663 return _IMP_atom.LennardJones_get_is_optimized(self, a0)
5667 """get_check_level(LennardJones self) -> IMP::CheckLevel"""
5668 return _IMP_atom.LennardJones_get_check_level(self)
5671 def __eq__(self, *args):
5673 __eq__(LennardJones self, LennardJones o) -> bool
5674 __eq__(LennardJones self, Particle d) -> bool
5676 return _IMP_atom.LennardJones___eq__(self, *args)
5679 def __ne__(self, *args):
5681 __ne__(LennardJones self, LennardJones o) -> bool
5682 __ne__(LennardJones self, Particle d) -> bool
5684 return _IMP_atom.LennardJones___ne__(self, *args)
5687 def __le__(self, *args):
5689 __le__(LennardJones self, LennardJones o) -> bool
5690 __le__(LennardJones self, Particle d) -> bool
5692 return _IMP_atom.LennardJones___le__(self, *args)
5695 def __lt__(self, *args):
5697 __lt__(LennardJones self, LennardJones o) -> bool
5698 __lt__(LennardJones self, Particle d) -> bool
5700 return _IMP_atom.LennardJones___lt__(self, *args)
5703 def __ge__(self, *args):
5705 __ge__(LennardJones self, LennardJones o) -> bool
5706 __ge__(LennardJones self, Particle d) -> bool
5708 return _IMP_atom.LennardJones___ge__(self, *args)
5711 def __gt__(self, *args):
5713 __gt__(LennardJones self, LennardJones o) -> bool
5714 __gt__(LennardJones self, Particle d) -> bool
5716 return _IMP_atom.LennardJones___gt__(self, *args)
5720 """__hash__(LennardJones self) -> std::size_t"""
5721 return _IMP_atom.LennardJones___hash__(self)
5725 """__str__(LennardJones self) -> std::string"""
5726 return _IMP_atom.LennardJones___str__(self)
5730 """__repr__(LennardJones self) -> std::string"""
5731 return _IMP_atom.LennardJones___repr__(self)
5733 __swig_destroy__ = _IMP_atom.delete_LennardJones
5734 __del__ =
lambda self:
None
5735 LennardJones_swigregister = _IMP_atom.LennardJones_swigregister
5736 LennardJones_swigregister(LennardJones)
5738 def LennardJones_setup_particle(*args):
5740 setup_particle(Model m, ParticleIndex pi) -> LennardJones
5741 setup_particle(_ParticleAdaptor decorator) -> LennardJones
5742 setup_particle(Model m, ParticleIndex pi, IMP::Float well_depth) -> LennardJones
5743 LennardJones_setup_particle(_ParticleAdaptor decorator, IMP::Float well_depth) -> LennardJones
5745 return _IMP_atom.LennardJones_setup_particle(*args)
5747 def LennardJones_get_is_setup(*args):
5749 get_is_setup(_ParticleAdaptor p) -> bool
5750 LennardJones_get_is_setup(Model m, ParticleIndex pi) -> bool
5752 return _IMP_atom.LennardJones_get_is_setup(*args)
5754 def LennardJones_get_well_depth_key():
5755 """LennardJones_get_well_depth_key() -> FloatKey"""
5756 return _IMP_atom.LennardJones_get_well_depth_key()
5759 """Proxy of C++ IMP::atom::LennardJonesPairScore class"""
5760 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5762 def __init__(self, f):
5763 """__init__(IMP::atom::LennardJonesPairScore self, SmoothingFunction f) -> LennardJonesPairScore"""
5764 this = _IMP_atom.new_LennardJonesPairScore(f)
5766 self.this.append(this)
5770 def set_repulsive_weight(self, repulsive_weight):
5771 """set_repulsive_weight(LennardJonesPairScore self, double repulsive_weight)"""
5772 return _IMP_atom.LennardJonesPairScore_set_repulsive_weight(self, repulsive_weight)
5775 def get_repulsive_weight(self):
5776 """get_repulsive_weight(LennardJonesPairScore self) -> double"""
5777 return _IMP_atom.LennardJonesPairScore_get_repulsive_weight(self)
5780 def set_attractive_weight(self, attractive_weight):
5781 """set_attractive_weight(LennardJonesPairScore self, double attractive_weight)"""
5782 return _IMP_atom.LennardJonesPairScore_set_attractive_weight(self, attractive_weight)
5785 def get_attractive_weight(self):
5786 """get_attractive_weight(LennardJonesPairScore self) -> double"""
5787 return _IMP_atom.LennardJonesPairScore_get_attractive_weight(self)
5790 def do_get_inputs(self, m, pis):
5791 """do_get_inputs(LennardJonesPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
5792 return _IMP_atom.LennardJonesPairScore_do_get_inputs(self, m, pis)
5795 def get_version_info(self):
5796 """get_version_info(LennardJonesPairScore self) -> VersionInfo"""
5797 return _IMP_atom.LennardJonesPairScore_get_version_info(self)
5801 """__str__(LennardJonesPairScore self) -> std::string"""
5802 return _IMP_atom.LennardJonesPairScore___str__(self)
5806 """__repr__(LennardJonesPairScore self) -> std::string"""
5807 return _IMP_atom.LennardJonesPairScore___repr__(self)
5812 return _object_cast_to_LennardJonesPairScore(o)
5814 LennardJonesPairScore_swigregister = _IMP_atom.LennardJonesPairScore_swigregister
5815 LennardJonesPairScore_swigregister(LennardJonesPairScore)
5818 """Proxy of C++ IMP::atom::LinearVelocity class"""
5819 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
5821 def get_velocity_key(i):
5822 """get_velocity_key(unsigned int i) -> FloatKey"""
5823 return _IMP_atom.LinearVelocity_get_velocity_key(i)
5825 get_velocity_key = staticmethod(get_velocity_key)
5827 def __init__(self, *args):
5829 __init__(IMP::atom::LinearVelocity self) -> LinearVelocity
5830 __init__(IMP::atom::LinearVelocity self, Model m, ParticleIndex id) -> LinearVelocity
5831 __init__(IMP::atom::LinearVelocity self, _ParticleAdaptor d) -> LinearVelocity
5833 this = _IMP_atom.new_LinearVelocity(*args)
5835 self.this.append(this)
5839 def get_is_setup(*args):
5841 get_is_setup(Model m, ParticleIndex pi) -> bool
5842 get_is_setup(_ParticleAdaptor p) -> bool
5844 return _IMP_atom.LinearVelocity_get_is_setup(*args)
5846 get_is_setup = staticmethod(get_is_setup)
5848 def show(self, *args):
5850 show(LinearVelocity self, _ostream out)
5851 show(LinearVelocity self)
5853 return _IMP_atom.LinearVelocity_show(self, *args)
5856 def setup_particle(*args):
5858 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
5859 setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
5860 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
5861 setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
5863 return _IMP_atom.LinearVelocity_setup_particle(*args)
5865 setup_particle = staticmethod(setup_particle)
5867 def set_velocity(self, v):
5868 """set_velocity(LinearVelocity self, Vector3D v)"""
5869 return _IMP_atom.LinearVelocity_set_velocity(self, v)
5872 def get_velocity(self):
5873 """get_velocity(LinearVelocity self) -> Vector3D"""
5874 return _IMP_atom.LinearVelocity_get_velocity(self)
5877 def add_attribute(self, *args):
5879 add_attribute(LinearVelocity self, FloatKey k, IMP::Float v, bool opt)
5880 add_attribute(LinearVelocity self, FloatKey a0, IMP::Float a1)
5881 add_attribute(LinearVelocity self, IntKey a0, IMP::Int a1)
5882 add_attribute(LinearVelocity self, StringKey a0, IMP::String a1)
5883 add_attribute(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5884 add_attribute(LinearVelocity self, ObjectKey a0, Object a1)
5886 return _IMP_atom.LinearVelocity_add_attribute(self, *args)
5889 def get_value(self, *args):
5891 get_value(LinearVelocity self, FloatKey a0) -> IMP::Float
5892 get_value(LinearVelocity self, IntKey a0) -> IMP::Int
5893 get_value(LinearVelocity self, StringKey a0) -> IMP::String
5894 get_value(LinearVelocity self, ParticleIndexKey a0) -> Particle
5895 get_value(LinearVelocity self, ObjectKey a0) -> Object
5897 return _IMP_atom.LinearVelocity_get_value(self, *args)
5900 def set_value(self, *args):
5902 set_value(LinearVelocity self, FloatKey a0, IMP::Float a1)
5903 set_value(LinearVelocity self, IntKey a0, IMP::Int a1)
5904 set_value(LinearVelocity self, StringKey a0, IMP::String a1)
5905 set_value(LinearVelocity self, ParticleIndexKey a0, Particle a1)
5906 set_value(LinearVelocity self, ObjectKey a0, Object a1)
5908 return _IMP_atom.LinearVelocity_set_value(self, *args)
5911 def remove_attribute(self, *args):
5913 remove_attribute(LinearVelocity self, FloatKey a0)
5914 remove_attribute(LinearVelocity self, IntKey a0)
5915 remove_attribute(LinearVelocity self, StringKey a0)
5916 remove_attribute(LinearVelocity self, ParticleIndexKey a0)
5917 remove_attribute(LinearVelocity self, ObjectKey a0)
5919 return _IMP_atom.LinearVelocity_remove_attribute(self, *args)
5922 def has_attribute(self, *args):
5924 has_attribute(LinearVelocity self, FloatKey a0) -> bool
5925 has_attribute(LinearVelocity self, IntKey a0) -> bool
5926 has_attribute(LinearVelocity self, StringKey a0) -> bool
5927 has_attribute(LinearVelocity self, ParticleIndexKey a0) -> bool
5928 has_attribute(LinearVelocity self, ObjectKey a0) -> bool
5930 return _IMP_atom.LinearVelocity_has_attribute(self, *args)
5933 def get_derivative(self, a0):
5934 """get_derivative(LinearVelocity self, FloatKey a0) -> double"""
5935 return _IMP_atom.LinearVelocity_get_derivative(self, a0)
5939 """get_name(LinearVelocity self) -> std::string"""
5940 return _IMP_atom.LinearVelocity_get_name(self)
5943 def clear_caches(self):
5944 """clear_caches(LinearVelocity self)"""
5945 return _IMP_atom.LinearVelocity_clear_caches(self)
5948 def set_name(self, a0):
5949 """set_name(LinearVelocity self, std::string a0)"""
5950 return _IMP_atom.LinearVelocity_set_name(self, a0)
5954 """set_check_level(LinearVelocity self, IMP::CheckLevel a0)"""
5955 return _IMP_atom.LinearVelocity_set_check_level(self, a0)
5958 def add_to_derivative(self, a0, a1, a2):
5959 """add_to_derivative(LinearVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
5960 return _IMP_atom.LinearVelocity_add_to_derivative(self, a0, a1, a2)
5963 def set_is_optimized(self, a0, a1):
5964 """set_is_optimized(LinearVelocity self, FloatKey a0, bool a1)"""
5965 return _IMP_atom.LinearVelocity_set_is_optimized(self, a0, a1)
5968 def get_is_optimized(self, a0):
5969 """get_is_optimized(LinearVelocity self, FloatKey a0) -> bool"""
5970 return _IMP_atom.LinearVelocity_get_is_optimized(self, a0)
5974 """get_check_level(LinearVelocity self) -> IMP::CheckLevel"""
5975 return _IMP_atom.LinearVelocity_get_check_level(self)
5978 def __eq__(self, *args):
5980 __eq__(LinearVelocity self, LinearVelocity o) -> bool
5981 __eq__(LinearVelocity self, Particle d) -> bool
5983 return _IMP_atom.LinearVelocity___eq__(self, *args)
5986 def __ne__(self, *args):
5988 __ne__(LinearVelocity self, LinearVelocity o) -> bool
5989 __ne__(LinearVelocity self, Particle d) -> bool
5991 return _IMP_atom.LinearVelocity___ne__(self, *args)
5994 def __le__(self, *args):
5996 __le__(LinearVelocity self, LinearVelocity o) -> bool
5997 __le__(LinearVelocity self, Particle d) -> bool
5999 return _IMP_atom.LinearVelocity___le__(self, *args)
6002 def __lt__(self, *args):
6004 __lt__(LinearVelocity self, LinearVelocity o) -> bool
6005 __lt__(LinearVelocity self, Particle d) -> bool
6007 return _IMP_atom.LinearVelocity___lt__(self, *args)
6010 def __ge__(self, *args):
6012 __ge__(LinearVelocity self, LinearVelocity o) -> bool
6013 __ge__(LinearVelocity self, Particle d) -> bool
6015 return _IMP_atom.LinearVelocity___ge__(self, *args)
6018 def __gt__(self, *args):
6020 __gt__(LinearVelocity self, LinearVelocity o) -> bool
6021 __gt__(LinearVelocity self, Particle d) -> bool
6023 return _IMP_atom.LinearVelocity___gt__(self, *args)
6027 """__hash__(LinearVelocity self) -> std::size_t"""
6028 return _IMP_atom.LinearVelocity___hash__(self)
6032 """__str__(LinearVelocity self) -> std::string"""
6033 return _IMP_atom.LinearVelocity___str__(self)
6037 """__repr__(LinearVelocity self) -> std::string"""
6038 return _IMP_atom.LinearVelocity___repr__(self)
6040 __swig_destroy__ = _IMP_atom.delete_LinearVelocity
6041 __del__ =
lambda self:
None
6042 LinearVelocity_swigregister = _IMP_atom.LinearVelocity_swigregister
6043 LinearVelocity_swigregister(LinearVelocity)
6045 def LinearVelocity_get_velocity_key(i):
6046 """LinearVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
6047 return _IMP_atom.LinearVelocity_get_velocity_key(i)
6049 def LinearVelocity_get_is_setup(*args):
6051 get_is_setup(Model m, ParticleIndex pi) -> bool
6052 LinearVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6054 return _IMP_atom.LinearVelocity_get_is_setup(*args)
6056 def LinearVelocity_setup_particle(*args):
6058 setup_particle(Model m, ParticleIndex pi) -> LinearVelocity
6059 setup_particle(_ParticleAdaptor decorator) -> LinearVelocity
6060 setup_particle(Model m, ParticleIndex pi, Vector3D v) -> LinearVelocity
6061 LinearVelocity_setup_particle(_ParticleAdaptor decorator, Vector3D v) -> LinearVelocity
6063 return _IMP_atom.LinearVelocity_setup_particle(*args)
6066 """Proxy of C++ IMP::atom::AngularVelocity class"""
6067 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6069 def get_velocity_key(i):
6070 """get_velocity_key(unsigned int i) -> FloatKey"""
6071 return _IMP_atom.AngularVelocity_get_velocity_key(i)
6073 get_velocity_key = staticmethod(get_velocity_key)
6075 def __init__(self, *args):
6077 __init__(IMP::atom::AngularVelocity self) -> AngularVelocity
6078 __init__(IMP::atom::AngularVelocity self, Model m, ParticleIndex id) -> AngularVelocity
6079 __init__(IMP::atom::AngularVelocity self, _ParticleAdaptor d) -> AngularVelocity
6081 this = _IMP_atom.new_AngularVelocity(*args)
6083 self.this.append(this)
6087 def get_is_setup(*args):
6089 get_is_setup(Model m, ParticleIndex pi) -> bool
6090 get_is_setup(_ParticleAdaptor p) -> bool
6092 return _IMP_atom.AngularVelocity_get_is_setup(*args)
6094 get_is_setup = staticmethod(get_is_setup)
6096 def show(self, *args):
6098 show(AngularVelocity self, _ostream out)
6099 show(AngularVelocity self)
6101 return _IMP_atom.AngularVelocity_show(self, *args)
6104 def setup_particle(*args):
6106 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6107 setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6108 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6109 setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6111 return _IMP_atom.AngularVelocity_setup_particle(*args)
6113 setup_particle = staticmethod(setup_particle)
6115 def set_velocity(self, v):
6116 """set_velocity(AngularVelocity self, Vector4D v)"""
6117 return _IMP_atom.AngularVelocity_set_velocity(self, v)
6120 def get_velocity(self):
6121 """get_velocity(AngularVelocity self) -> Vector4D"""
6122 return _IMP_atom.AngularVelocity_get_velocity(self)
6125 def add_attribute(self, *args):
6127 add_attribute(AngularVelocity self, FloatKey k, IMP::Float v, bool opt)
6128 add_attribute(AngularVelocity self, FloatKey a0, IMP::Float a1)
6129 add_attribute(AngularVelocity self, IntKey a0, IMP::Int a1)
6130 add_attribute(AngularVelocity self, StringKey a0, IMP::String a1)
6131 add_attribute(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6132 add_attribute(AngularVelocity self, ObjectKey a0, Object a1)
6134 return _IMP_atom.AngularVelocity_add_attribute(self, *args)
6137 def get_value(self, *args):
6139 get_value(AngularVelocity self, FloatKey a0) -> IMP::Float
6140 get_value(AngularVelocity self, IntKey a0) -> IMP::Int
6141 get_value(AngularVelocity self, StringKey a0) -> IMP::String
6142 get_value(AngularVelocity self, ParticleIndexKey a0) -> Particle
6143 get_value(AngularVelocity self, ObjectKey a0) -> Object
6145 return _IMP_atom.AngularVelocity_get_value(self, *args)
6148 def set_value(self, *args):
6150 set_value(AngularVelocity self, FloatKey a0, IMP::Float a1)
6151 set_value(AngularVelocity self, IntKey a0, IMP::Int a1)
6152 set_value(AngularVelocity self, StringKey a0, IMP::String a1)
6153 set_value(AngularVelocity self, ParticleIndexKey a0, Particle a1)
6154 set_value(AngularVelocity self, ObjectKey a0, Object a1)
6156 return _IMP_atom.AngularVelocity_set_value(self, *args)
6159 def remove_attribute(self, *args):
6161 remove_attribute(AngularVelocity self, FloatKey a0)
6162 remove_attribute(AngularVelocity self, IntKey a0)
6163 remove_attribute(AngularVelocity self, StringKey a0)
6164 remove_attribute(AngularVelocity self, ParticleIndexKey a0)
6165 remove_attribute(AngularVelocity self, ObjectKey a0)
6167 return _IMP_atom.AngularVelocity_remove_attribute(self, *args)
6170 def has_attribute(self, *args):
6172 has_attribute(AngularVelocity self, FloatKey a0) -> bool
6173 has_attribute(AngularVelocity self, IntKey a0) -> bool
6174 has_attribute(AngularVelocity self, StringKey a0) -> bool
6175 has_attribute(AngularVelocity self, ParticleIndexKey a0) -> bool
6176 has_attribute(AngularVelocity self, ObjectKey a0) -> bool
6178 return _IMP_atom.AngularVelocity_has_attribute(self, *args)
6181 def get_derivative(self, a0):
6182 """get_derivative(AngularVelocity self, FloatKey a0) -> double"""
6183 return _IMP_atom.AngularVelocity_get_derivative(self, a0)
6187 """get_name(AngularVelocity self) -> std::string"""
6188 return _IMP_atom.AngularVelocity_get_name(self)
6191 def clear_caches(self):
6192 """clear_caches(AngularVelocity self)"""
6193 return _IMP_atom.AngularVelocity_clear_caches(self)
6196 def set_name(self, a0):
6197 """set_name(AngularVelocity self, std::string a0)"""
6198 return _IMP_atom.AngularVelocity_set_name(self, a0)
6202 """set_check_level(AngularVelocity self, IMP::CheckLevel a0)"""
6203 return _IMP_atom.AngularVelocity_set_check_level(self, a0)
6206 def add_to_derivative(self, a0, a1, a2):
6207 """add_to_derivative(AngularVelocity self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6208 return _IMP_atom.AngularVelocity_add_to_derivative(self, a0, a1, a2)
6211 def set_is_optimized(self, a0, a1):
6212 """set_is_optimized(AngularVelocity self, FloatKey a0, bool a1)"""
6213 return _IMP_atom.AngularVelocity_set_is_optimized(self, a0, a1)
6216 def get_is_optimized(self, a0):
6217 """get_is_optimized(AngularVelocity self, FloatKey a0) -> bool"""
6218 return _IMP_atom.AngularVelocity_get_is_optimized(self, a0)
6222 """get_check_level(AngularVelocity self) -> IMP::CheckLevel"""
6223 return _IMP_atom.AngularVelocity_get_check_level(self)
6226 def __eq__(self, *args):
6228 __eq__(AngularVelocity self, AngularVelocity o) -> bool
6229 __eq__(AngularVelocity self, Particle d) -> bool
6231 return _IMP_atom.AngularVelocity___eq__(self, *args)
6234 def __ne__(self, *args):
6236 __ne__(AngularVelocity self, AngularVelocity o) -> bool
6237 __ne__(AngularVelocity self, Particle d) -> bool
6239 return _IMP_atom.AngularVelocity___ne__(self, *args)
6242 def __le__(self, *args):
6244 __le__(AngularVelocity self, AngularVelocity o) -> bool
6245 __le__(AngularVelocity self, Particle d) -> bool
6247 return _IMP_atom.AngularVelocity___le__(self, *args)
6250 def __lt__(self, *args):
6252 __lt__(AngularVelocity self, AngularVelocity o) -> bool
6253 __lt__(AngularVelocity self, Particle d) -> bool
6255 return _IMP_atom.AngularVelocity___lt__(self, *args)
6258 def __ge__(self, *args):
6260 __ge__(AngularVelocity self, AngularVelocity o) -> bool
6261 __ge__(AngularVelocity self, Particle d) -> bool
6263 return _IMP_atom.AngularVelocity___ge__(self, *args)
6266 def __gt__(self, *args):
6268 __gt__(AngularVelocity self, AngularVelocity o) -> bool
6269 __gt__(AngularVelocity self, Particle d) -> bool
6271 return _IMP_atom.AngularVelocity___gt__(self, *args)
6275 """__hash__(AngularVelocity self) -> std::size_t"""
6276 return _IMP_atom.AngularVelocity___hash__(self)
6280 """__str__(AngularVelocity self) -> std::string"""
6281 return _IMP_atom.AngularVelocity___str__(self)
6285 """__repr__(AngularVelocity self) -> std::string"""
6286 return _IMP_atom.AngularVelocity___repr__(self)
6288 __swig_destroy__ = _IMP_atom.delete_AngularVelocity
6289 __del__ =
lambda self:
None
6290 AngularVelocity_swigregister = _IMP_atom.AngularVelocity_swigregister
6291 AngularVelocity_swigregister(AngularVelocity)
6293 def AngularVelocity_get_velocity_key(i):
6294 """AngularVelocity_get_velocity_key(unsigned int i) -> FloatKey"""
6295 return _IMP_atom.AngularVelocity_get_velocity_key(i)
6297 def AngularVelocity_get_is_setup(*args):
6299 get_is_setup(Model m, ParticleIndex pi) -> bool
6300 AngularVelocity_get_is_setup(_ParticleAdaptor p) -> bool
6302 return _IMP_atom.AngularVelocity_get_is_setup(*args)
6304 def AngularVelocity_setup_particle(*args):
6306 setup_particle(Model m, ParticleIndex pi) -> AngularVelocity
6307 setup_particle(_ParticleAdaptor decorator) -> AngularVelocity
6308 setup_particle(Model m, ParticleIndex pi, Vector4D v) -> AngularVelocity
6309 AngularVelocity_setup_particle(_ParticleAdaptor decorator, Vector4D v) -> AngularVelocity
6311 return _IMP_atom.AngularVelocity_setup_particle(*args)
6313 class MolecularDynamics(Simulator):
6314 """Proxy of C++ IMP::atom::MolecularDynamics class"""
6315 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6317 def __init__(self, m):
6318 """__init__(IMP::atom::MolecularDynamics self, Model m) -> MolecularDynamics"""
6319 this = _IMP_atom.new_MolecularDynamics(m)
6321 self.this.append(this)
6325 def get_kinetic_energy(self):
6326 """get_kinetic_energy(MolecularDynamics self) -> IMP::Float"""
6327 return _IMP_atom.MolecularDynamics_get_kinetic_energy(self)
6330 def get_kinetic_temperature(self, ekinetic):
6331 """get_kinetic_temperature(MolecularDynamics self, IMP::Float ekinetic) -> IMP::Float"""
6332 return _IMP_atom.MolecularDynamics_get_kinetic_temperature(self, ekinetic)
6335 def set_velocity_cap(self, velocity_cap):
6336 """set_velocity_cap(MolecularDynamics self, IMP::Float velocity_cap)"""
6337 return _IMP_atom.MolecularDynamics_set_velocity_cap(self, velocity_cap)
6340 def assign_velocities(self, temperature):
6341 """assign_velocities(MolecularDynamics self, IMP::Float temperature)"""
6342 return _IMP_atom.MolecularDynamics_assign_velocities(self, temperature)
6345 def setup(self, ps):
6346 """setup(MolecularDynamics self, IMP::ParticleIndexes const & ps)"""
6347 return _IMP_atom.MolecularDynamics_setup(self, ps)
6350 def do_step(self, sc, dt):
6351 """do_step(MolecularDynamics self, IMP::ParticleIndexes const & sc, double dt) -> double"""
6352 return _IMP_atom.MolecularDynamics_do_step(self, sc, dt)
6355 def get_is_simulation_particle(self, p):
6356 """get_is_simulation_particle(MolecularDynamics self, ParticleIndex p) -> bool"""
6357 return _IMP_atom.MolecularDynamics_get_is_simulation_particle(self, p)
6360 def get_version_info(self):
6361 """get_version_info(MolecularDynamics self) -> VersionInfo"""
6362 return _IMP_atom.MolecularDynamics_get_version_info(self)
6366 """__str__(MolecularDynamics self) -> std::string"""
6367 return _IMP_atom.MolecularDynamics___str__(self)
6371 """__repr__(MolecularDynamics self) -> std::string"""
6372 return _IMP_atom.MolecularDynamics___repr__(self)
6377 return _object_cast_to_MolecularDynamics(o)
6379 MolecularDynamics_swigregister = _IMP_atom.MolecularDynamics_swigregister
6380 MolecularDynamics_swigregister(MolecularDynamics)
6383 """Proxy of C++ IMP::atom::VelocityScalingOptimizerState class"""
6384 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6386 def __init__(self, m, pis, temperature):
6387 """__init__(IMP::atom::VelocityScalingOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature) -> VelocityScalingOptimizerState"""
6388 this = _IMP_atom.new_VelocityScalingOptimizerState(m, pis, temperature)
6390 self.this.append(this)
6394 def set_particles(self, pis):
6395 """set_particles(VelocityScalingOptimizerState self, IMP::Particles const & pis)"""
6396 return _IMP_atom.VelocityScalingOptimizerState_set_particles(self, pis)
6399 def set_temperature(self, temperature):
6400 """set_temperature(VelocityScalingOptimizerState self, IMP::Float temperature)"""
6401 return _IMP_atom.VelocityScalingOptimizerState_set_temperature(self, temperature)
6404 def rescale_velocities(self):
6405 """rescale_velocities(VelocityScalingOptimizerState self)"""
6406 return _IMP_atom.VelocityScalingOptimizerState_rescale_velocities(self)
6409 def get_version_info(self):
6410 """get_version_info(VelocityScalingOptimizerState self) -> VersionInfo"""
6411 return _IMP_atom.VelocityScalingOptimizerState_get_version_info(self)
6415 """__str__(VelocityScalingOptimizerState self) -> std::string"""
6416 return _IMP_atom.VelocityScalingOptimizerState___str__(self)
6420 """__repr__(VelocityScalingOptimizerState self) -> std::string"""
6421 return _IMP_atom.VelocityScalingOptimizerState___repr__(self)
6426 return _object_cast_to_VelocityScalingOptimizerState(o)
6428 VelocityScalingOptimizerState_swigregister = _IMP_atom.VelocityScalingOptimizerState_swigregister
6429 VelocityScalingOptimizerState_swigregister(VelocityScalingOptimizerState)
6431 class Fragment(Hierarchy):
6432 """Proxy of C++ IMP::atom::Fragment class"""
6433 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6435 def set_residue_indexes(self, o):
6436 """set_residue_indexes(Fragment self, IMP::Ints o)"""
6437 return _IMP_atom.Fragment_set_residue_indexes(self, o)
6440 def get_residue_indexes(self):
6441 """get_residue_indexes(Fragment self) -> IMP::Ints"""
6442 return _IMP_atom.Fragment_get_residue_indexes(self)
6445 def get_contains_residue(self, rindex):
6446 """get_contains_residue(Fragment self, int rindex) -> bool"""
6447 return _IMP_atom.Fragment_get_contains_residue(self, rindex)
6450 def __init__(self, *args):
6452 __init__(IMP::atom::Fragment self) -> Fragment
6453 __init__(IMP::atom::Fragment self, Model m, ParticleIndex id) -> Fragment
6454 __init__(IMP::atom::Fragment self, _ParticleAdaptor d) -> Fragment
6456 this = _IMP_atom.new_Fragment(*args)
6458 self.this.append(this)
6462 def get_is_setup(*args):
6464 get_is_setup(Model m, ParticleIndex pi) -> bool
6465 get_is_setup(_ParticleAdaptor p) -> bool
6467 return _IMP_atom.Fragment_get_is_setup(*args)
6469 get_is_setup = staticmethod(get_is_setup)
6471 def show(self, *args):
6473 show(Fragment self, _ostream out)
6476 return _IMP_atom.Fragment_show(self, *args)
6479 def setup_particle(*args):
6481 setup_particle(Model m, ParticleIndex pi) -> Fragment
6482 setup_particle(_ParticleAdaptor decorator) -> Fragment
6483 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6484 setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6485 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6486 setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6488 return _IMP_atom.Fragment_setup_particle(*args)
6490 setup_particle = staticmethod(setup_particle)
6492 def add_attribute(self, *args):
6494 add_attribute(Fragment self, FloatKey k, IMP::Float v, bool opt)
6495 add_attribute(Fragment self, FloatKey a0, IMP::Float a1)
6496 add_attribute(Fragment self, IntKey a0, IMP::Int a1)
6497 add_attribute(Fragment self, StringKey a0, IMP::String a1)
6498 add_attribute(Fragment self, ParticleIndexKey a0, Particle a1)
6499 add_attribute(Fragment self, ObjectKey a0, Object a1)
6501 return _IMP_atom.Fragment_add_attribute(self, *args)
6504 def get_value(self, *args):
6506 get_value(Fragment self, FloatKey a0) -> IMP::Float
6507 get_value(Fragment self, IntKey a0) -> IMP::Int
6508 get_value(Fragment self, StringKey a0) -> IMP::String
6509 get_value(Fragment self, ParticleIndexKey a0) -> Particle
6510 get_value(Fragment self, ObjectKey a0) -> Object
6512 return _IMP_atom.Fragment_get_value(self, *args)
6515 def set_value(self, *args):
6517 set_value(Fragment self, FloatKey a0, IMP::Float a1)
6518 set_value(Fragment self, IntKey a0, IMP::Int a1)
6519 set_value(Fragment self, StringKey a0, IMP::String a1)
6520 set_value(Fragment self, ParticleIndexKey a0, Particle a1)
6521 set_value(Fragment self, ObjectKey a0, Object a1)
6523 return _IMP_atom.Fragment_set_value(self, *args)
6526 def remove_attribute(self, *args):
6528 remove_attribute(Fragment self, FloatKey a0)
6529 remove_attribute(Fragment self, IntKey a0)
6530 remove_attribute(Fragment self, StringKey a0)
6531 remove_attribute(Fragment self, ParticleIndexKey a0)
6532 remove_attribute(Fragment self, ObjectKey a0)
6534 return _IMP_atom.Fragment_remove_attribute(self, *args)
6537 def has_attribute(self, *args):
6539 has_attribute(Fragment self, FloatKey a0) -> bool
6540 has_attribute(Fragment self, IntKey a0) -> bool
6541 has_attribute(Fragment self, StringKey a0) -> bool
6542 has_attribute(Fragment self, ParticleIndexKey a0) -> bool
6543 has_attribute(Fragment self, ObjectKey a0) -> bool
6545 return _IMP_atom.Fragment_has_attribute(self, *args)
6548 def get_derivative(self, a0):
6549 """get_derivative(Fragment self, FloatKey a0) -> double"""
6550 return _IMP_atom.Fragment_get_derivative(self, a0)
6554 """get_name(Fragment self) -> std::string"""
6555 return _IMP_atom.Fragment_get_name(self)
6558 def clear_caches(self):
6559 """clear_caches(Fragment self)"""
6560 return _IMP_atom.Fragment_clear_caches(self)
6563 def set_name(self, a0):
6564 """set_name(Fragment self, std::string a0)"""
6565 return _IMP_atom.Fragment_set_name(self, a0)
6569 """set_check_level(Fragment self, IMP::CheckLevel a0)"""
6570 return _IMP_atom.Fragment_set_check_level(self, a0)
6573 def add_to_derivative(self, a0, a1, a2):
6574 """add_to_derivative(Fragment self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6575 return _IMP_atom.Fragment_add_to_derivative(self, a0, a1, a2)
6578 def set_is_optimized(self, a0, a1):
6579 """set_is_optimized(Fragment self, FloatKey a0, bool a1)"""
6580 return _IMP_atom.Fragment_set_is_optimized(self, a0, a1)
6583 def get_is_optimized(self, a0):
6584 """get_is_optimized(Fragment self, FloatKey a0) -> bool"""
6585 return _IMP_atom.Fragment_get_is_optimized(self, a0)
6589 """get_check_level(Fragment self) -> IMP::CheckLevel"""
6590 return _IMP_atom.Fragment_get_check_level(self)
6593 def __eq__(self, *args):
6595 __eq__(Fragment self, Fragment o) -> bool
6596 __eq__(Fragment self, Particle d) -> bool
6598 return _IMP_atom.Fragment___eq__(self, *args)
6601 def __ne__(self, *args):
6603 __ne__(Fragment self, Fragment o) -> bool
6604 __ne__(Fragment self, Particle d) -> bool
6606 return _IMP_atom.Fragment___ne__(self, *args)
6609 def __le__(self, *args):
6611 __le__(Fragment self, Fragment o) -> bool
6612 __le__(Fragment self, Particle d) -> bool
6614 return _IMP_atom.Fragment___le__(self, *args)
6617 def __lt__(self, *args):
6619 __lt__(Fragment self, Fragment o) -> bool
6620 __lt__(Fragment self, Particle d) -> bool
6622 return _IMP_atom.Fragment___lt__(self, *args)
6625 def __ge__(self, *args):
6627 __ge__(Fragment self, Fragment o) -> bool
6628 __ge__(Fragment self, Particle d) -> bool
6630 return _IMP_atom.Fragment___ge__(self, *args)
6633 def __gt__(self, *args):
6635 __gt__(Fragment self, Fragment o) -> bool
6636 __gt__(Fragment self, Particle d) -> bool
6638 return _IMP_atom.Fragment___gt__(self, *args)
6642 """__hash__(Fragment self) -> std::size_t"""
6643 return _IMP_atom.Fragment___hash__(self)
6647 """__str__(Fragment self) -> std::string"""
6648 return _IMP_atom.Fragment___str__(self)
6652 """__repr__(Fragment self) -> std::string"""
6653 return _IMP_atom.Fragment___repr__(self)
6655 __swig_destroy__ = _IMP_atom.delete_Fragment
6656 __del__ =
lambda self:
None
6657 Fragment_swigregister = _IMP_atom.Fragment_swigregister
6658 Fragment_swigregister(Fragment)
6660 def Fragment_get_is_setup(*args):
6662 get_is_setup(Model m, ParticleIndex pi) -> bool
6663 Fragment_get_is_setup(_ParticleAdaptor p) -> bool
6665 return _IMP_atom.Fragment_get_is_setup(*args)
6667 def Fragment_setup_particle(*args):
6669 setup_particle(Model m, ParticleIndex pi) -> Fragment
6670 setup_particle(_ParticleAdaptor decorator) -> Fragment
6671 setup_particle(Model m, ParticleIndex pi, Fragment other) -> Fragment
6672 setup_particle(_ParticleAdaptor decorator, Fragment other) -> Fragment
6673 setup_particle(Model m, ParticleIndex pi, IMP::Ints residue_indexes) -> Fragment
6674 Fragment_setup_particle(_ParticleAdaptor decorator, IMP::Ints residue_indexes) -> Fragment
6676 return _IMP_atom.Fragment_setup_particle(*args)
6679 """Proxy of C++ IMP::atom::StereochemistryPairFilter class"""
6680 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6683 """__init__(IMP::atom::StereochemistryPairFilter self) -> StereochemistryPairFilter"""
6684 this = _IMP_atom.new_StereochemistryPairFilter()
6686 self.this.append(this)
6690 def set_bonds(self, bonds):
6691 """set_bonds(StereochemistryPairFilter self, IMP::Particles const & bonds)"""
6692 return _IMP_atom.StereochemistryPairFilter_set_bonds(self, bonds)
6695 def set_angles(self, angles):
6696 """set_angles(StereochemistryPairFilter self, IMP::Particles const & angles)"""
6697 return _IMP_atom.StereochemistryPairFilter_set_angles(self, angles)
6700 def set_dihedrals(self, dihedrals):
6701 """set_dihedrals(StereochemistryPairFilter self, IMP::Particles const & dihedrals)"""
6702 return _IMP_atom.StereochemistryPairFilter_set_dihedrals(self, dihedrals)
6705 def do_get_inputs(self, m, pis):
6706 """do_get_inputs(StereochemistryPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6707 return _IMP_atom.StereochemistryPairFilter_do_get_inputs(self, m, pis)
6710 def get_value(self, *args):
6712 get_value(StereochemistryPairFilter self, IMP::ParticlePair const & a) -> int
6713 get_value(StereochemistryPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6715 return _IMP_atom.StereochemistryPairFilter_get_value(self, *args)
6718 def get_value_index(self, *args):
6720 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6721 get_value_index(StereochemistryPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6723 return _IMP_atom.StereochemistryPairFilter_get_value_index(self, *args)
6726 def get_version_info(self):
6727 """get_version_info(StereochemistryPairFilter self) -> VersionInfo"""
6728 return _IMP_atom.StereochemistryPairFilter_get_version_info(self)
6732 """__str__(StereochemistryPairFilter self) -> std::string"""
6733 return _IMP_atom.StereochemistryPairFilter___str__(self)
6737 """__repr__(StereochemistryPairFilter self) -> std::string"""
6738 return _IMP_atom.StereochemistryPairFilter___repr__(self)
6743 return _object_cast_to_StereochemistryPairFilter(o)
6745 StereochemistryPairFilter_swigregister = _IMP_atom.StereochemistryPairFilter_swigregister
6746 StereochemistryPairFilter_swigregister(StereochemistryPairFilter)
6749 """Proxy of C++ IMP::atom::SoapPairFilter class"""
6750 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6752 def __init__(self, library):
6753 """__init__(IMP::atom::SoapPairFilter self, std::string library) -> SoapPairFilter"""
6754 this = _IMP_atom.new_SoapPairFilter(library)
6756 self.this.append(this)
6760 def do_get_inputs(self, m, pis):
6761 """do_get_inputs(SoapPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6762 return _IMP_atom.SoapPairFilter_do_get_inputs(self, m, pis)
6765 def get_value(self, *args):
6767 get_value(SoapPairFilter self, IMP::ParticlePair const & a) -> int
6768 get_value(SoapPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
6770 return _IMP_atom.SoapPairFilter_get_value(self, *args)
6773 def get_value_index(self, *args):
6775 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
6776 get_value_index(SoapPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6778 return _IMP_atom.SoapPairFilter_get_value_index(self, *args)
6781 def get_version_info(self):
6782 """get_version_info(SoapPairFilter self) -> VersionInfo"""
6783 return _IMP_atom.SoapPairFilter_get_version_info(self)
6787 """__str__(SoapPairFilter self) -> std::string"""
6788 return _IMP_atom.SoapPairFilter___str__(self)
6792 """__repr__(SoapPairFilter self) -> std::string"""
6793 return _IMP_atom.SoapPairFilter___repr__(self)
6798 return _object_cast_to_SoapPairFilter(o)
6800 SoapPairFilter_swigregister = _IMP_atom.SoapPairFilter_swigregister
6801 SoapPairFilter_swigregister(SoapPairFilter)
6804 """Proxy of C++ IMP::atom::Mass class"""
6805 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
6808 """get_mass(Mass self) -> IMP::Float"""
6809 return _IMP_atom.Mass_get_mass(self)
6812 def set_mass(self, d):
6813 """set_mass(Mass self, IMP::Float d)"""
6814 return _IMP_atom.Mass_set_mass(self, d)
6817 def __init__(self, *args):
6819 __init__(IMP::atom::Mass self) -> Mass
6820 __init__(IMP::atom::Mass self, Model m, ParticleIndex id) -> Mass
6821 __init__(IMP::atom::Mass self, _ParticleAdaptor d) -> Mass
6823 this = _IMP_atom.new_Mass(*args)
6825 self.this.append(this)
6829 def get_is_setup(*args):
6831 get_is_setup(Model m, ParticleIndex pi) -> bool
6832 get_is_setup(_ParticleAdaptor p) -> bool
6834 return _IMP_atom.Mass_get_is_setup(*args)
6836 get_is_setup = staticmethod(get_is_setup)
6838 def show(self, *args):
6840 show(Mass self, _ostream out)
6843 return _IMP_atom.Mass_show(self, *args)
6846 def setup_particle(*args):
6848 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
6849 setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
6851 return _IMP_atom.Mass_setup_particle(*args)
6853 setup_particle = staticmethod(setup_particle)
6856 """get_mass_key() -> FloatKey"""
6857 return _IMP_atom.Mass_get_mass_key()
6859 get_mass_key = staticmethod(get_mass_key)
6861 def add_attribute(self, *args):
6863 add_attribute(Mass self, FloatKey k, IMP::Float v, bool opt)
6864 add_attribute(Mass self, FloatKey a0, IMP::Float a1)
6865 add_attribute(Mass self, IntKey a0, IMP::Int a1)
6866 add_attribute(Mass self, StringKey a0, IMP::String a1)
6867 add_attribute(Mass self, ParticleIndexKey a0, Particle a1)
6868 add_attribute(Mass self, ObjectKey a0, Object a1)
6870 return _IMP_atom.Mass_add_attribute(self, *args)
6873 def get_value(self, *args):
6875 get_value(Mass self, FloatKey a0) -> IMP::Float
6876 get_value(Mass self, IntKey a0) -> IMP::Int
6877 get_value(Mass self, StringKey a0) -> IMP::String
6878 get_value(Mass self, ParticleIndexKey a0) -> Particle
6879 get_value(Mass self, ObjectKey a0) -> Object
6881 return _IMP_atom.Mass_get_value(self, *args)
6884 def set_value(self, *args):
6886 set_value(Mass self, FloatKey a0, IMP::Float a1)
6887 set_value(Mass self, IntKey a0, IMP::Int a1)
6888 set_value(Mass self, StringKey a0, IMP::String a1)
6889 set_value(Mass self, ParticleIndexKey a0, Particle a1)
6890 set_value(Mass self, ObjectKey a0, Object a1)
6892 return _IMP_atom.Mass_set_value(self, *args)
6895 def remove_attribute(self, *args):
6897 remove_attribute(Mass self, FloatKey a0)
6898 remove_attribute(Mass self, IntKey a0)
6899 remove_attribute(Mass self, StringKey a0)
6900 remove_attribute(Mass self, ParticleIndexKey a0)
6901 remove_attribute(Mass self, ObjectKey a0)
6903 return _IMP_atom.Mass_remove_attribute(self, *args)
6906 def has_attribute(self, *args):
6908 has_attribute(Mass self, FloatKey a0) -> bool
6909 has_attribute(Mass self, IntKey a0) -> bool
6910 has_attribute(Mass self, StringKey a0) -> bool
6911 has_attribute(Mass self, ParticleIndexKey a0) -> bool
6912 has_attribute(Mass self, ObjectKey a0) -> bool
6914 return _IMP_atom.Mass_has_attribute(self, *args)
6917 def get_derivative(self, a0):
6918 """get_derivative(Mass self, FloatKey a0) -> double"""
6919 return _IMP_atom.Mass_get_derivative(self, a0)
6923 """get_name(Mass self) -> std::string"""
6924 return _IMP_atom.Mass_get_name(self)
6927 def clear_caches(self):
6928 """clear_caches(Mass self)"""
6929 return _IMP_atom.Mass_clear_caches(self)
6932 def set_name(self, a0):
6933 """set_name(Mass self, std::string a0)"""
6934 return _IMP_atom.Mass_set_name(self, a0)
6938 """set_check_level(Mass self, IMP::CheckLevel a0)"""
6939 return _IMP_atom.Mass_set_check_level(self, a0)
6942 def add_to_derivative(self, a0, a1, a2):
6943 """add_to_derivative(Mass self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
6944 return _IMP_atom.Mass_add_to_derivative(self, a0, a1, a2)
6947 def set_is_optimized(self, a0, a1):
6948 """set_is_optimized(Mass self, FloatKey a0, bool a1)"""
6949 return _IMP_atom.Mass_set_is_optimized(self, a0, a1)
6952 def get_is_optimized(self, a0):
6953 """get_is_optimized(Mass self, FloatKey a0) -> bool"""
6954 return _IMP_atom.Mass_get_is_optimized(self, a0)
6958 """get_check_level(Mass self) -> IMP::CheckLevel"""
6959 return _IMP_atom.Mass_get_check_level(self)
6962 def __eq__(self, *args):
6964 __eq__(Mass self, Mass o) -> bool
6965 __eq__(Mass self, Particle d) -> bool
6967 return _IMP_atom.Mass___eq__(self, *args)
6970 def __ne__(self, *args):
6972 __ne__(Mass self, Mass o) -> bool
6973 __ne__(Mass self, Particle d) -> bool
6975 return _IMP_atom.Mass___ne__(self, *args)
6978 def __le__(self, *args):
6980 __le__(Mass self, Mass o) -> bool
6981 __le__(Mass self, Particle d) -> bool
6983 return _IMP_atom.Mass___le__(self, *args)
6986 def __lt__(self, *args):
6988 __lt__(Mass self, Mass o) -> bool
6989 __lt__(Mass self, Particle d) -> bool
6991 return _IMP_atom.Mass___lt__(self, *args)
6994 def __ge__(self, *args):
6996 __ge__(Mass self, Mass o) -> bool
6997 __ge__(Mass self, Particle d) -> bool
6999 return _IMP_atom.Mass___ge__(self, *args)
7002 def __gt__(self, *args):
7004 __gt__(Mass self, Mass o) -> bool
7005 __gt__(Mass self, Particle d) -> bool
7007 return _IMP_atom.Mass___gt__(self, *args)
7011 """__hash__(Mass self) -> std::size_t"""
7012 return _IMP_atom.Mass___hash__(self)
7016 """__str__(Mass self) -> std::string"""
7017 return _IMP_atom.Mass___str__(self)
7021 """__repr__(Mass self) -> std::string"""
7022 return _IMP_atom.Mass___repr__(self)
7024 __swig_destroy__ = _IMP_atom.delete_Mass
7025 __del__ =
lambda self:
None
7026 Mass_swigregister = _IMP_atom.Mass_swigregister
7027 Mass_swigregister(Mass)
7029 def Mass_get_is_setup(*args):
7031 get_is_setup(Model m, ParticleIndex pi) -> bool
7032 Mass_get_is_setup(_ParticleAdaptor p) -> bool
7034 return _IMP_atom.Mass_get_is_setup(*args)
7036 def Mass_setup_particle(*args):
7038 setup_particle(Model m, ParticleIndex pi, IMP::Float mass) -> Mass
7039 Mass_setup_particle(_ParticleAdaptor decorator, IMP::Float mass) -> Mass
7041 return _IMP_atom.Mass_setup_particle(*args)
7043 def Mass_get_mass_key():
7044 """Mass_get_mass_key() -> FloatKey"""
7045 return _IMP_atom.Mass_get_mass_key()
7048 """Proxy of C++ IMP::atom::BondedPairFilter class"""
7049 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7052 """__init__(IMP::atom::BondedPairFilter self) -> BondedPairFilter"""
7053 this = _IMP_atom.new_BondedPairFilter()
7055 self.this.append(this)
7059 def do_get_inputs(self, m, pis):
7060 """do_get_inputs(BondedPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7061 return _IMP_atom.BondedPairFilter_do_get_inputs(self, m, pis)
7064 def get_value(self, *args):
7066 get_value(BondedPairFilter self, IMP::ParticlePair const & a) -> int
7067 get_value(BondedPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
7069 return _IMP_atom.BondedPairFilter_get_value(self, *args)
7072 def get_value_index(self, *args):
7074 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
7075 get_value_index(BondedPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
7077 return _IMP_atom.BondedPairFilter_get_value_index(self, *args)
7080 def get_version_info(self):
7081 """get_version_info(BondedPairFilter self) -> VersionInfo"""
7082 return _IMP_atom.BondedPairFilter_get_version_info(self)
7086 """__str__(BondedPairFilter self) -> std::string"""
7087 return _IMP_atom.BondedPairFilter___str__(self)
7091 """__repr__(BondedPairFilter self) -> std::string"""
7092 return _IMP_atom.BondedPairFilter___repr__(self)
7097 return _object_cast_to_BondedPairFilter(o)
7099 BondedPairFilter_swigregister = _IMP_atom.BondedPairFilter_swigregister
7100 BondedPairFilter_swigregister(BondedPairFilter)
7103 """Proxy of C++ IMP::atom::Mol2Selector class"""
7104 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7106 def __init__(self, *args, **kwargs):
7107 raise AttributeError(
"No constructor defined - class is abstract")
7109 def get_is_selected(self, atom_line):
7110 """get_is_selected(Mol2Selector self, std::string const & atom_line) -> bool"""
7111 return _IMP_atom.Mol2Selector_get_is_selected(self, atom_line)
7113 __swig_destroy__ = _IMP_atom.delete_Mol2Selector
7114 __del__ =
lambda self:
None
7117 """__str__(Mol2Selector self) -> std::string"""
7118 return _IMP_atom.Mol2Selector___str__(self)
7122 """__repr__(Mol2Selector self) -> std::string"""
7123 return _IMP_atom.Mol2Selector___repr__(self)
7128 return _object_cast_to_Mol2Selector(o)
7130 Mol2Selector_swigregister = _IMP_atom.Mol2Selector_swigregister
7131 Mol2Selector_swigregister(Mol2Selector)
7133 class AllMol2Selector(Mol2Selector):
7134 """Proxy of C++ IMP::atom::AllMol2Selector class"""
7135 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7138 """__str__(AllMol2Selector self) -> std::string"""
7139 return _IMP_atom.AllMol2Selector___str__(self)
7143 """__repr__(AllMol2Selector self) -> std::string"""
7144 return _IMP_atom.AllMol2Selector___repr__(self)
7149 return _object_cast_to_AllMol2Selector(o)
7153 """__init__(IMP::atom::AllMol2Selector self) -> AllMol2Selector"""
7154 this = _IMP_atom.new_AllMol2Selector()
7156 self.this.append(this)
7159 __swig_destroy__ = _IMP_atom.delete_AllMol2Selector
7160 __del__ =
lambda self:
None
7161 AllMol2Selector_swigregister = _IMP_atom.AllMol2Selector_swigregister
7162 AllMol2Selector_swigregister(AllMol2Selector)
7164 class NonHydrogenMol2Selector(Mol2Selector):
7165 """Proxy of C++ IMP::atom::NonHydrogenMol2Selector class"""
7166 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7169 """__str__(NonHydrogenMol2Selector self) -> std::string"""
7170 return _IMP_atom.NonHydrogenMol2Selector___str__(self)
7174 """__repr__(NonHydrogenMol2Selector self) -> std::string"""
7175 return _IMP_atom.NonHydrogenMol2Selector___repr__(self)
7180 return _object_cast_to_NonHydrogenMol2Selector(o)
7184 """__init__(IMP::atom::NonHydrogenMol2Selector self) -> NonHydrogenMol2Selector"""
7185 this = _IMP_atom.new_NonHydrogenMol2Selector()
7187 self.this.append(this)
7190 __swig_destroy__ = _IMP_atom.delete_NonHydrogenMol2Selector
7191 __del__ =
lambda self:
None
7192 NonHydrogenMol2Selector_swigregister = _IMP_atom.NonHydrogenMol2Selector_swigregister
7193 NonHydrogenMol2Selector_swigregister(NonHydrogenMol2Selector)
7196 def read_mol2(mol2_file, model, mol2sel=None):
7198 read_mol2(TextInput mol2_file, Model model, Mol2Selector mol2sel=None) -> Hierarchy
7199 read_mol2(TextInput mol2_file, Model model) -> Hierarchy
7201 return _IMP_atom.read_mol2(mol2_file, model, mol2sel)
7204 """write_mol2(Hierarchy rhd, TextOutput file_name)"""
7205 return _IMP_atom.write_mol2(rhd, file_name)
7207 """Proxy of C++ IMP::atom::SecondaryStructureResidue class"""
7208 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7210 def __init__(self, *args):
7212 __init__(IMP::atom::SecondaryStructureResidue self) -> SecondaryStructureResidue
7213 __init__(IMP::atom::SecondaryStructureResidue self, Model m, ParticleIndex id) -> SecondaryStructureResidue
7214 __init__(IMP::atom::SecondaryStructureResidue self, _ParticleAdaptor d) -> SecondaryStructureResidue
7216 this = _IMP_atom.new_SecondaryStructureResidue(*args)
7218 self.this.append(this)
7222 def show(self, *args):
7224 show(SecondaryStructureResidue self, _ostream out)
7225 show(SecondaryStructureResidue self)
7227 return _IMP_atom.SecondaryStructureResidue_show(self, *args)
7230 def setup_particle(*args):
7232 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7233 setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7234 setup_particle(Particle res_p) -> SecondaryStructureResidue
7236 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7238 setup_particle = staticmethod(setup_particle)
7240 def get_is_setup(*args):
7242 get_is_setup(_ParticleAdaptor p) -> bool
7243 get_is_setup(Model m, ParticleIndex pi) -> bool
7245 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7247 get_is_setup = staticmethod(get_is_setup)
7249 def get_particle(self):
7250 """get_particle(SecondaryStructureResidue self) -> Particle"""
7251 return _IMP_atom.SecondaryStructureResidue_get_particle(self)
7254 def get_all_probabilities(self):
7255 """get_all_probabilities(SecondaryStructureResidue self) -> IMP::Floats"""
7256 return _IMP_atom.SecondaryStructureResidue_get_all_probabilities(self)
7259 def get_prob_helix(self):
7260 """get_prob_helix(SecondaryStructureResidue self) -> IMP::Float"""
7261 return _IMP_atom.SecondaryStructureResidue_get_prob_helix(self)
7264 def set_prob_helix(self, t):
7265 """set_prob_helix(SecondaryStructureResidue self, IMP::Float t)"""
7266 return _IMP_atom.SecondaryStructureResidue_set_prob_helix(self, t)
7269 def get_prob_strand(self):
7270 """get_prob_strand(SecondaryStructureResidue self) -> IMP::Float"""
7271 return _IMP_atom.SecondaryStructureResidue_get_prob_strand(self)
7274 def set_prob_strand(self, t):
7275 """set_prob_strand(SecondaryStructureResidue self, IMP::Float t)"""
7276 return _IMP_atom.SecondaryStructureResidue_set_prob_strand(self, t)
7279 def get_prob_coil(self):
7280 """get_prob_coil(SecondaryStructureResidue self) -> IMP::Float"""
7281 return _IMP_atom.SecondaryStructureResidue_get_prob_coil(self)
7284 def set_prob_coil(self, t):
7285 """set_prob_coil(SecondaryStructureResidue self, IMP::Float t)"""
7286 return _IMP_atom.SecondaryStructureResidue_set_prob_coil(self, t)
7289 def get_prob_helix_key():
7290 """get_prob_helix_key() -> FloatKey"""
7291 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7293 get_prob_helix_key = staticmethod(get_prob_helix_key)
7295 def get_prob_strand_key():
7296 """get_prob_strand_key() -> FloatKey"""
7297 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7299 get_prob_strand_key = staticmethod(get_prob_strand_key)
7301 def get_prob_coil_key():
7302 """get_prob_coil_key() -> FloatKey"""
7303 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7305 get_prob_coil_key = staticmethod(get_prob_coil_key)
7307 def add_attribute(self, *args):
7309 add_attribute(SecondaryStructureResidue self, FloatKey k, IMP::Float v, bool opt)
7310 add_attribute(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7311 add_attribute(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7312 add_attribute(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7313 add_attribute(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7314 add_attribute(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7316 return _IMP_atom.SecondaryStructureResidue_add_attribute(self, *args)
7319 def get_value(self, *args):
7321 get_value(SecondaryStructureResidue self, FloatKey a0) -> IMP::Float
7322 get_value(SecondaryStructureResidue self, IntKey a0) -> IMP::Int
7323 get_value(SecondaryStructureResidue self, StringKey a0) -> IMP::String
7324 get_value(SecondaryStructureResidue self, ParticleIndexKey a0) -> Particle
7325 get_value(SecondaryStructureResidue self, ObjectKey a0) -> Object
7327 return _IMP_atom.SecondaryStructureResidue_get_value(self, *args)
7330 def set_value(self, *args):
7332 set_value(SecondaryStructureResidue self, FloatKey a0, IMP::Float a1)
7333 set_value(SecondaryStructureResidue self, IntKey a0, IMP::Int a1)
7334 set_value(SecondaryStructureResidue self, StringKey a0, IMP::String a1)
7335 set_value(SecondaryStructureResidue self, ParticleIndexKey a0, Particle a1)
7336 set_value(SecondaryStructureResidue self, ObjectKey a0, Object a1)
7338 return _IMP_atom.SecondaryStructureResidue_set_value(self, *args)
7341 def remove_attribute(self, *args):
7343 remove_attribute(SecondaryStructureResidue self, FloatKey a0)
7344 remove_attribute(SecondaryStructureResidue self, IntKey a0)
7345 remove_attribute(SecondaryStructureResidue self, StringKey a0)
7346 remove_attribute(SecondaryStructureResidue self, ParticleIndexKey a0)
7347 remove_attribute(SecondaryStructureResidue self, ObjectKey a0)
7349 return _IMP_atom.SecondaryStructureResidue_remove_attribute(self, *args)
7352 def has_attribute(self, *args):
7354 has_attribute(SecondaryStructureResidue self, FloatKey a0) -> bool
7355 has_attribute(SecondaryStructureResidue self, IntKey a0) -> bool
7356 has_attribute(SecondaryStructureResidue self, StringKey a0) -> bool
7357 has_attribute(SecondaryStructureResidue self, ParticleIndexKey a0) -> bool
7358 has_attribute(SecondaryStructureResidue self, ObjectKey a0) -> bool
7360 return _IMP_atom.SecondaryStructureResidue_has_attribute(self, *args)
7363 def get_derivative(self, a0):
7364 """get_derivative(SecondaryStructureResidue self, FloatKey a0) -> double"""
7365 return _IMP_atom.SecondaryStructureResidue_get_derivative(self, a0)
7369 """get_name(SecondaryStructureResidue self) -> std::string"""
7370 return _IMP_atom.SecondaryStructureResidue_get_name(self)
7373 def clear_caches(self):
7374 """clear_caches(SecondaryStructureResidue self)"""
7375 return _IMP_atom.SecondaryStructureResidue_clear_caches(self)
7378 def set_name(self, a0):
7379 """set_name(SecondaryStructureResidue self, std::string a0)"""
7380 return _IMP_atom.SecondaryStructureResidue_set_name(self, a0)
7384 """set_check_level(SecondaryStructureResidue self, IMP::CheckLevel a0)"""
7385 return _IMP_atom.SecondaryStructureResidue_set_check_level(self, a0)
7388 def add_to_derivative(self, a0, a1, a2):
7389 """add_to_derivative(SecondaryStructureResidue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
7390 return _IMP_atom.SecondaryStructureResidue_add_to_derivative(self, a0, a1, a2)
7393 def set_is_optimized(self, a0, a1):
7394 """set_is_optimized(SecondaryStructureResidue self, FloatKey a0, bool a1)"""
7395 return _IMP_atom.SecondaryStructureResidue_set_is_optimized(self, a0, a1)
7398 def get_is_optimized(self, a0):
7399 """get_is_optimized(SecondaryStructureResidue self, FloatKey a0) -> bool"""
7400 return _IMP_atom.SecondaryStructureResidue_get_is_optimized(self, a0)
7404 """get_check_level(SecondaryStructureResidue self) -> IMP::CheckLevel"""
7405 return _IMP_atom.SecondaryStructureResidue_get_check_level(self)
7408 def __eq__(self, *args):
7410 __eq__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7411 __eq__(SecondaryStructureResidue self, Particle d) -> bool
7413 return _IMP_atom.SecondaryStructureResidue___eq__(self, *args)
7416 def __ne__(self, *args):
7418 __ne__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7419 __ne__(SecondaryStructureResidue self, Particle d) -> bool
7421 return _IMP_atom.SecondaryStructureResidue___ne__(self, *args)
7424 def __le__(self, *args):
7426 __le__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7427 __le__(SecondaryStructureResidue self, Particle d) -> bool
7429 return _IMP_atom.SecondaryStructureResidue___le__(self, *args)
7432 def __lt__(self, *args):
7434 __lt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7435 __lt__(SecondaryStructureResidue self, Particle d) -> bool
7437 return _IMP_atom.SecondaryStructureResidue___lt__(self, *args)
7440 def __ge__(self, *args):
7442 __ge__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7443 __ge__(SecondaryStructureResidue self, Particle d) -> bool
7445 return _IMP_atom.SecondaryStructureResidue___ge__(self, *args)
7448 def __gt__(self, *args):
7450 __gt__(SecondaryStructureResidue self, SecondaryStructureResidue o) -> bool
7451 __gt__(SecondaryStructureResidue self, Particle d) -> bool
7453 return _IMP_atom.SecondaryStructureResidue___gt__(self, *args)
7457 """__hash__(SecondaryStructureResidue self) -> std::size_t"""
7458 return _IMP_atom.SecondaryStructureResidue___hash__(self)
7462 """__str__(SecondaryStructureResidue self) -> std::string"""
7463 return _IMP_atom.SecondaryStructureResidue___str__(self)
7467 """__repr__(SecondaryStructureResidue self) -> std::string"""
7468 return _IMP_atom.SecondaryStructureResidue___repr__(self)
7470 __swig_destroy__ = _IMP_atom.delete_SecondaryStructureResidue
7471 __del__ =
lambda self:
None
7472 SecondaryStructureResidue_swigregister = _IMP_atom.SecondaryStructureResidue_swigregister
7473 SecondaryStructureResidue_swigregister(SecondaryStructureResidue)
7475 def SecondaryStructureResidue_setup_particle(*args):
7477 setup_particle(Model m, ParticleIndex pi, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7478 setup_particle(_ParticleAdaptor decorator, IMP::Float prob_helix, IMP::Float prob_strand, IMP::Float prob_coil) -> SecondaryStructureResidue
7479 SecondaryStructureResidue_setup_particle(Particle res_p) -> SecondaryStructureResidue
7481 return _IMP_atom.SecondaryStructureResidue_setup_particle(*args)
7483 def SecondaryStructureResidue_get_is_setup(*args):
7485 get_is_setup(_ParticleAdaptor p) -> bool
7486 SecondaryStructureResidue_get_is_setup(Model m, ParticleIndex pi) -> bool
7488 return _IMP_atom.SecondaryStructureResidue_get_is_setup(*args)
7490 def SecondaryStructureResidue_get_prob_helix_key():
7491 """SecondaryStructureResidue_get_prob_helix_key() -> FloatKey"""
7492 return _IMP_atom.SecondaryStructureResidue_get_prob_helix_key()
7494 def SecondaryStructureResidue_get_prob_strand_key():
7495 """SecondaryStructureResidue_get_prob_strand_key() -> FloatKey"""
7496 return _IMP_atom.SecondaryStructureResidue_get_prob_strand_key()
7498 def SecondaryStructureResidue_get_prob_coil_key():
7499 """SecondaryStructureResidue_get_prob_coil_key() -> FloatKey"""
7500 return _IMP_atom.SecondaryStructureResidue_get_prob_coil_key()
7505 setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl, bool winner_takes_all_per_res=False) -> SecondaryStructureResidue
7506 setup_coarse_secondary_structure_residue(IMP::Particles const & ssr_ps, Model mdl) -> SecondaryStructureResidue
7508 return _IMP_atom.setup_coarse_secondary_structure_residue(ssr_ps, mdl, winner_takes_all_per_res)
7512 setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=False) -> IMP::atom::SecondaryStructureResidues
7513 setup_coarse_secondary_structure_residues(IMP::Particles const & ssr_ps, Model mdl, int coarse_factor, int start_res_num) -> IMP::atom::SecondaryStructureResidues
7515 return _IMP_atom.setup_coarse_secondary_structure_residues(ssr_ps, mdl, coarse_factor, start_res_num, winner_takes_all_per_res)
7518 """get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2) -> IMP::Float"""
7519 return _IMP_atom.get_secondary_structure_match_score(ssr1, ssr2)
7521 def read_psipred(*args):
7523 read_psipred(TextInput inf, Model mdl) -> IMP::atom::SecondaryStructureResidues
7524 read_psipred(TextInput inf, IMP::Particles ps) -> IMP::atom::SecondaryStructureResidues
7526 return _IMP_atom.read_psipred(*args)
7528 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> class"""
7529 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7530 __repr__ = _swig_repr
7532 def __init__(self, *args):
7534 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0, std::string name) -> _ADopeBase
7535 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Dope)> self, Dope t0) -> _ADopeBase
7537 this = _IMP_atom.new__ADopeBase(*args)
7539 self.this.append(this)
7543 def do_get_inputs(self, m, pis):
7544 """do_get_inputs(_ADopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7545 return _IMP_atom._ADopeBase_do_get_inputs(self, m, pis)
7548 def get_score_functor(self):
7549 """get_score_functor(_ADopeBase self) -> Dope"""
7550 return _IMP_atom._ADopeBase_get_score_functor(self)
7553 def get_version_info(self):
7554 """get_version_info(_ADopeBase self) -> VersionInfo"""
7555 return _IMP_atom._ADopeBase_get_version_info(self)
7557 _ADopeBase_swigregister = _IMP_atom._ADopeBase_swigregister
7558 _ADopeBase_swigregister(_ADopeBase)
7561 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> class"""
7562 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7563 __repr__ = _swig_repr
7565 def __init__(self, *args):
7567 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0, std::string name) -> _BDopeBase
7568 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::DopeType,false,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::DopeType,false,true,false > >::DistanceScore const & t0) -> _BDopeBase
7570 this = _IMP_atom.new__BDopeBase(*args)
7572 self.this.append(this)
7576 def do_get_inputs(self, m, pis):
7577 """do_get_inputs(_BDopeBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7578 return _IMP_atom._BDopeBase_do_get_inputs(self, m, pis)
7581 def get_score_functor(self):
7582 """get_score_functor(_BDopeBase self) -> _DopeBase"""
7583 return _IMP_atom._BDopeBase_get_score_functor(self)
7586 def get_version_info(self):
7587 """get_version_info(_BDopeBase self) -> VersionInfo"""
7588 return _IMP_atom._BDopeBase_get_version_info(self)
7590 _BDopeBase_swigregister = _IMP_atom._BDopeBase_swigregister
7591 _BDopeBase_swigregister(_BDopeBase)
7594 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> class"""
7595 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7596 __repr__ = _swig_repr
7598 def __init__(self, *args):
7600 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0, std::string name) -> _OrientedSoapBase
7601 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::OrientedSoap)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::OrientedSoap >::DistanceScore const & t0) -> _OrientedSoapBase
7603 this = _IMP_atom.new__OrientedSoapBase(*args)
7605 self.this.append(this)
7609 def do_get_inputs(self, m, pis):
7610 """do_get_inputs(_OrientedSoapBase self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7611 return _IMP_atom._OrientedSoapBase_do_get_inputs(self, m, pis)
7614 def get_score_functor(self):
7615 """get_score_functor(_OrientedSoapBase self) -> IMP::score_functor::OrientedSoap &"""
7616 return _IMP_atom._OrientedSoapBase_get_score_functor(self)
7619 def get_version_info(self):
7620 """get_version_info(_OrientedSoapBase self) -> VersionInfo"""
7621 return _IMP_atom._OrientedSoapBase_get_version_info(self)
7623 _OrientedSoapBase_swigregister = _IMP_atom._OrientedSoapBase_swigregister
7624 _OrientedSoapBase_swigregister(_OrientedSoapBase)
7627 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> class"""
7628 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7629 __repr__ = _swig_repr
7631 def __init__(self, *args):
7633 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0, std::string name) -> _SPSFTB
7634 __init__(IMP::score_functor::DistancePairScore<(IMP::score_functor::Statistical<(IMP::atom::ProteinLigandType,true,false)>)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false > >::DistanceScore const & t0) -> _SPSFTB
7636 this = _IMP_atom.new__SPSFTB(*args)
7638 self.this.append(this)
7642 def do_get_inputs(self, m, pis):
7643 """do_get_inputs(_SPSFTB self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7644 return _IMP_atom._SPSFTB_do_get_inputs(self, m, pis)
7647 def get_score_functor(self):
7648 """get_score_functor(_SPSFTB self) -> IMP::score_functor::Statistical< IMP::atom::ProteinLigandType,true,false,false > &"""
7649 return _IMP_atom._SPSFTB_get_score_functor(self)
7652 def get_version_info(self):
7653 """get_version_info(_SPSFTB self) -> VersionInfo"""
7654 return _IMP_atom._SPSFTB_get_version_info(self)
7656 _SPSFTB_swigregister = _IMP_atom._SPSFTB_swigregister
7657 _SPSFTB_swigregister(_SPSFTB)
7659 class _SPSTF(_SPSFTB):
7660 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> class"""
7661 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7662 __repr__ = _swig_repr
7664 def __init__(self, *args):
7666 __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file) -> _SPSTF
7667 __init__(IMP::core::StatisticalPairScore<(IMP::atom::ProteinLigandType,true,false)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSTF
7669 this = _IMP_atom.new__SPSTF(*args)
7671 self.this.append(this)
7674 __swig_destroy__ = _IMP_atom.delete__SPSTF
7675 __del__ =
lambda self:
None
7676 _SPSTF_swigregister = _IMP_atom._SPSTF_swigregister
7677 _SPSTF_swigregister(_SPSTF)
7679 class _SPSFT(_BDopeBase):
7680 """Proxy of C++ IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> class"""
7681 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7682 __repr__ = _swig_repr
7684 def __init__(self, *args):
7686 __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file) -> _SPSFT
7687 __init__(IMP::core::StatisticalPairScore<(IMP::atom::DopeType,false,true)> self, IntKey k, double threshold, TextInput data_file, unsigned int shift) -> _SPSFT
7689 this = _IMP_atom.new__SPSFT(*args)
7691 self.this.append(this)
7694 __swig_destroy__ = _IMP_atom.delete__SPSFT
7695 __del__ =
lambda self:
None
7696 _SPSFT_swigregister = _IMP_atom._SPSFT_swigregister
7697 _SPSFT_swigregister(_SPSFT)
7699 class ProteinLigandAtomPairScore(_SPSTF):
7700 """Proxy of C++ IMP::atom::ProteinLigandAtomPairScore class"""
7701 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7703 def __init__(self, *args):
7705 __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold) -> ProteinLigandAtomPairScore
7706 __init__(IMP::atom::ProteinLigandAtomPairScore self) -> ProteinLigandAtomPairScore
7707 __init__(IMP::atom::ProteinLigandAtomPairScore self, double threshold, TextInput data_file) -> ProteinLigandAtomPairScore
7709 this = _IMP_atom.new_ProteinLigandAtomPairScore(*args)
7711 self.this.append(this)
7715 def get_maximum_distance(self):
7716 """get_maximum_distance(ProteinLigandAtomPairScore self) -> double"""
7717 return _IMP_atom.ProteinLigandAtomPairScore_get_maximum_distance(self)
7721 """__str__(ProteinLigandAtomPairScore self) -> std::string"""
7722 return _IMP_atom.ProteinLigandAtomPairScore___str__(self)
7726 """__repr__(ProteinLigandAtomPairScore self) -> std::string"""
7727 return _IMP_atom.ProteinLigandAtomPairScore___repr__(self)
7732 return _object_cast_to_ProteinLigandAtomPairScore(o)
7734 __swig_destroy__ = _IMP_atom.delete_ProteinLigandAtomPairScore
7735 __del__ =
lambda self:
None
7736 ProteinLigandAtomPairScore_swigregister = _IMP_atom.ProteinLigandAtomPairScore_swigregister
7737 ProteinLigandAtomPairScore_swigregister(ProteinLigandAtomPairScore)
7740 """Proxy of C++ IMP::atom::ProteinLigandRestraint class"""
7741 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7743 def __init__(self, *args):
7745 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold) -> ProteinLigandRestraint
7746 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand) -> ProteinLigandRestraint
7747 __init__(IMP::atom::ProteinLigandRestraint self, Hierarchy protein, Hierarchy ligand, double threshold, TextInput data_file) -> ProteinLigandRestraint
7749 this = _IMP_atom.new_ProteinLigandRestraint(*args)
7751 self.this.append(this)
7756 """__str__(ProteinLigandRestraint self) -> std::string"""
7757 return _IMP_atom.ProteinLigandRestraint___str__(self)
7761 """__repr__(ProteinLigandRestraint self) -> std::string"""
7762 return _IMP_atom.ProteinLigandRestraint___repr__(self)
7767 return _object_cast_to_ProteinLigandRestraint(o)
7769 __swig_destroy__ = _IMP_atom.delete_ProteinLigandRestraint
7770 __del__ =
lambda self:
None
7771 ProteinLigandRestraint_swigregister = _IMP_atom.ProteinLigandRestraint_swigregister
7772 ProteinLigandRestraint_swigregister(ProteinLigandRestraint)
7776 """add_protein_ligand_score_data(Hierarchy h)"""
7777 return _IMP_atom.add_protein_ligand_score_data(h)
7778 class AtomType(IMP._Value):
7779 """Proxy of C++ IMP::Key<(8974343,false)> class"""
7780 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7782 def __init__(self, *args):
7784 __init__(IMP::Key<(8974343,false)> self) -> AtomType
7785 __init__(IMP::Key<(8974343,false)> self, std::string c) -> AtomType
7786 __init__(IMP::Key<(8974343,false)> self, unsigned int i) -> AtomType
7788 this = _IMP_atom.new_AtomType(*args)
7790 self.this.append(this)
7795 """add_key(std::string sc) -> unsigned int"""
7796 return _IMP_atom.AtomType_add_key(sc)
7798 add_key = staticmethod(add_key)
7800 def get_key_exists(sc):
7801 """get_key_exists(std::string sc) -> bool"""
7802 return _IMP_atom.AtomType_get_key_exists(sc)
7804 get_key_exists = staticmethod(get_key_exists)
7806 def get_string(self):
7807 """get_string(AtomType self) -> std::string const"""
7808 return _IMP_atom.AtomType_get_string(self)
7811 def __cmp__(self, o):
7812 """__cmp__(AtomType self, AtomType o) -> int"""
7813 return _IMP_atom.AtomType___cmp__(self, o)
7816 def __eq__(self, o):
7817 """__eq__(AtomType self, AtomType o) -> bool"""
7818 return _IMP_atom.AtomType___eq__(self, o)
7821 def __ne__(self, o):
7822 """__ne__(AtomType self, AtomType o) -> bool"""
7823 return _IMP_atom.AtomType___ne__(self, o)
7826 def __lt__(self, o):
7827 """__lt__(AtomType self, AtomType o) -> bool"""
7828 return _IMP_atom.AtomType___lt__(self, o)
7831 def __gt__(self, o):
7832 """__gt__(AtomType self, AtomType o) -> bool"""
7833 return _IMP_atom.AtomType___gt__(self, o)
7836 def __ge__(self, o):
7837 """__ge__(AtomType self, AtomType o) -> bool"""
7838 return _IMP_atom.AtomType___ge__(self, o)
7841 def __le__(self, o):
7842 """__le__(AtomType self, AtomType o) -> bool"""
7843 return _IMP_atom.AtomType___le__(self, o)
7847 """__hash__(AtomType self) -> std::size_t"""
7848 return _IMP_atom.AtomType___hash__(self)
7851 def show(self, *args):
7853 show(AtomType self, _ostream out)
7856 return _IMP_atom.AtomType_show(self, *args)
7859 def add_alias(old_key, new_name):
7860 """add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7861 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7863 add_alias = staticmethod(add_alias)
7866 """get_index(AtomType self) -> unsigned int"""
7867 return _IMP_atom.AtomType_get_index(self)
7871 """show_all(_ostream out)"""
7872 return _IMP_atom.AtomType_show_all(out)
7874 show_all = staticmethod(show_all)
7876 def get_all_strings():
7877 """get_all_strings() -> IMP::Vector< std::string >"""
7878 return _IMP_atom.AtomType_get_all_strings()
7880 get_all_strings = staticmethod(get_all_strings)
7882 def get_number_unique():
7883 """get_number_unique() -> unsigned int"""
7884 return _IMP_atom.AtomType_get_number_unique()
7886 get_number_unique = staticmethod(get_number_unique)
7889 """__str__(AtomType self) -> std::string"""
7890 return _IMP_atom.AtomType___str__(self)
7894 """__repr__(AtomType self) -> std::string"""
7895 return _IMP_atom.AtomType___repr__(self)
7897 __swig_destroy__ = _IMP_atom.delete_AtomType
7898 __del__ =
lambda self:
None
7899 AtomType_swigregister = _IMP_atom.AtomType_swigregister
7900 AtomType_swigregister(AtomType)
7902 def AtomType_add_key(sc):
7903 """AtomType_add_key(std::string sc) -> unsigned int"""
7904 return _IMP_atom.AtomType_add_key(sc)
7906 def AtomType_get_key_exists(sc):
7907 """AtomType_get_key_exists(std::string sc) -> bool"""
7908 return _IMP_atom.AtomType_get_key_exists(sc)
7910 def AtomType_add_alias(old_key, new_name):
7911 """AtomType_add_alias(AtomType old_key, std::string new_name) -> AtomType"""
7912 return _IMP_atom.AtomType_add_alias(old_key, new_name)
7914 def AtomType_show_all(out):
7915 """AtomType_show_all(_ostream out)"""
7916 return _IMP_atom.AtomType_show_all(out)
7918 def AtomType_get_all_strings():
7919 """AtomType_get_all_strings() -> IMP::Vector< std::string >"""
7920 return _IMP_atom.AtomType_get_all_strings()
7922 def AtomType_get_number_unique():
7923 """AtomType_get_number_unique() -> unsigned int"""
7924 return _IMP_atom.AtomType_get_number_unique()
7926 class ResidueType(IMP._Value):
7927 """Proxy of C++ IMP::Key<(90784334,true)> class"""
7928 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
7930 def __init__(self, *args):
7932 __init__(IMP::Key<(90784334,true)> self) -> ResidueType
7933 __init__(IMP::Key<(90784334,true)> self, std::string c) -> ResidueType
7934 __init__(IMP::Key<(90784334,true)> self, unsigned int i) -> ResidueType
7936 this = _IMP_atom.new_ResidueType(*args)
7938 self.this.append(this)
7943 """add_key(std::string sc) -> unsigned int"""
7944 return _IMP_atom.ResidueType_add_key(sc)
7946 add_key = staticmethod(add_key)
7948 def get_key_exists(sc):
7949 """get_key_exists(std::string sc) -> bool"""
7950 return _IMP_atom.ResidueType_get_key_exists(sc)
7952 get_key_exists = staticmethod(get_key_exists)
7954 def get_string(self):
7955 """get_string(ResidueType self) -> std::string const"""
7956 return _IMP_atom.ResidueType_get_string(self)
7959 def __cmp__(self, o):
7960 """__cmp__(ResidueType self, ResidueType o) -> int"""
7961 return _IMP_atom.ResidueType___cmp__(self, o)
7964 def __eq__(self, o):
7965 """__eq__(ResidueType self, ResidueType o) -> bool"""
7966 return _IMP_atom.ResidueType___eq__(self, o)
7969 def __ne__(self, o):
7970 """__ne__(ResidueType self, ResidueType o) -> bool"""
7971 return _IMP_atom.ResidueType___ne__(self, o)
7974 def __lt__(self, o):
7975 """__lt__(ResidueType self, ResidueType o) -> bool"""
7976 return _IMP_atom.ResidueType___lt__(self, o)
7979 def __gt__(self, o):
7980 """__gt__(ResidueType self, ResidueType o) -> bool"""
7981 return _IMP_atom.ResidueType___gt__(self, o)
7984 def __ge__(self, o):
7985 """__ge__(ResidueType self, ResidueType o) -> bool"""
7986 return _IMP_atom.ResidueType___ge__(self, o)
7989 def __le__(self, o):
7990 """__le__(ResidueType self, ResidueType o) -> bool"""
7991 return _IMP_atom.ResidueType___le__(self, o)
7995 """__hash__(ResidueType self) -> std::size_t"""
7996 return _IMP_atom.ResidueType___hash__(self)
7999 def show(self, *args):
8001 show(ResidueType self, _ostream out)
8002 show(ResidueType self)
8004 return _IMP_atom.ResidueType_show(self, *args)
8007 def add_alias(old_key, new_name):
8008 """add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8009 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8011 add_alias = staticmethod(add_alias)
8014 """get_index(ResidueType self) -> unsigned int"""
8015 return _IMP_atom.ResidueType_get_index(self)
8019 """show_all(_ostream out)"""
8020 return _IMP_atom.ResidueType_show_all(out)
8022 show_all = staticmethod(show_all)
8024 def get_all_strings():
8025 """get_all_strings() -> IMP::Vector< std::string >"""
8026 return _IMP_atom.ResidueType_get_all_strings()
8028 get_all_strings = staticmethod(get_all_strings)
8030 def get_number_unique():
8031 """get_number_unique() -> unsigned int"""
8032 return _IMP_atom.ResidueType_get_number_unique()
8034 get_number_unique = staticmethod(get_number_unique)
8037 """__str__(ResidueType self) -> std::string"""
8038 return _IMP_atom.ResidueType___str__(self)
8042 """__repr__(ResidueType self) -> std::string"""
8043 return _IMP_atom.ResidueType___repr__(self)
8045 __swig_destroy__ = _IMP_atom.delete_ResidueType
8046 __del__ =
lambda self:
None
8047 ResidueType_swigregister = _IMP_atom.ResidueType_swigregister
8048 ResidueType_swigregister(ResidueType)
8050 def ResidueType_add_key(sc):
8051 """ResidueType_add_key(std::string sc) -> unsigned int"""
8052 return _IMP_atom.ResidueType_add_key(sc)
8054 def ResidueType_get_key_exists(sc):
8055 """ResidueType_get_key_exists(std::string sc) -> bool"""
8056 return _IMP_atom.ResidueType_get_key_exists(sc)
8058 def ResidueType_add_alias(old_key, new_name):
8059 """ResidueType_add_alias(ResidueType old_key, std::string new_name) -> ResidueType"""
8060 return _IMP_atom.ResidueType_add_alias(old_key, new_name)
8062 def ResidueType_show_all(out):
8063 """ResidueType_show_all(_ostream out)"""
8064 return _IMP_atom.ResidueType_show_all(out)
8066 def ResidueType_get_all_strings():
8067 """ResidueType_get_all_strings() -> IMP::Vector< std::string >"""
8068 return _IMP_atom.ResidueType_get_all_strings()
8070 def ResidueType_get_number_unique():
8071 """ResidueType_get_number_unique() -> unsigned int"""
8072 return _IMP_atom.ResidueType_get_number_unique()
8075 _IMP_atom.UNKNOWN_ELEMENT_swigconstant(_IMP_atom)
8076 UNKNOWN_ELEMENT = _IMP_atom.UNKNOWN_ELEMENT
8078 _IMP_atom.OH_swigconstant(_IMP_atom)
8081 _IMP_atom.H2O_swigconstant(_IMP_atom)
8084 _IMP_atom.H_swigconstant(_IMP_atom)
8087 _IMP_atom.He_swigconstant(_IMP_atom)
8090 _IMP_atom.Li_swigconstant(_IMP_atom)
8093 _IMP_atom.Be_swigconstant(_IMP_atom)
8096 _IMP_atom.B_swigconstant(_IMP_atom)
8099 _IMP_atom.C_swigconstant(_IMP_atom)
8102 _IMP_atom.N_swigconstant(_IMP_atom)
8105 _IMP_atom.O_swigconstant(_IMP_atom)
8108 _IMP_atom.F_swigconstant(_IMP_atom)
8111 _IMP_atom.Ne_swigconstant(_IMP_atom)
8114 _IMP_atom.Na_swigconstant(_IMP_atom)
8117 _IMP_atom.Mg_swigconstant(_IMP_atom)
8120 _IMP_atom.Al_swigconstant(_IMP_atom)
8123 _IMP_atom.Si_swigconstant(_IMP_atom)
8126 _IMP_atom.P_swigconstant(_IMP_atom)
8129 _IMP_atom.S_swigconstant(_IMP_atom)
8132 _IMP_atom.Cl_swigconstant(_IMP_atom)
8135 _IMP_atom.Ar_swigconstant(_IMP_atom)
8138 _IMP_atom.K_swigconstant(_IMP_atom)
8141 _IMP_atom.Ca_swigconstant(_IMP_atom)
8144 _IMP_atom.Sc_swigconstant(_IMP_atom)
8147 _IMP_atom.Ti_swigconstant(_IMP_atom)
8150 _IMP_atom.V_swigconstant(_IMP_atom)
8153 _IMP_atom.Cr_swigconstant(_IMP_atom)
8156 _IMP_atom.Mn_swigconstant(_IMP_atom)
8159 _IMP_atom.Fe_swigconstant(_IMP_atom)
8162 _IMP_atom.Co_swigconstant(_IMP_atom)
8165 _IMP_atom.Ni_swigconstant(_IMP_atom)
8168 _IMP_atom.Cu_swigconstant(_IMP_atom)
8171 _IMP_atom.Zn_swigconstant(_IMP_atom)
8174 _IMP_atom.Ga_swigconstant(_IMP_atom)
8177 _IMP_atom.Ge_swigconstant(_IMP_atom)
8180 _IMP_atom.As_swigconstant(_IMP_atom)
8183 _IMP_atom.Se_swigconstant(_IMP_atom)
8186 _IMP_atom.Br_swigconstant(_IMP_atom)
8189 _IMP_atom.Kr_swigconstant(_IMP_atom)
8192 _IMP_atom.Rb_swigconstant(_IMP_atom)
8195 _IMP_atom.Sr_swigconstant(_IMP_atom)
8198 _IMP_atom.Y_swigconstant(_IMP_atom)
8201 _IMP_atom.Zr_swigconstant(_IMP_atom)
8204 _IMP_atom.Nb_swigconstant(_IMP_atom)
8207 _IMP_atom.Mo_swigconstant(_IMP_atom)
8210 _IMP_atom.Tc_swigconstant(_IMP_atom)
8213 _IMP_atom.Ru_swigconstant(_IMP_atom)
8216 _IMP_atom.Rh_swigconstant(_IMP_atom)
8219 _IMP_atom.Pd_swigconstant(_IMP_atom)
8222 _IMP_atom.Ag_swigconstant(_IMP_atom)
8225 _IMP_atom.Cd_swigconstant(_IMP_atom)
8228 _IMP_atom.In_swigconstant(_IMP_atom)
8231 _IMP_atom.Sn_swigconstant(_IMP_atom)
8234 _IMP_atom.Sb_swigconstant(_IMP_atom)
8237 _IMP_atom.Te_swigconstant(_IMP_atom)
8240 _IMP_atom.I_swigconstant(_IMP_atom)
8243 _IMP_atom.Xe_swigconstant(_IMP_atom)
8246 _IMP_atom.Cs_swigconstant(_IMP_atom)
8249 _IMP_atom.Ba_swigconstant(_IMP_atom)
8252 _IMP_atom.La_swigconstant(_IMP_atom)
8255 _IMP_atom.Ce_swigconstant(_IMP_atom)
8258 _IMP_atom.Pr_swigconstant(_IMP_atom)
8261 _IMP_atom.Nd_swigconstant(_IMP_atom)
8264 _IMP_atom.Pm_swigconstant(_IMP_atom)
8267 _IMP_atom.Sm_swigconstant(_IMP_atom)
8270 _IMP_atom.Eu_swigconstant(_IMP_atom)
8273 _IMP_atom.Gd_swigconstant(_IMP_atom)
8276 _IMP_atom.Tb_swigconstant(_IMP_atom)
8279 _IMP_atom.Dy_swigconstant(_IMP_atom)
8282 _IMP_atom.Ho_swigconstant(_IMP_atom)
8285 _IMP_atom.Er_swigconstant(_IMP_atom)
8288 _IMP_atom.Tm_swigconstant(_IMP_atom)
8291 _IMP_atom.Yb_swigconstant(_IMP_atom)
8294 _IMP_atom.Lu_swigconstant(_IMP_atom)
8297 _IMP_atom.Hf_swigconstant(_IMP_atom)
8300 _IMP_atom.Ta_swigconstant(_IMP_atom)
8303 _IMP_atom.W_swigconstant(_IMP_atom)
8306 _IMP_atom.Re_swigconstant(_IMP_atom)
8309 _IMP_atom.Os_swigconstant(_IMP_atom)
8312 _IMP_atom.Ir_swigconstant(_IMP_atom)
8315 _IMP_atom.Pt_swigconstant(_IMP_atom)
8318 _IMP_atom.Au_swigconstant(_IMP_atom)
8321 _IMP_atom.Hg_swigconstant(_IMP_atom)
8324 _IMP_atom.Tl_swigconstant(_IMP_atom)
8327 _IMP_atom.Pb_swigconstant(_IMP_atom)
8330 _IMP_atom.Bi_swigconstant(_IMP_atom)
8333 _IMP_atom.Po_swigconstant(_IMP_atom)
8336 _IMP_atom.At_swigconstant(_IMP_atom)
8339 _IMP_atom.Rn_swigconstant(_IMP_atom)
8342 _IMP_atom.Fr_swigconstant(_IMP_atom)
8345 _IMP_atom.Ra_swigconstant(_IMP_atom)
8348 _IMP_atom.Ac_swigconstant(_IMP_atom)
8351 _IMP_atom.Th_swigconstant(_IMP_atom)
8354 _IMP_atom.Pa_swigconstant(_IMP_atom)
8357 _IMP_atom.U_swigconstant(_IMP_atom)
8360 _IMP_atom.Np_swigconstant(_IMP_atom)
8363 _IMP_atom.Pu_swigconstant(_IMP_atom)
8366 _IMP_atom.Am_swigconstant(_IMP_atom)
8369 _IMP_atom.Cm_swigconstant(_IMP_atom)
8372 _IMP_atom.Bk_swigconstant(_IMP_atom)
8375 _IMP_atom.Cf_swigconstant(_IMP_atom)
8378 _IMP_atom.Es_swigconstant(_IMP_atom)
8381 _IMP_atom.Fm_swigconstant(_IMP_atom)
8384 _IMP_atom.Md_swigconstant(_IMP_atom)
8387 _IMP_atom.No_swigconstant(_IMP_atom)
8390 _IMP_atom.Lr_swigconstant(_IMP_atom)
8393 _IMP_atom.Db_swigconstant(_IMP_atom)
8396 _IMP_atom.Jl_swigconstant(_IMP_atom)
8399 _IMP_atom.Rf_swigconstant(_IMP_atom)
8402 _IMP_atom.NUMBER_OF_ELEMENTS_swigconstant(_IMP_atom)
8403 NUMBER_OF_ELEMENTS = _IMP_atom.NUMBER_OF_ELEMENTS
8406 """hash_value(IMP::atom::Element e) -> size_t"""
8407 return _IMP_atom.hash_value(e)
8408 class ElementTable(object):
8409 """Proxy of C++ IMP::atom::ElementTable class"""
8410 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8411 __repr__ = _swig_repr
8414 """__init__(IMP::atom::ElementTable self) -> ElementTable"""
8415 this = _IMP_atom.new_ElementTable()
8417 self.this.append(this)
8421 def get_element(self, s):
8422 """get_element(ElementTable self, std::string const & s) -> IMP::atom::Element"""
8423 return _IMP_atom.ElementTable_get_element(self, s)
8426 def get_name(self, e):
8427 """get_name(ElementTable self, IMP::atom::Element e) -> std::string"""
8428 return _IMP_atom.ElementTable_get_name(self, e)
8432 """get_mass(ElementTable self, IMP::atom::Element e) -> IMP::Float"""
8433 return _IMP_atom.ElementTable_get_mass(self, e)
8435 __swig_destroy__ = _IMP_atom.delete_ElementTable
8436 __del__ =
lambda self:
None
8437 ElementTable_swigregister = _IMP_atom.ElementTable_swigregister
8438 ElementTable_swigregister(ElementTable)
8441 def get_element_table():
8442 """get_element_table() -> ElementTable"""
8443 return _IMP_atom.get_element_table()
8444 class Atom(Hierarchy):
8445 """Proxy of C++ IMP::atom::Atom class"""
8446 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8448 def __init__(self, *args):
8450 __init__(IMP::atom::Atom self) -> Atom
8451 __init__(IMP::atom::Atom self, Model m, ParticleIndex id) -> Atom
8452 __init__(IMP::atom::Atom self, _ParticleAdaptor d) -> Atom
8454 this = _IMP_atom.new_Atom(*args)
8456 self.this.append(this)
8460 def show(self, *args):
8462 show(Atom self, _ostream out)
8465 return _IMP_atom.Atom_show(self, *args)
8468 def setup_particle(*args):
8470 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8471 setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8472 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8473 setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8475 return _IMP_atom.Atom_setup_particle(*args)
8477 setup_particle = staticmethod(setup_particle)
8479 def get_is_setup(*args):
8481 get_is_setup(_ParticleAdaptor p) -> bool
8482 get_is_setup(Model m, ParticleIndex pi) -> bool
8484 return _IMP_atom.Atom_get_is_setup(*args)
8486 get_is_setup = staticmethod(get_is_setup)
8488 def get_atom_type(self):
8489 """get_atom_type(Atom self) -> AtomType"""
8490 return _IMP_atom.Atom_get_atom_type(self)
8493 def set_atom_type(self, t):
8494 """set_atom_type(Atom self, AtomType t)"""
8495 return _IMP_atom.Atom_set_atom_type(self, t)
8498 def get_element(self):
8499 """get_element(Atom self) -> IMP::atom::Element"""
8500 return _IMP_atom.Atom_get_element(self)
8503 def set_element(self, e):
8504 """set_element(Atom self, IMP::atom::Element e)"""
8505 return _IMP_atom.Atom_set_element(self, e)
8508 def get_occupancy(self):
8509 """get_occupancy(Atom self) -> double"""
8510 return _IMP_atom.Atom_get_occupancy(self)
8513 def set_occupancy(self, occupancy):
8514 """set_occupancy(Atom self, double occupancy)"""
8515 return _IMP_atom.Atom_set_occupancy(self, occupancy)
8518 def get_temperature_factor(self):
8519 """get_temperature_factor(Atom self) -> double"""
8520 return _IMP_atom.Atom_get_temperature_factor(self)
8523 def set_temperature_factor(self, tempFactor):
8524 """set_temperature_factor(Atom self, double tempFactor)"""
8525 return _IMP_atom.Atom_set_temperature_factor(self, tempFactor)
8528 def get_input_index(self):
8529 """get_input_index(Atom self) -> IMP::Int"""
8530 return _IMP_atom.Atom_get_input_index(self)
8533 def set_input_index(self, t):
8534 """set_input_index(Atom self, IMP::Int t)"""
8535 return _IMP_atom.Atom_set_input_index(self, t)
8538 def get_atom_type_key():
8539 """get_atom_type_key() -> IntKey"""
8540 return _IMP_atom.Atom_get_atom_type_key()
8542 get_atom_type_key = staticmethod(get_atom_type_key)
8544 def get_element_key():
8545 """get_element_key() -> IntKey"""
8546 return _IMP_atom.Atom_get_element_key()
8548 get_element_key = staticmethod(get_element_key)
8550 def get_input_index_key():
8551 """get_input_index_key() -> IntKey"""
8552 return _IMP_atom.Atom_get_input_index_key()
8554 get_input_index_key = staticmethod(get_input_index_key)
8556 def get_occupancy_key():
8557 """get_occupancy_key() -> FloatKey"""
8558 return _IMP_atom.Atom_get_occupancy_key()
8560 get_occupancy_key = staticmethod(get_occupancy_key)
8562 def get_temperature_factor_key():
8563 """get_temperature_factor_key() -> FloatKey"""
8564 return _IMP_atom.Atom_get_temperature_factor_key()
8566 get_temperature_factor_key = staticmethod(get_temperature_factor_key)
8568 def add_attribute(self, *args):
8570 add_attribute(Atom self, FloatKey k, IMP::Float v, bool opt)
8571 add_attribute(Atom self, FloatKey a0, IMP::Float a1)
8572 add_attribute(Atom self, IntKey a0, IMP::Int a1)
8573 add_attribute(Atom self, StringKey a0, IMP::String a1)
8574 add_attribute(Atom self, ParticleIndexKey a0, Particle a1)
8575 add_attribute(Atom self, ObjectKey a0, Object a1)
8577 return _IMP_atom.Atom_add_attribute(self, *args)
8580 def get_value(self, *args):
8582 get_value(Atom self, FloatKey a0) -> IMP::Float
8583 get_value(Atom self, IntKey a0) -> IMP::Int
8584 get_value(Atom self, StringKey a0) -> IMP::String
8585 get_value(Atom self, ParticleIndexKey a0) -> Particle
8586 get_value(Atom self, ObjectKey a0) -> Object
8588 return _IMP_atom.Atom_get_value(self, *args)
8591 def set_value(self, *args):
8593 set_value(Atom self, FloatKey a0, IMP::Float a1)
8594 set_value(Atom self, IntKey a0, IMP::Int a1)
8595 set_value(Atom self, StringKey a0, IMP::String a1)
8596 set_value(Atom self, ParticleIndexKey a0, Particle a1)
8597 set_value(Atom self, ObjectKey a0, Object a1)
8599 return _IMP_atom.Atom_set_value(self, *args)
8602 def remove_attribute(self, *args):
8604 remove_attribute(Atom self, FloatKey a0)
8605 remove_attribute(Atom self, IntKey a0)
8606 remove_attribute(Atom self, StringKey a0)
8607 remove_attribute(Atom self, ParticleIndexKey a0)
8608 remove_attribute(Atom self, ObjectKey a0)
8610 return _IMP_atom.Atom_remove_attribute(self, *args)
8613 def has_attribute(self, *args):
8615 has_attribute(Atom self, FloatKey a0) -> bool
8616 has_attribute(Atom self, IntKey a0) -> bool
8617 has_attribute(Atom self, StringKey a0) -> bool
8618 has_attribute(Atom self, ParticleIndexKey a0) -> bool
8619 has_attribute(Atom self, ObjectKey a0) -> bool
8621 return _IMP_atom.Atom_has_attribute(self, *args)
8624 def get_derivative(self, a0):
8625 """get_derivative(Atom self, FloatKey a0) -> double"""
8626 return _IMP_atom.Atom_get_derivative(self, a0)
8630 """get_name(Atom self) -> std::string"""
8631 return _IMP_atom.Atom_get_name(self)
8634 def clear_caches(self):
8635 """clear_caches(Atom self)"""
8636 return _IMP_atom.Atom_clear_caches(self)
8639 def set_name(self, a0):
8640 """set_name(Atom self, std::string a0)"""
8641 return _IMP_atom.Atom_set_name(self, a0)
8645 """set_check_level(Atom self, IMP::CheckLevel a0)"""
8646 return _IMP_atom.Atom_set_check_level(self, a0)
8649 def add_to_derivative(self, a0, a1, a2):
8650 """add_to_derivative(Atom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8651 return _IMP_atom.Atom_add_to_derivative(self, a0, a1, a2)
8654 def set_is_optimized(self, a0, a1):
8655 """set_is_optimized(Atom self, FloatKey a0, bool a1)"""
8656 return _IMP_atom.Atom_set_is_optimized(self, a0, a1)
8659 def get_is_optimized(self, a0):
8660 """get_is_optimized(Atom self, FloatKey a0) -> bool"""
8661 return _IMP_atom.Atom_get_is_optimized(self, a0)
8665 """get_check_level(Atom self) -> IMP::CheckLevel"""
8666 return _IMP_atom.Atom_get_check_level(self)
8669 def __eq__(self, *args):
8671 __eq__(Atom self, Atom o) -> bool
8672 __eq__(Atom self, Particle d) -> bool
8674 return _IMP_atom.Atom___eq__(self, *args)
8677 def __ne__(self, *args):
8679 __ne__(Atom self, Atom o) -> bool
8680 __ne__(Atom self, Particle d) -> bool
8682 return _IMP_atom.Atom___ne__(self, *args)
8685 def __le__(self, *args):
8687 __le__(Atom self, Atom o) -> bool
8688 __le__(Atom self, Particle d) -> bool
8690 return _IMP_atom.Atom___le__(self, *args)
8693 def __lt__(self, *args):
8695 __lt__(Atom self, Atom o) -> bool
8696 __lt__(Atom self, Particle d) -> bool
8698 return _IMP_atom.Atom___lt__(self, *args)
8701 def __ge__(self, *args):
8703 __ge__(Atom self, Atom o) -> bool
8704 __ge__(Atom self, Particle d) -> bool
8706 return _IMP_atom.Atom___ge__(self, *args)
8709 def __gt__(self, *args):
8711 __gt__(Atom self, Atom o) -> bool
8712 __gt__(Atom self, Particle d) -> bool
8714 return _IMP_atom.Atom___gt__(self, *args)
8718 """__hash__(Atom self) -> std::size_t"""
8719 return _IMP_atom.Atom___hash__(self)
8723 """__str__(Atom self) -> std::string"""
8724 return _IMP_atom.Atom___str__(self)
8728 """__repr__(Atom self) -> std::string"""
8729 return _IMP_atom.Atom___repr__(self)
8731 __swig_destroy__ = _IMP_atom.delete_Atom
8732 __del__ =
lambda self:
None
8733 Atom_swigregister = _IMP_atom.Atom_swigregister
8734 Atom_swigregister(Atom)
8735 cvar = _IMP_atom.cvar
8736 AT_UNKNOWN = cvar.AT_UNKNOWN
8746 AT_HA1 = cvar.AT_HA1
8747 AT_HA2 = cvar.AT_HA2
8748 AT_HA3 = cvar.AT_HA3
8751 AT_HB1 = cvar.AT_HB1
8752 AT_HB2 = cvar.AT_HB2
8753 AT_HB3 = cvar.AT_HB3
8754 AT_OXT = cvar.AT_OXT
8755 AT_CH3 = cvar.AT_CH3
8758 AT_CG1 = cvar.AT_CG1
8759 AT_CG2 = cvar.AT_CG2
8761 AT_HG1 = cvar.AT_HG1
8762 AT_HG2 = cvar.AT_HG2
8763 AT_HG3 = cvar.AT_HG3
8764 AT_HG11 = cvar.AT_HG11
8765 AT_HG21 = cvar.AT_HG21
8766 AT_HG31 = cvar.AT_HG31
8767 AT_HG12 = cvar.AT_HG12
8768 AT_HG13 = cvar.AT_HG13
8769 AT_HG22 = cvar.AT_HG22
8770 AT_HG23 = cvar.AT_HG23
8771 AT_HG32 = cvar.AT_HG32
8773 AT_OG1 = cvar.AT_OG1
8776 AT_CD1 = cvar.AT_CD1
8777 AT_CD2 = cvar.AT_CD2
8779 AT_HD1 = cvar.AT_HD1
8780 AT_HD2 = cvar.AT_HD2
8781 AT_HD3 = cvar.AT_HD3
8782 AT_HD11 = cvar.AT_HD11
8783 AT_HD21 = cvar.AT_HD21
8784 AT_HD31 = cvar.AT_HD31
8785 AT_HD12 = cvar.AT_HD12
8786 AT_HD13 = cvar.AT_HD13
8787 AT_HD22 = cvar.AT_HD22
8788 AT_HD23 = cvar.AT_HD23
8789 AT_HD32 = cvar.AT_HD32
8791 AT_OD1 = cvar.AT_OD1
8792 AT_OD2 = cvar.AT_OD2
8793 AT_ND1 = cvar.AT_ND1
8794 AT_ND2 = cvar.AT_ND2
8796 AT_CE1 = cvar.AT_CE1
8797 AT_CE2 = cvar.AT_CE2
8798 AT_CE3 = cvar.AT_CE3
8800 AT_HE1 = cvar.AT_HE1
8801 AT_HE2 = cvar.AT_HE2
8802 AT_HE3 = cvar.AT_HE3
8803 AT_HE21 = cvar.AT_HE21
8804 AT_HE22 = cvar.AT_HE22
8805 AT_OE1 = cvar.AT_OE1
8806 AT_OE2 = cvar.AT_OE2
8808 AT_NE1 = cvar.AT_NE1
8809 AT_NE2 = cvar.AT_NE2
8811 AT_CZ2 = cvar.AT_CZ2
8812 AT_CZ3 = cvar.AT_CZ3
8815 AT_HZ1 = cvar.AT_HZ1
8816 AT_HZ2 = cvar.AT_HZ2
8817 AT_HZ3 = cvar.AT_HZ3
8818 AT_CH2 = cvar.AT_CH2
8819 AT_NH1 = cvar.AT_NH1
8820 AT_NH2 = cvar.AT_NH2
8823 AT_HH11 = cvar.AT_HH11
8824 AT_HH21 = cvar.AT_HH21
8825 AT_HH2 = cvar.AT_HH2
8826 AT_HH12 = cvar.AT_HH12
8827 AT_HH22 = cvar.AT_HH22
8828 AT_HH13 = cvar.AT_HH13
8829 AT_HH23 = cvar.AT_HH23
8830 AT_HH33 = cvar.AT_HH33
8832 AT_OP1 = cvar.AT_OP1
8833 AT_OP2 = cvar.AT_OP2
8834 AT_OP3 = cvar.AT_OP3
8835 AT_O5p = cvar.AT_O5p
8836 AT_C5p = cvar.AT_C5p
8837 AT_H5p = cvar.AT_H5p
8838 AT_H5pp = cvar.AT_H5pp
8839 AT_C4p = cvar.AT_C4p
8840 AT_H4p = cvar.AT_H4p
8841 AT_O4p = cvar.AT_O4p
8842 AT_C1p = cvar.AT_C1p
8843 AT_H1p = cvar.AT_H1p
8844 AT_C3p = cvar.AT_C3p
8845 AT_H3p = cvar.AT_H3p
8846 AT_O3p = cvar.AT_O3p
8847 AT_C2p = cvar.AT_C2p
8848 AT_H2p = cvar.AT_H2p
8849 AT_H2pp = cvar.AT_H2pp
8850 AT_O2p = cvar.AT_O2p
8851 AT_HO2p = cvar.AT_HO2p
8863 AT_H61 = cvar.AT_H61
8864 AT_H62 = cvar.AT_H62
8868 AT_H21 = cvar.AT_H21
8869 AT_H22 = cvar.AT_H22
8874 AT_H41 = cvar.AT_H41
8875 AT_H42 = cvar.AT_H42
8878 AT_H71 = cvar.AT_H71
8879 AT_H72 = cvar.AT_H72
8880 AT_H73 = cvar.AT_H73
8881 AT_O1A = cvar.AT_O1A
8882 AT_O2A = cvar.AT_O2A
8883 AT_O3A = cvar.AT_O3A
8884 AT_O1B = cvar.AT_O1B
8885 AT_O2B = cvar.AT_O2B
8886 AT_O3B = cvar.AT_O3B
8888 def Atom_setup_particle(*args):
8890 setup_particle(Model m, ParticleIndex pi, Atom other) -> Atom
8891 setup_particle(_ParticleAdaptor decorator, Atom other) -> Atom
8892 setup_particle(Model m, ParticleIndex pi, AtomType atom_type) -> Atom
8893 Atom_setup_particle(_ParticleAdaptor decorator, AtomType atom_type) -> Atom
8895 return _IMP_atom.Atom_setup_particle(*args)
8897 def Atom_get_is_setup(*args):
8899 get_is_setup(_ParticleAdaptor p) -> bool
8900 Atom_get_is_setup(Model m, ParticleIndex pi) -> bool
8902 return _IMP_atom.Atom_get_is_setup(*args)
8904 def Atom_get_atom_type_key():
8905 """Atom_get_atom_type_key() -> IntKey"""
8906 return _IMP_atom.Atom_get_atom_type_key()
8908 def Atom_get_element_key():
8909 """Atom_get_element_key() -> IntKey"""
8910 return _IMP_atom.Atom_get_element_key()
8912 def Atom_get_input_index_key():
8913 """Atom_get_input_index_key() -> IntKey"""
8914 return _IMP_atom.Atom_get_input_index_key()
8916 def Atom_get_occupancy_key():
8917 """Atom_get_occupancy_key() -> FloatKey"""
8918 return _IMP_atom.Atom_get_occupancy_key()
8920 def Atom_get_temperature_factor_key():
8921 """Atom_get_temperature_factor_key() -> FloatKey"""
8922 return _IMP_atom.Atom_get_temperature_factor_key()
8927 get_residue(Hierarchy mhd, unsigned int index) -> Hierarchy
8928 get_residue(Atom d, bool nothrow=False) -> Residue
8929 get_residue(Atom d) -> Residue
8931 return _IMP_atom.get_residue(*args)
8934 """get_atom(Residue rd, AtomType at) -> Atom"""
8935 return _IMP_atom.get_atom(rd, at)
8938 """add_atom_type(std::string name, IMP::atom::Element e) -> AtomType"""
8939 return _IMP_atom.add_atom_type(name, e)
8941 def get_element_for_atom_type(at):
8942 """get_element_for_atom_type(AtomType at) -> IMP::atom::Element"""
8943 return _IMP_atom.get_element_for_atom_type(at)
8946 """get_atom_type_exists(std::string name) -> bool"""
8947 return _IMP_atom.get_atom_type_exists(name)
8948 class Residue(Hierarchy):
8949 """Proxy of C++ IMP::atom::Residue class"""
8950 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
8952 def __init__(self, *args):
8954 __init__(IMP::atom::Residue self) -> Residue
8955 __init__(IMP::atom::Residue self, Model m, ParticleIndex id) -> Residue
8956 __init__(IMP::atom::Residue self, _ParticleAdaptor d) -> Residue
8958 this = _IMP_atom.new_Residue(*args)
8960 self.this.append(this)
8964 def show(self, *args):
8966 show(Residue self, _ostream out)
8969 return _IMP_atom.Residue_show(self, *args)
8972 def setup_particle(*args):
8974 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
8975 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
8976 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
8977 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
8978 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
8979 setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
8980 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
8981 setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
8983 return _IMP_atom.Residue_setup_particle(*args)
8985 setup_particle = staticmethod(setup_particle)
8987 def get_is_setup(*args):
8989 get_is_setup(_ParticleAdaptor p) -> bool
8990 get_is_setup(Model m, ParticleIndex pi) -> bool
8992 return _IMP_atom.Residue_get_is_setup(*args)
8994 get_is_setup = staticmethod(get_is_setup)
8996 def get_residue_type(self):
8997 """get_residue_type(Residue self) -> ResidueType"""
8998 return _IMP_atom.Residue_get_residue_type(self)
9001 def set_residue_type(self, t):
9002 """set_residue_type(Residue self, ResidueType t)"""
9003 return _IMP_atom.Residue_set_residue_type(self, t)
9006 def get_is_protein(self):
9007 """get_is_protein(Residue self) -> bool"""
9008 return _IMP_atom.Residue_get_is_protein(self)
9011 def get_is_dna(self):
9012 """get_is_dna(Residue self) -> bool"""
9013 return _IMP_atom.Residue_get_is_dna(self)
9016 def get_is_rna(self):
9017 """get_is_rna(Residue self) -> bool"""
9018 return _IMP_atom.Residue_get_is_rna(self)
9022 """get_index(Residue self) -> IMP::Int"""
9023 return _IMP_atom.Residue_get_index(self)
9026 def set_index(self, t):
9027 """set_index(Residue self, IMP::Int t)"""
9028 return _IMP_atom.Residue_set_index(self, t)
9031 def get_insertion_code(self):
9032 """get_insertion_code(Residue self) -> char"""
9033 return _IMP_atom.Residue_get_insertion_code(self)
9036 def set_insertion_code(self, insertion_code):
9037 """set_insertion_code(Residue self, char insertion_code)"""
9038 return _IMP_atom.Residue_set_insertion_code(self, insertion_code)
9041 def get_index_key():
9042 """get_index_key() -> IntKey"""
9043 return _IMP_atom.Residue_get_index_key()
9045 get_index_key = staticmethod(get_index_key)
9047 def get_residue_type_key():
9048 """get_residue_type_key() -> IntKey"""
9049 return _IMP_atom.Residue_get_residue_type_key()
9051 get_residue_type_key = staticmethod(get_residue_type_key)
9053 def get_insertion_code_key():
9054 """get_insertion_code_key() -> IntKey"""
9055 return _IMP_atom.Residue_get_insertion_code_key()
9057 get_insertion_code_key = staticmethod(get_insertion_code_key)
9059 def add_attribute(self, *args):
9061 add_attribute(Residue self, FloatKey k, IMP::Float v, bool opt)
9062 add_attribute(Residue self, FloatKey a0, IMP::Float a1)
9063 add_attribute(Residue self, IntKey a0, IMP::Int a1)
9064 add_attribute(Residue self, StringKey a0, IMP::String a1)
9065 add_attribute(Residue self, ParticleIndexKey a0, Particle a1)
9066 add_attribute(Residue self, ObjectKey a0, Object a1)
9068 return _IMP_atom.Residue_add_attribute(self, *args)
9071 def get_value(self, *args):
9073 get_value(Residue self, FloatKey a0) -> IMP::Float
9074 get_value(Residue self, IntKey a0) -> IMP::Int
9075 get_value(Residue self, StringKey a0) -> IMP::String
9076 get_value(Residue self, ParticleIndexKey a0) -> Particle
9077 get_value(Residue self, ObjectKey a0) -> Object
9079 return _IMP_atom.Residue_get_value(self, *args)
9082 def set_value(self, *args):
9084 set_value(Residue self, FloatKey a0, IMP::Float a1)
9085 set_value(Residue self, IntKey a0, IMP::Int a1)
9086 set_value(Residue self, StringKey a0, IMP::String a1)
9087 set_value(Residue self, ParticleIndexKey a0, Particle a1)
9088 set_value(Residue self, ObjectKey a0, Object a1)
9090 return _IMP_atom.Residue_set_value(self, *args)
9093 def remove_attribute(self, *args):
9095 remove_attribute(Residue self, FloatKey a0)
9096 remove_attribute(Residue self, IntKey a0)
9097 remove_attribute(Residue self, StringKey a0)
9098 remove_attribute(Residue self, ParticleIndexKey a0)
9099 remove_attribute(Residue self, ObjectKey a0)
9101 return _IMP_atom.Residue_remove_attribute(self, *args)
9104 def has_attribute(self, *args):
9106 has_attribute(Residue self, FloatKey a0) -> bool
9107 has_attribute(Residue self, IntKey a0) -> bool
9108 has_attribute(Residue self, StringKey a0) -> bool
9109 has_attribute(Residue self, ParticleIndexKey a0) -> bool
9110 has_attribute(Residue self, ObjectKey a0) -> bool
9112 return _IMP_atom.Residue_has_attribute(self, *args)
9115 def get_derivative(self, a0):
9116 """get_derivative(Residue self, FloatKey a0) -> double"""
9117 return _IMP_atom.Residue_get_derivative(self, a0)
9121 """get_name(Residue self) -> std::string"""
9122 return _IMP_atom.Residue_get_name(self)
9125 def clear_caches(self):
9126 """clear_caches(Residue self)"""
9127 return _IMP_atom.Residue_clear_caches(self)
9130 def set_name(self, a0):
9131 """set_name(Residue self, std::string a0)"""
9132 return _IMP_atom.Residue_set_name(self, a0)
9136 """set_check_level(Residue self, IMP::CheckLevel a0)"""
9137 return _IMP_atom.Residue_set_check_level(self, a0)
9140 def add_to_derivative(self, a0, a1, a2):
9141 """add_to_derivative(Residue self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9142 return _IMP_atom.Residue_add_to_derivative(self, a0, a1, a2)
9145 def set_is_optimized(self, a0, a1):
9146 """set_is_optimized(Residue self, FloatKey a0, bool a1)"""
9147 return _IMP_atom.Residue_set_is_optimized(self, a0, a1)
9150 def get_is_optimized(self, a0):
9151 """get_is_optimized(Residue self, FloatKey a0) -> bool"""
9152 return _IMP_atom.Residue_get_is_optimized(self, a0)
9156 """get_check_level(Residue self) -> IMP::CheckLevel"""
9157 return _IMP_atom.Residue_get_check_level(self)
9160 def __eq__(self, *args):
9162 __eq__(Residue self, Residue o) -> bool
9163 __eq__(Residue self, Particle d) -> bool
9165 return _IMP_atom.Residue___eq__(self, *args)
9168 def __ne__(self, *args):
9170 __ne__(Residue self, Residue o) -> bool
9171 __ne__(Residue self, Particle d) -> bool
9173 return _IMP_atom.Residue___ne__(self, *args)
9176 def __le__(self, *args):
9178 __le__(Residue self, Residue o) -> bool
9179 __le__(Residue self, Particle d) -> bool
9181 return _IMP_atom.Residue___le__(self, *args)
9184 def __lt__(self, *args):
9186 __lt__(Residue self, Residue o) -> bool
9187 __lt__(Residue self, Particle d) -> bool
9189 return _IMP_atom.Residue___lt__(self, *args)
9192 def __ge__(self, *args):
9194 __ge__(Residue self, Residue o) -> bool
9195 __ge__(Residue self, Particle d) -> bool
9197 return _IMP_atom.Residue___ge__(self, *args)
9200 def __gt__(self, *args):
9202 __gt__(Residue self, Residue o) -> bool
9203 __gt__(Residue self, Particle d) -> bool
9205 return _IMP_atom.Residue___gt__(self, *args)
9209 """__hash__(Residue self) -> std::size_t"""
9210 return _IMP_atom.Residue___hash__(self)
9214 """__str__(Residue self) -> std::string"""
9215 return _IMP_atom.Residue___str__(self)
9219 """__repr__(Residue self) -> std::string"""
9220 return _IMP_atom.Residue___repr__(self)
9222 __swig_destroy__ = _IMP_atom.delete_Residue
9223 __del__ =
lambda self:
None
9224 Residue_swigregister = _IMP_atom.Residue_swigregister
9225 Residue_swigregister(Residue)
9262 def Residue_setup_particle(*args):
9264 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index, int insertion_code) -> Residue
9265 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index, int insertion_code) -> Residue
9266 setup_particle(Model m, ParticleIndex pi, ResidueType t, int index) -> Residue
9267 setup_particle(_ParticleAdaptor decorator, ResidueType t, int index) -> Residue
9268 setup_particle(Model m, ParticleIndex pi, ResidueType t) -> Residue
9269 setup_particle(_ParticleAdaptor decorator, ResidueType t) -> Residue
9270 setup_particle(Model m, ParticleIndex pi, Residue other) -> Residue
9271 Residue_setup_particle(_ParticleAdaptor decorator, Residue other) -> Residue
9273 return _IMP_atom.Residue_setup_particle(*args)
9275 def Residue_get_is_setup(*args):
9277 get_is_setup(_ParticleAdaptor p) -> bool
9278 Residue_get_is_setup(Model m, ParticleIndex pi) -> bool
9280 return _IMP_atom.Residue_get_is_setup(*args)
9282 def Residue_get_index_key():
9283 """Residue_get_index_key() -> IntKey"""
9284 return _IMP_atom.Residue_get_index_key()
9286 def Residue_get_residue_type_key():
9287 """Residue_get_residue_type_key() -> IntKey"""
9288 return _IMP_atom.Residue_get_residue_type_key()
9290 def Residue_get_insertion_code_key():
9291 """Residue_get_insertion_code_key() -> IntKey"""
9292 return _IMP_atom.Residue_get_insertion_code_key()
9296 """get_next_residue(Residue rd) -> Hierarchy"""
9297 return _IMP_atom.get_next_residue(rd)
9300 """get_previous_residue(Residue rd) -> Hierarchy"""
9301 return _IMP_atom.get_previous_residue(rd)
9304 """get_one_letter_code(ResidueType c) -> char"""
9305 return _IMP_atom.get_one_letter_code(c)
9307 _IMP_atom.BALLS_swigconstant(_IMP_atom)
9308 BALLS = _IMP_atom.BALLS
9310 _IMP_atom.DENSITIES_swigconstant(_IMP_atom)
9311 DENSITIES = _IMP_atom.DENSITIES
9312 class Representation(Hierarchy):
9313 """Proxy of C++ IMP::atom::Representation class"""
9314 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9316 def setup_particle(*args):
9318 setup_particle(Model m, ParticleIndex pi) -> Representation
9319 setup_particle(_ParticleAdaptor decorator) -> Representation
9320 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9321 setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9323 return _IMP_atom.Representation_setup_particle(*args)
9325 setup_particle = staticmethod(setup_particle)
9327 def __init__(self, *args):
9329 __init__(IMP::atom::Representation self) -> Representation
9330 __init__(IMP::atom::Representation self, Model m, ParticleIndex id) -> Representation
9331 __init__(IMP::atom::Representation self, _ParticleAdaptor d) -> Representation
9333 this = _IMP_atom.new_Representation(*args)
9335 self.this.append(this)
9339 def show(self, *args):
9341 show(Representation self, _ostream out)
9342 show(Representation self)
9344 return _IMP_atom.Representation_show(self, *args)
9347 def get_is_setup(*args):
9349 get_is_setup(_ParticleAdaptor p) -> bool
9350 get_is_setup(Model m, ParticleIndex pi) -> bool
9352 return _IMP_atom.Representation_get_is_setup(*args)
9354 get_is_setup = staticmethod(get_is_setup)
9358 get_representation(Representation self, double resolution, IMP::atom::RepresentationType type) -> Hierarchy
9359 get_representation(Representation self, double resolution) -> Hierarchy
9361 return _IMP_atom.Representation_get_representation(self, *args)
9364 def get_representations(self, *args):
9366 get_representations(Representation self, IMP::atom::RepresentationType type) -> IMP::atom::Hierarchies
9367 get_representations(Representation self) -> IMP::atom::Hierarchies
9369 return _IMP_atom.Representation_get_representations(self, *args)
9372 def add_representation(self, *args):
9374 add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type, double resolution=-1)
9375 add_representation(Representation self, _ParticleIndexAdaptor rep, IMP::atom::RepresentationType type)
9376 add_representation(Representation self, _ParticleIndexAdaptor rep)
9378 return _IMP_atom.Representation_add_representation(self, *args)
9381 def get_resolutions(self, *args):
9383 get_resolutions(Representation self, IMP::atom::RepresentationType type) -> IMP::Floats
9384 get_resolutions(Representation self) -> IMP::Floats
9386 return _IMP_atom.Representation_get_resolutions(self, *args)
9389 def add_attribute(self, *args):
9391 add_attribute(Representation self, FloatKey k, IMP::Float v, bool opt)
9392 add_attribute(Representation self, FloatKey a0, IMP::Float a1)
9393 add_attribute(Representation self, IntKey a0, IMP::Int a1)
9394 add_attribute(Representation self, StringKey a0, IMP::String a1)
9395 add_attribute(Representation self, ParticleIndexKey a0, Particle a1)
9396 add_attribute(Representation self, ObjectKey a0, Object a1)
9398 return _IMP_atom.Representation_add_attribute(self, *args)
9401 def get_value(self, *args):
9403 get_value(Representation self, FloatKey a0) -> IMP::Float
9404 get_value(Representation self, IntKey a0) -> IMP::Int
9405 get_value(Representation self, StringKey a0) -> IMP::String
9406 get_value(Representation self, ParticleIndexKey a0) -> Particle
9407 get_value(Representation self, ObjectKey a0) -> Object
9409 return _IMP_atom.Representation_get_value(self, *args)
9412 def set_value(self, *args):
9414 set_value(Representation self, FloatKey a0, IMP::Float a1)
9415 set_value(Representation self, IntKey a0, IMP::Int a1)
9416 set_value(Representation self, StringKey a0, IMP::String a1)
9417 set_value(Representation self, ParticleIndexKey a0, Particle a1)
9418 set_value(Representation self, ObjectKey a0, Object a1)
9420 return _IMP_atom.Representation_set_value(self, *args)
9423 def remove_attribute(self, *args):
9425 remove_attribute(Representation self, FloatKey a0)
9426 remove_attribute(Representation self, IntKey a0)
9427 remove_attribute(Representation self, StringKey a0)
9428 remove_attribute(Representation self, ParticleIndexKey a0)
9429 remove_attribute(Representation self, ObjectKey a0)
9431 return _IMP_atom.Representation_remove_attribute(self, *args)
9434 def has_attribute(self, *args):
9436 has_attribute(Representation self, FloatKey a0) -> bool
9437 has_attribute(Representation self, IntKey a0) -> bool
9438 has_attribute(Representation self, StringKey a0) -> bool
9439 has_attribute(Representation self, ParticleIndexKey a0) -> bool
9440 has_attribute(Representation self, ObjectKey a0) -> bool
9442 return _IMP_atom.Representation_has_attribute(self, *args)
9445 def get_derivative(self, a0):
9446 """get_derivative(Representation self, FloatKey a0) -> double"""
9447 return _IMP_atom.Representation_get_derivative(self, a0)
9451 """get_name(Representation self) -> std::string"""
9452 return _IMP_atom.Representation_get_name(self)
9455 def clear_caches(self):
9456 """clear_caches(Representation self)"""
9457 return _IMP_atom.Representation_clear_caches(self)
9460 def set_name(self, a0):
9461 """set_name(Representation self, std::string a0)"""
9462 return _IMP_atom.Representation_set_name(self, a0)
9466 """set_check_level(Representation self, IMP::CheckLevel a0)"""
9467 return _IMP_atom.Representation_set_check_level(self, a0)
9470 def add_to_derivative(self, a0, a1, a2):
9471 """add_to_derivative(Representation self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9472 return _IMP_atom.Representation_add_to_derivative(self, a0, a1, a2)
9475 def set_is_optimized(self, a0, a1):
9476 """set_is_optimized(Representation self, FloatKey a0, bool a1)"""
9477 return _IMP_atom.Representation_set_is_optimized(self, a0, a1)
9480 def get_is_optimized(self, a0):
9481 """get_is_optimized(Representation self, FloatKey a0) -> bool"""
9482 return _IMP_atom.Representation_get_is_optimized(self, a0)
9486 """get_check_level(Representation self) -> IMP::CheckLevel"""
9487 return _IMP_atom.Representation_get_check_level(self)
9490 def __eq__(self, *args):
9492 __eq__(Representation self, Representation o) -> bool
9493 __eq__(Representation self, Particle d) -> bool
9495 return _IMP_atom.Representation___eq__(self, *args)
9498 def __ne__(self, *args):
9500 __ne__(Representation self, Representation o) -> bool
9501 __ne__(Representation self, Particle d) -> bool
9503 return _IMP_atom.Representation___ne__(self, *args)
9506 def __le__(self, *args):
9508 __le__(Representation self, Representation o) -> bool
9509 __le__(Representation self, Particle d) -> bool
9511 return _IMP_atom.Representation___le__(self, *args)
9514 def __lt__(self, *args):
9516 __lt__(Representation self, Representation o) -> bool
9517 __lt__(Representation self, Particle d) -> bool
9519 return _IMP_atom.Representation___lt__(self, *args)
9522 def __ge__(self, *args):
9524 __ge__(Representation self, Representation o) -> bool
9525 __ge__(Representation self, Particle d) -> bool
9527 return _IMP_atom.Representation___ge__(self, *args)
9530 def __gt__(self, *args):
9532 __gt__(Representation self, Representation o) -> bool
9533 __gt__(Representation self, Particle d) -> bool
9535 return _IMP_atom.Representation___gt__(self, *args)
9539 """__hash__(Representation self) -> std::size_t"""
9540 return _IMP_atom.Representation___hash__(self)
9544 """__str__(Representation self) -> std::string"""
9545 return _IMP_atom.Representation___str__(self)
9549 """__repr__(Representation self) -> std::string"""
9550 return _IMP_atom.Representation___repr__(self)
9552 __swig_destroy__ = _IMP_atom.delete_Representation
9553 __del__ =
lambda self:
None
9554 Representation_swigregister = _IMP_atom.Representation_swigregister
9555 Representation_swigregister(Representation)
9556 ALL_RESOLUTIONS = cvar.ALL_RESOLUTIONS
9558 def Representation_setup_particle(*args):
9560 setup_particle(Model m, ParticleIndex pi) -> Representation
9561 setup_particle(_ParticleAdaptor decorator) -> Representation
9562 setup_particle(Model m, ParticleIndex pi, double resolution) -> Representation
9563 Representation_setup_particle(_ParticleAdaptor decorator, double resolution) -> Representation
9565 return _IMP_atom.Representation_setup_particle(*args)
9567 def Representation_get_is_setup(*args):
9569 get_is_setup(_ParticleAdaptor p) -> bool
9570 Representation_get_is_setup(Model m, ParticleIndex pi) -> bool
9572 return _IMP_atom.Representation_get_is_setup(*args)
9577 get_resolution(Model m, ParticleIndex pi) -> double
9578 get_resolution(Hierarchy h) -> double
9580 return _IMP_atom.get_resolution(*args)
9584 get_representation(Hierarchy h, bool nothrow=False) -> Representation
9585 get_representation(Hierarchy h) -> Representation
9587 return _IMP_atom.get_representation(h, nothrow)
9591 show_with_representations(Hierarchy h, _ostream out)
9592 show_with_representations(Hierarchy h)
9594 return _IMP_atom.show_with_representations(*args)
9595 class State(Hierarchy):
9596 """Proxy of C++ IMP::atom::State class"""
9597 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9599 def setup_particle(*args):
9601 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9602 setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9604 return _IMP_atom.State_setup_particle(*args)
9606 setup_particle = staticmethod(setup_particle)
9608 def __init__(self, *args):
9610 __init__(IMP::atom::State self) -> State
9611 __init__(IMP::atom::State self, Model m, ParticleIndex id) -> State
9612 __init__(IMP::atom::State self, _ParticleAdaptor d) -> State
9614 this = _IMP_atom.new_State(*args)
9616 self.this.append(this)
9620 def show(self, *args):
9622 show(State self, _ostream out)
9625 return _IMP_atom.State_show(self, *args)
9628 def get_is_setup(*args):
9630 get_is_setup(_ParticleAdaptor p) -> bool
9631 get_is_setup(Model m, ParticleIndex pi) -> bool
9633 return _IMP_atom.State_get_is_setup(*args)
9635 get_is_setup = staticmethod(get_is_setup)
9638 """get_state_index(State self) -> unsigned int"""
9639 return _IMP_atom.State_get_state_index(self)
9642 def add_attribute(self, *args):
9644 add_attribute(State self, FloatKey k, IMP::Float v, bool opt)
9645 add_attribute(State self, FloatKey a0, IMP::Float a1)
9646 add_attribute(State self, IntKey a0, IMP::Int a1)
9647 add_attribute(State self, StringKey a0, IMP::String a1)
9648 add_attribute(State self, ParticleIndexKey a0, Particle a1)
9649 add_attribute(State self, ObjectKey a0, Object a1)
9651 return _IMP_atom.State_add_attribute(self, *args)
9654 def get_value(self, *args):
9656 get_value(State self, FloatKey a0) -> IMP::Float
9657 get_value(State self, IntKey a0) -> IMP::Int
9658 get_value(State self, StringKey a0) -> IMP::String
9659 get_value(State self, ParticleIndexKey a0) -> Particle
9660 get_value(State self, ObjectKey a0) -> Object
9662 return _IMP_atom.State_get_value(self, *args)
9665 def set_value(self, *args):
9667 set_value(State self, FloatKey a0, IMP::Float a1)
9668 set_value(State self, IntKey a0, IMP::Int a1)
9669 set_value(State self, StringKey a0, IMP::String a1)
9670 set_value(State self, ParticleIndexKey a0, Particle a1)
9671 set_value(State self, ObjectKey a0, Object a1)
9673 return _IMP_atom.State_set_value(self, *args)
9676 def remove_attribute(self, *args):
9678 remove_attribute(State self, FloatKey a0)
9679 remove_attribute(State self, IntKey a0)
9680 remove_attribute(State self, StringKey a0)
9681 remove_attribute(State self, ParticleIndexKey a0)
9682 remove_attribute(State self, ObjectKey a0)
9684 return _IMP_atom.State_remove_attribute(self, *args)
9687 def has_attribute(self, *args):
9689 has_attribute(State self, FloatKey a0) -> bool
9690 has_attribute(State self, IntKey a0) -> bool
9691 has_attribute(State self, StringKey a0) -> bool
9692 has_attribute(State self, ParticleIndexKey a0) -> bool
9693 has_attribute(State self, ObjectKey a0) -> bool
9695 return _IMP_atom.State_has_attribute(self, *args)
9698 def get_derivative(self, a0):
9699 """get_derivative(State self, FloatKey a0) -> double"""
9700 return _IMP_atom.State_get_derivative(self, a0)
9704 """get_name(State self) -> std::string"""
9705 return _IMP_atom.State_get_name(self)
9708 def clear_caches(self):
9709 """clear_caches(State self)"""
9710 return _IMP_atom.State_clear_caches(self)
9713 def set_name(self, a0):
9714 """set_name(State self, std::string a0)"""
9715 return _IMP_atom.State_set_name(self, a0)
9719 """set_check_level(State self, IMP::CheckLevel a0)"""
9720 return _IMP_atom.State_set_check_level(self, a0)
9723 def add_to_derivative(self, a0, a1, a2):
9724 """add_to_derivative(State self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9725 return _IMP_atom.State_add_to_derivative(self, a0, a1, a2)
9728 def set_is_optimized(self, a0, a1):
9729 """set_is_optimized(State self, FloatKey a0, bool a1)"""
9730 return _IMP_atom.State_set_is_optimized(self, a0, a1)
9733 def get_is_optimized(self, a0):
9734 """get_is_optimized(State self, FloatKey a0) -> bool"""
9735 return _IMP_atom.State_get_is_optimized(self, a0)
9739 """get_check_level(State self) -> IMP::CheckLevel"""
9740 return _IMP_atom.State_get_check_level(self)
9743 def __eq__(self, *args):
9745 __eq__(State self, State o) -> bool
9746 __eq__(State self, Particle d) -> bool
9748 return _IMP_atom.State___eq__(self, *args)
9751 def __ne__(self, *args):
9753 __ne__(State self, State o) -> bool
9754 __ne__(State self, Particle d) -> bool
9756 return _IMP_atom.State___ne__(self, *args)
9759 def __le__(self, *args):
9761 __le__(State self, State o) -> bool
9762 __le__(State self, Particle d) -> bool
9764 return _IMP_atom.State___le__(self, *args)
9767 def __lt__(self, *args):
9769 __lt__(State self, State o) -> bool
9770 __lt__(State self, Particle d) -> bool
9772 return _IMP_atom.State___lt__(self, *args)
9775 def __ge__(self, *args):
9777 __ge__(State self, State o) -> bool
9778 __ge__(State self, Particle d) -> bool
9780 return _IMP_atom.State___ge__(self, *args)
9783 def __gt__(self, *args):
9785 __gt__(State self, State o) -> bool
9786 __gt__(State self, Particle d) -> bool
9788 return _IMP_atom.State___gt__(self, *args)
9792 """__hash__(State self) -> std::size_t"""
9793 return _IMP_atom.State___hash__(self)
9797 """__str__(State self) -> std::string"""
9798 return _IMP_atom.State___str__(self)
9802 """__repr__(State self) -> std::string"""
9803 return _IMP_atom.State___repr__(self)
9805 __swig_destroy__ = _IMP_atom.delete_State
9806 __del__ =
lambda self:
None
9807 State_swigregister = _IMP_atom.State_swigregister
9808 State_swigregister(State)
9810 def State_setup_particle(*args):
9812 setup_particle(Model m, ParticleIndex pi, unsigned int index) -> State
9813 State_setup_particle(_ParticleAdaptor decorator, unsigned int index) -> State
9815 return _IMP_atom.State_setup_particle(*args)
9817 def State_get_is_setup(*args):
9819 get_is_setup(_ParticleAdaptor p) -> bool
9820 State_get_is_setup(Model m, ParticleIndex pi) -> bool
9822 return _IMP_atom.State_get_is_setup(*args)
9826 """get_state_index(Hierarchy h) -> int"""
9827 return _IMP_atom.get_state_index(h)
9830 """get_phi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9831 return _IMP_atom.get_phi_dihedral_atoms(rd)
9834 """get_psi_dihedral_atoms(Residue rd) -> IMP::atom::Atoms"""
9835 return _IMP_atom.get_psi_dihedral_atoms(rd)
9836 class Molecule(Hierarchy):
9837 """Proxy of C++ IMP::atom::Molecule class"""
9838 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
9840 def __init__(self, *args):
9842 __init__(IMP::atom::Molecule self) -> Molecule
9843 __init__(IMP::atom::Molecule self, Model m, ParticleIndex id) -> Molecule
9844 __init__(IMP::atom::Molecule self, _ParticleAdaptor d) -> Molecule
9846 this = _IMP_atom.new_Molecule(*args)
9848 self.this.append(this)
9852 def show(self, *args):
9854 show(Molecule self, _ostream out)
9857 return _IMP_atom.Molecule_show(self, *args)
9860 def setup_particle(*args):
9862 setup_particle(Model m, ParticleIndex pi) -> Molecule
9863 setup_particle(_ParticleAdaptor decorator) -> Molecule
9864 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
9865 setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
9867 return _IMP_atom.Molecule_setup_particle(*args)
9869 setup_particle = staticmethod(setup_particle)
9871 def get_is_setup(*args):
9873 get_is_setup(_ParticleAdaptor p) -> bool
9874 get_is_setup(Model m, ParticleIndex pi) -> bool
9876 return _IMP_atom.Molecule_get_is_setup(*args)
9878 get_is_setup = staticmethod(get_is_setup)
9880 def add_attribute(self, *args):
9882 add_attribute(Molecule self, FloatKey k, IMP::Float v, bool opt)
9883 add_attribute(Molecule self, FloatKey a0, IMP::Float a1)
9884 add_attribute(Molecule self, IntKey a0, IMP::Int a1)
9885 add_attribute(Molecule self, StringKey a0, IMP::String a1)
9886 add_attribute(Molecule self, ParticleIndexKey a0, Particle a1)
9887 add_attribute(Molecule self, ObjectKey a0, Object a1)
9889 return _IMP_atom.Molecule_add_attribute(self, *args)
9892 def get_value(self, *args):
9894 get_value(Molecule self, FloatKey a0) -> IMP::Float
9895 get_value(Molecule self, IntKey a0) -> IMP::Int
9896 get_value(Molecule self, StringKey a0) -> IMP::String
9897 get_value(Molecule self, ParticleIndexKey a0) -> Particle
9898 get_value(Molecule self, ObjectKey a0) -> Object
9900 return _IMP_atom.Molecule_get_value(self, *args)
9903 def set_value(self, *args):
9905 set_value(Molecule self, FloatKey a0, IMP::Float a1)
9906 set_value(Molecule self, IntKey a0, IMP::Int a1)
9907 set_value(Molecule self, StringKey a0, IMP::String a1)
9908 set_value(Molecule self, ParticleIndexKey a0, Particle a1)
9909 set_value(Molecule self, ObjectKey a0, Object a1)
9911 return _IMP_atom.Molecule_set_value(self, *args)
9914 def remove_attribute(self, *args):
9916 remove_attribute(Molecule self, FloatKey a0)
9917 remove_attribute(Molecule self, IntKey a0)
9918 remove_attribute(Molecule self, StringKey a0)
9919 remove_attribute(Molecule self, ParticleIndexKey a0)
9920 remove_attribute(Molecule self, ObjectKey a0)
9922 return _IMP_atom.Molecule_remove_attribute(self, *args)
9925 def has_attribute(self, *args):
9927 has_attribute(Molecule self, FloatKey a0) -> bool
9928 has_attribute(Molecule self, IntKey a0) -> bool
9929 has_attribute(Molecule self, StringKey a0) -> bool
9930 has_attribute(Molecule self, ParticleIndexKey a0) -> bool
9931 has_attribute(Molecule self, ObjectKey a0) -> bool
9933 return _IMP_atom.Molecule_has_attribute(self, *args)
9936 def get_derivative(self, a0):
9937 """get_derivative(Molecule self, FloatKey a0) -> double"""
9938 return _IMP_atom.Molecule_get_derivative(self, a0)
9942 """get_name(Molecule self) -> std::string"""
9943 return _IMP_atom.Molecule_get_name(self)
9946 def clear_caches(self):
9947 """clear_caches(Molecule self)"""
9948 return _IMP_atom.Molecule_clear_caches(self)
9951 def set_name(self, a0):
9952 """set_name(Molecule self, std::string a0)"""
9953 return _IMP_atom.Molecule_set_name(self, a0)
9957 """set_check_level(Molecule self, IMP::CheckLevel a0)"""
9958 return _IMP_atom.Molecule_set_check_level(self, a0)
9961 def add_to_derivative(self, a0, a1, a2):
9962 """add_to_derivative(Molecule self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9963 return _IMP_atom.Molecule_add_to_derivative(self, a0, a1, a2)
9966 def set_is_optimized(self, a0, a1):
9967 """set_is_optimized(Molecule self, FloatKey a0, bool a1)"""
9968 return _IMP_atom.Molecule_set_is_optimized(self, a0, a1)
9971 def get_is_optimized(self, a0):
9972 """get_is_optimized(Molecule self, FloatKey a0) -> bool"""
9973 return _IMP_atom.Molecule_get_is_optimized(self, a0)
9977 """get_check_level(Molecule self) -> IMP::CheckLevel"""
9978 return _IMP_atom.Molecule_get_check_level(self)
9981 def __eq__(self, *args):
9983 __eq__(Molecule self, Molecule o) -> bool
9984 __eq__(Molecule self, Particle d) -> bool
9986 return _IMP_atom.Molecule___eq__(self, *args)
9989 def __ne__(self, *args):
9991 __ne__(Molecule self, Molecule o) -> bool
9992 __ne__(Molecule self, Particle d) -> bool
9994 return _IMP_atom.Molecule___ne__(self, *args)
9997 def __le__(self, *args):
9999 __le__(Molecule self, Molecule o) -> bool
10000 __le__(Molecule self, Particle d) -> bool
10002 return _IMP_atom.Molecule___le__(self, *args)
10005 def __lt__(self, *args):
10007 __lt__(Molecule self, Molecule o) -> bool
10008 __lt__(Molecule self, Particle d) -> bool
10010 return _IMP_atom.Molecule___lt__(self, *args)
10013 def __ge__(self, *args):
10015 __ge__(Molecule self, Molecule o) -> bool
10016 __ge__(Molecule self, Particle d) -> bool
10018 return _IMP_atom.Molecule___ge__(self, *args)
10021 def __gt__(self, *args):
10023 __gt__(Molecule self, Molecule o) -> bool
10024 __gt__(Molecule self, Particle d) -> bool
10026 return _IMP_atom.Molecule___gt__(self, *args)
10029 def __hash__(self):
10030 """__hash__(Molecule self) -> std::size_t"""
10031 return _IMP_atom.Molecule___hash__(self)
10035 """__str__(Molecule self) -> std::string"""
10036 return _IMP_atom.Molecule___str__(self)
10039 def __repr__(self):
10040 """__repr__(Molecule self) -> std::string"""
10041 return _IMP_atom.Molecule___repr__(self)
10043 __swig_destroy__ = _IMP_atom.delete_Molecule
10044 __del__ =
lambda self:
None
10045 Molecule_swigregister = _IMP_atom.Molecule_swigregister
10046 Molecule_swigregister(Molecule)
10048 def Molecule_setup_particle(*args):
10050 setup_particle(Model m, ParticleIndex pi) -> Molecule
10051 setup_particle(_ParticleAdaptor decorator) -> Molecule
10052 setup_particle(Model m, ParticleIndex pi, Molecule other) -> Molecule
10053 Molecule_setup_particle(_ParticleAdaptor decorator, Molecule other) -> Molecule
10055 return _IMP_atom.Molecule_setup_particle(*args)
10057 def Molecule_get_is_setup(*args):
10059 get_is_setup(_ParticleAdaptor p) -> bool
10060 Molecule_get_is_setup(Model m, ParticleIndex pi) -> bool
10062 return _IMP_atom.Molecule_get_is_setup(*args)
10066 """get_molecule_name(Hierarchy h) -> std::string"""
10067 return _IMP_atom.get_molecule_name(h)
10068 class Copy(Molecule):
10069 """Proxy of C++ IMP::atom::Copy class"""
10070 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10072 def get_copy_index_key():
10073 """get_copy_index_key() -> IntKey"""
10074 return _IMP_atom.Copy_get_copy_index_key()
10076 get_copy_index_key = staticmethod(get_copy_index_key)
10078 def __init__(self, *args):
10080 __init__(IMP::atom::Copy self) -> Copy
10081 __init__(IMP::atom::Copy self, Model m, ParticleIndex id) -> Copy
10082 __init__(IMP::atom::Copy self, _ParticleAdaptor d) -> Copy
10084 this = _IMP_atom.new_Copy(*args)
10086 self.this.append(this)
10090 def show(self, *args):
10092 show(Copy self, _ostream out)
10095 return _IMP_atom.Copy_show(self, *args)
10098 def setup_particle(*args):
10100 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10101 setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10103 return _IMP_atom.Copy_setup_particle(*args)
10105 setup_particle = staticmethod(setup_particle)
10107 def get_is_setup(*args):
10109 get_is_setup(_ParticleAdaptor p) -> bool
10110 get_is_setup(Model m, ParticleIndex pi) -> bool
10112 return _IMP_atom.Copy_get_is_setup(*args)
10114 get_is_setup = staticmethod(get_is_setup)
10117 """get_copy_index(Copy self) -> int"""
10118 return _IMP_atom.Copy_get_copy_index(self)
10121 def add_attribute(self, *args):
10123 add_attribute(Copy self, FloatKey k, IMP::Float v, bool opt)
10124 add_attribute(Copy self, FloatKey a0, IMP::Float a1)
10125 add_attribute(Copy self, IntKey a0, IMP::Int a1)
10126 add_attribute(Copy self, StringKey a0, IMP::String a1)
10127 add_attribute(Copy self, ParticleIndexKey a0, Particle a1)
10128 add_attribute(Copy self, ObjectKey a0, Object a1)
10130 return _IMP_atom.Copy_add_attribute(self, *args)
10133 def get_value(self, *args):
10135 get_value(Copy self, FloatKey a0) -> IMP::Float
10136 get_value(Copy self, IntKey a0) -> IMP::Int
10137 get_value(Copy self, StringKey a0) -> IMP::String
10138 get_value(Copy self, ParticleIndexKey a0) -> Particle
10139 get_value(Copy self, ObjectKey a0) -> Object
10141 return _IMP_atom.Copy_get_value(self, *args)
10144 def set_value(self, *args):
10146 set_value(Copy self, FloatKey a0, IMP::Float a1)
10147 set_value(Copy self, IntKey a0, IMP::Int a1)
10148 set_value(Copy self, StringKey a0, IMP::String a1)
10149 set_value(Copy self, ParticleIndexKey a0, Particle a1)
10150 set_value(Copy self, ObjectKey a0, Object a1)
10152 return _IMP_atom.Copy_set_value(self, *args)
10155 def remove_attribute(self, *args):
10157 remove_attribute(Copy self, FloatKey a0)
10158 remove_attribute(Copy self, IntKey a0)
10159 remove_attribute(Copy self, StringKey a0)
10160 remove_attribute(Copy self, ParticleIndexKey a0)
10161 remove_attribute(Copy self, ObjectKey a0)
10163 return _IMP_atom.Copy_remove_attribute(self, *args)
10166 def has_attribute(self, *args):
10168 has_attribute(Copy self, FloatKey a0) -> bool
10169 has_attribute(Copy self, IntKey a0) -> bool
10170 has_attribute(Copy self, StringKey a0) -> bool
10171 has_attribute(Copy self, ParticleIndexKey a0) -> bool
10172 has_attribute(Copy self, ObjectKey a0) -> bool
10174 return _IMP_atom.Copy_has_attribute(self, *args)
10177 def get_derivative(self, a0):
10178 """get_derivative(Copy self, FloatKey a0) -> double"""
10179 return _IMP_atom.Copy_get_derivative(self, a0)
10182 def get_name(self):
10183 """get_name(Copy self) -> std::string"""
10184 return _IMP_atom.Copy_get_name(self)
10187 def clear_caches(self):
10188 """clear_caches(Copy self)"""
10189 return _IMP_atom.Copy_clear_caches(self)
10192 def set_name(self, a0):
10193 """set_name(Copy self, std::string a0)"""
10194 return _IMP_atom.Copy_set_name(self, a0)
10198 """set_check_level(Copy self, IMP::CheckLevel a0)"""
10199 return _IMP_atom.Copy_set_check_level(self, a0)
10202 def add_to_derivative(self, a0, a1, a2):
10203 """add_to_derivative(Copy self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10204 return _IMP_atom.Copy_add_to_derivative(self, a0, a1, a2)
10207 def set_is_optimized(self, a0, a1):
10208 """set_is_optimized(Copy self, FloatKey a0, bool a1)"""
10209 return _IMP_atom.Copy_set_is_optimized(self, a0, a1)
10212 def get_is_optimized(self, a0):
10213 """get_is_optimized(Copy self, FloatKey a0) -> bool"""
10214 return _IMP_atom.Copy_get_is_optimized(self, a0)
10218 """get_check_level(Copy self) -> IMP::CheckLevel"""
10219 return _IMP_atom.Copy_get_check_level(self)
10222 def __eq__(self, *args):
10224 __eq__(Copy self, Copy o) -> bool
10225 __eq__(Copy self, Particle d) -> bool
10227 return _IMP_atom.Copy___eq__(self, *args)
10230 def __ne__(self, *args):
10232 __ne__(Copy self, Copy o) -> bool
10233 __ne__(Copy self, Particle d) -> bool
10235 return _IMP_atom.Copy___ne__(self, *args)
10238 def __le__(self, *args):
10240 __le__(Copy self, Copy o) -> bool
10241 __le__(Copy self, Particle d) -> bool
10243 return _IMP_atom.Copy___le__(self, *args)
10246 def __lt__(self, *args):
10248 __lt__(Copy self, Copy o) -> bool
10249 __lt__(Copy self, Particle d) -> bool
10251 return _IMP_atom.Copy___lt__(self, *args)
10254 def __ge__(self, *args):
10256 __ge__(Copy self, Copy o) -> bool
10257 __ge__(Copy self, Particle d) -> bool
10259 return _IMP_atom.Copy___ge__(self, *args)
10262 def __gt__(self, *args):
10264 __gt__(Copy self, Copy o) -> bool
10265 __gt__(Copy self, Particle d) -> bool
10267 return _IMP_atom.Copy___gt__(self, *args)
10270 def __hash__(self):
10271 """__hash__(Copy self) -> std::size_t"""
10272 return _IMP_atom.Copy___hash__(self)
10276 """__str__(Copy self) -> std::string"""
10277 return _IMP_atom.Copy___str__(self)
10280 def __repr__(self):
10281 """__repr__(Copy self) -> std::string"""
10282 return _IMP_atom.Copy___repr__(self)
10284 __swig_destroy__ = _IMP_atom.delete_Copy
10285 __del__ =
lambda self:
None
10286 Copy_swigregister = _IMP_atom.Copy_swigregister
10287 Copy_swigregister(Copy)
10289 def Copy_get_copy_index_key():
10290 """Copy_get_copy_index_key() -> IntKey"""
10291 return _IMP_atom.Copy_get_copy_index_key()
10293 def Copy_setup_particle(*args):
10295 setup_particle(Model m, ParticleIndex pi, IMP::Int number) -> Copy
10296 Copy_setup_particle(_ParticleAdaptor decorator, IMP::Int number) -> Copy
10298 return _IMP_atom.Copy_setup_particle(*args)
10300 def Copy_get_is_setup(*args):
10302 get_is_setup(_ParticleAdaptor p) -> bool
10303 Copy_get_is_setup(Model m, ParticleIndex pi) -> bool
10305 return _IMP_atom.Copy_get_is_setup(*args)
10309 """get_copy_index(Hierarchy h) -> int"""
10310 return _IMP_atom.get_copy_index(h)
10311 class Selection(IMP._ParticleIndexesAdaptor):
10312 """Proxy of C++ IMP::atom::Selection class"""
10313 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10314 NONE = _IMP_atom.Selection_NONE
10315 C = _IMP_atom.Selection_C
10316 N = _IMP_atom.Selection_N
10318 def __init__(self, *args):
10320 __init__(IMP::atom::Selection self) -> Selection
10321 __init__(IMP::atom::Selection self, Hierarchy h) -> Selection
10322 __init__(IMP::atom::Selection self, Particle h) -> Selection
10323 __init__(IMP::atom::Selection self, Model m, IMP::ParticleIndexes const & pis) -> Selection
10324 __init__(IMP::atom::Selection self, IMP::ParticlesTemp const & h) -> Selection
10326 this = _IMP_atom.new_Selection(*args)
10328 self.this.append(this)
10332 def create_clone(self):
10333 """create_clone(Selection self) -> Selection"""
10334 return _IMP_atom.Selection_create_clone(self)
10337 def get_hierarchies(self):
10338 """get_hierarchies(Selection self) -> IMP::atom::Hierarchies"""
10339 return _IMP_atom.Selection_get_hierarchies(self)
10342 def set_molecules(self, mols):
10343 """set_molecules(Selection self, IMP::Strings mols)"""
10344 return _IMP_atom.Selection_set_molecules(self, mols)
10347 def set_resolution(self, r):
10348 """set_resolution(Selection self, double r)"""
10349 return _IMP_atom.Selection_set_resolution(self, r)
10352 def set_representation_type(self, t):
10353 """set_representation_type(Selection self, IMP::atom::RepresentationType t)"""
10354 return _IMP_atom.Selection_set_representation_type(self, t)
10357 def set_state_index(self, state):
10358 """set_state_index(Selection self, int state)"""
10359 return _IMP_atom.Selection_set_state_index(self, state)
10362 def set_state_indexes(self, states):
10363 """set_state_indexes(Selection self, IMP::Ints states)"""
10364 return _IMP_atom.Selection_set_state_indexes(self, states)
10367 def set_terminus(self, t):
10368 """set_terminus(Selection self, IMP::atom::Selection::Terminus t)"""
10369 return _IMP_atom.Selection_set_terminus(self, t)
10372 def set_element(self, e):
10373 """set_element(Selection self, IMP::atom::Element e)"""
10374 return _IMP_atom.Selection_set_element(self, e)
10377 def set_chain_ids(self, chains):
10378 """set_chain_ids(Selection self, IMP::Strings chains)"""
10379 return _IMP_atom.Selection_set_chain_ids(self, chains)
10382 def set_chains(self, chains):
10383 """set_chains(Selection self, IMP::Strings chains)"""
10384 return _IMP_atom.Selection_set_chains(self, chains)
10387 def set_residue_indexes(self, indexes):
10388 """set_residue_indexes(Selection self, IMP::Ints indexes)"""
10389 return _IMP_atom.Selection_set_residue_indexes(self, indexes)
10392 def set_atom_types(self, types):
10393 """set_atom_types(Selection self, IMP::atom::AtomTypes types)"""
10394 return _IMP_atom.Selection_set_atom_types(self, types)
10397 def set_residue_types(self, types):
10398 """set_residue_types(Selection self, IMP::atom::ResidueTypes types)"""
10399 return _IMP_atom.Selection_set_residue_types(self, types)
10402 def set_domains(self, names):
10403 """set_domains(Selection self, IMP::Strings names)"""
10404 return _IMP_atom.Selection_set_domains(self, names)
10407 def set_molecule(self, mol):
10408 """set_molecule(Selection self, std::string mol)"""
10409 return _IMP_atom.Selection_set_molecule(self, mol)
10412 def set_chain_id(self, c):
10413 """set_chain_id(Selection self, std::string c)"""
10414 return _IMP_atom.Selection_set_chain_id(self, c)
10417 def set_chain(self, c):
10418 """set_chain(Selection self, std::string c)"""
10419 return _IMP_atom.Selection_set_chain(self, c)
10422 def set_residue_index(self, i):
10423 """set_residue_index(Selection self, int i)"""
10424 return _IMP_atom.Selection_set_residue_index(self, i)
10427 def set_atom_type(self, types):
10428 """set_atom_type(Selection self, AtomType types)"""
10429 return _IMP_atom.Selection_set_atom_type(self, types)
10432 def set_residue_type(self, type):
10433 """set_residue_type(Selection self, ResidueType type)"""
10434 return _IMP_atom.Selection_set_residue_type(self, type)
10437 def set_domain(self, name):
10438 """set_domain(Selection self, std::string name)"""
10439 return _IMP_atom.Selection_set_domain(self, name)
10442 def set_copy_index(self, copy):
10443 """set_copy_index(Selection self, unsigned int copy)"""
10444 return _IMP_atom.Selection_set_copy_index(self, copy)
10447 def set_copy_indexes(self, copies):
10448 """set_copy_indexes(Selection self, IMP::Ints copies)"""
10449 return _IMP_atom.Selection_set_copy_indexes(self, copies)
10452 def set_particle_type(self, t):
10453 """set_particle_type(Selection self, ParticleType t)"""
10454 return _IMP_atom.Selection_set_particle_type(self, t)
10457 def set_particle_types(self, t):
10458 """set_particle_types(Selection self, IMP::core::ParticleTypes t)"""
10459 return _IMP_atom.Selection_set_particle_types(self, t)
10462 def set_hierarchy_types(self, types):
10463 """set_hierarchy_types(Selection self, IMP::Ints types)"""
10464 return _IMP_atom.Selection_set_hierarchy_types(self, types)
10467 def set_intersection(self, s):
10468 """set_intersection(Selection self, Selection s)"""
10469 return _IMP_atom.Selection_set_intersection(self, s)
10472 def set_union(self, s):
10473 """set_union(Selection self, Selection s)"""
10474 return _IMP_atom.Selection_set_union(self, s)
10477 def set_symmetric_difference(self, s):
10478 """set_symmetric_difference(Selection self, Selection s)"""
10479 return _IMP_atom.Selection_set_symmetric_difference(self, s)
10482 def set_difference(self, s):
10483 """set_difference(Selection self, Selection s)"""
10484 return _IMP_atom.Selection_set_difference(self, s)
10487 def get_selected_particles(self, with_representation=True):
10489 get_selected_particles(Selection self, bool with_representation=True) -> IMP::ParticlesTemp
10490 get_selected_particles(Selection self) -> IMP::ParticlesTemp
10492 return _IMP_atom.Selection_get_selected_particles(self, with_representation)
10495 def get_selected_particle_indexes(self, with_representation=True):
10497 get_selected_particle_indexes(Selection self, bool with_representation=True) -> IMP::ParticleIndexes
10498 get_selected_particle_indexes(Selection self) -> IMP::ParticleIndexes
10500 return _IMP_atom.Selection_get_selected_particle_indexes(self, with_representation)
10503 def show(self, *args):
10505 show(Selection self, _ostream out)
10506 show(Selection self)
10508 return _IMP_atom.Selection_show(self, *args)
10512 """__str__(Selection self) -> std::string"""
10513 return _IMP_atom.Selection___str__(self)
10516 def __repr__(self):
10517 """__repr__(Selection self) -> std::string"""
10518 return _IMP_atom.Selection___repr__(self)
10521 def __init__(self, hierarchy=None,
10522 hierarchies=
None, **params):
10523 if hierarchy
and hierarchies:
10524 raise RuntimeError(
"You can't pass both hierarchy and hierarchies to Selection")
10526 this = _IMP_atom.new_Selection(hierarchy)
10527 try: self.this.append(this)
10528 except: self.this = this
10530 this = _IMP_atom.new_Selection(hierarchies)
10531 try: self.this.append(this)
10532 except: self.this = this
10534 raise ValueError(
"Either hierarchy or hierarchies must be provided.")
10535 for k
in params.keys():
10536 eval(
"self.set_%s(params[k])"%k)
10538 def union(self, s):
10539 news = self.create_clone()
10540 news.union_update(s)
10542 def intersection(self, s):
10543 news = self.create_clone()
10544 news.intersection_update(s)
10546 def symmetric_difference(self, s):
10547 news = self.create_clone()
10548 news.symmetric_difference_update(s)
10550 def difference(self, s):
10551 news = self.create_clone()
10552 news.difference_update(s)
10554 def union_update(self, s):
10557 def intersection_update(self, s):
10558 self.set_intersection(s)
10560 def symmetric_difference_update(self, s):
10561 self.set_symmetric_difference(s)
10563 def difference_update(self, s):
10564 self.set_difference(s)
10567 __and__ = intersection
10568 __xor__ = symmetric_difference
10569 __sub__ = difference
10570 __ior__ = union_update
10571 __iand__ = intersection_update
10572 __ixor__ = symmetric_difference_update
10573 __isub__ = difference_update
10575 __swig_destroy__ = _IMP_atom.delete_Selection
10576 __del__ =
lambda self:
None
10577 Selection_swigregister = _IMP_atom.Selection_swigregister
10578 Selection_swigregister(Selection)
10583 create_distance_restraint(Selection n0, Selection n1, double x0, double k, std::string name) -> Restraint
10584 create_distance_restraint(Selection n0, Selection n1, double x0, double k) -> Restraint
10586 return _IMP_atom.create_distance_restraint(*args)
10590 create_connectivity_restraint(IMP::atom::Selections const & s, double k, std::string name) -> Restraint
10591 create_connectivity_restraint(IMP::atom::Selections const & s, double k) -> Restraint
10592 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k, std::string name) -> Restraint
10593 create_connectivity_restraint(IMP::atom::Selections const & s, double x0, double k) -> Restraint
10595 return _IMP_atom.create_connectivity_restraint(*args)
10599 create_internal_connectivity_restraint(Selection s, double k, std::string name) -> Restraint
10600 create_internal_connectivity_restraint(Selection s, double k) -> Restraint
10601 create_internal_connectivity_restraint(Selection s, double x0, double k, std::string name) -> Restraint
10602 create_internal_connectivity_restraint(Selection s, double x0, double k) -> Restraint
10604 return _IMP_atom.create_internal_connectivity_restraint(*args)
10608 create_cover(Selection s, std::string name) -> XYZR
10609 create_cover(Selection s) -> XYZR
10611 return _IMP_atom.create_cover(*args)
10615 get_mass(ResidueType c) -> double
10616 get_mass(Selection s) -> double
10618 return _IMP_atom.get_mass(*args)
10621 """get_volume(Selection s) -> double"""
10622 return _IMP_atom.get_volume(s)
10625 """get_surface_area(Selection s) -> double"""
10626 return _IMP_atom.get_surface_area(s)
10630 get_leaves(Hierarchy h) -> IMP::atom::Hierarchies
10631 get_leaves(IMP::atom::Hierarchies const & h) -> IMP::atom::Hierarchies
10632 get_leaves(Selection h) -> IMP::atom::Hierarchies
10634 return _IMP_atom.get_leaves(*args)
10636 """Proxy of C++ IMP::atom::SelectionGeometry class"""
10637 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10639 def __init__(self, *args):
10641 __init__(IMP::atom::SelectionGeometry self, Selection d, std::string name) -> SelectionGeometry
10642 __init__(IMP::atom::SelectionGeometry self, Selection d) -> SelectionGeometry
10644 this = _IMP_atom.new_SelectionGeometry(*args)
10646 self.this.append(this)
10650 def get_version_info(self):
10651 """get_version_info(SelectionGeometry self) -> VersionInfo"""
10652 return _IMP_atom.SelectionGeometry_get_version_info(self)
10656 """__str__(SelectionGeometry self) -> std::string"""
10657 return _IMP_atom.SelectionGeometry___str__(self)
10660 def __repr__(self):
10661 """__repr__(SelectionGeometry self) -> std::string"""
10662 return _IMP_atom.SelectionGeometry___repr__(self)
10667 return _object_cast_to_SelectionGeometry(o)
10669 SelectionGeometry_swigregister = _IMP_atom.SelectionGeometry_swigregister
10670 SelectionGeometry_swigregister(SelectionGeometry)
10675 get_rmsd(IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10676 get_rmsd(Selection s0, Selection s1) -> double
10678 return _IMP_atom.get_rmsd(*args)
10682 get_rmsd_transforming_first(Transformation3D tr, IMP::core::XYZs const & s0, IMP::core::XYZs const & s1) -> double
10683 get_rmsd_transforming_first(Transformation3D tr, Selection s0, Selection s1) -> double
10685 return _IMP_atom.get_rmsd_transforming_first(*args)
10688 """get_placement_score(IMP::core::XYZs const & source, IMP::core::XYZs const & target) -> IMP::FloatPair"""
10689 return _IMP_atom.get_placement_score(source, target)
10692 """get_component_placement_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> IMP::FloatPair"""
10693 return _IMP_atom.get_component_placement_score(ref1, ref2, mdl1, mdl2)
10696 """get_pairwise_rmsd_score(IMP::core::XYZs const & ref1, IMP::core::XYZs const & ref2, IMP::core::XYZs const & mdl1, IMP::core::XYZs const & mdl2) -> double"""
10697 return _IMP_atom.get_pairwise_rmsd_score(ref1, ref2, mdl1, mdl2)
10701 get_radius_of_gyration(Selection s) -> double
10702 get_radius_of_gyration(IMP::ParticlesTemp const & ps) -> double
10704 return _IMP_atom.get_radius_of_gyration(*args)
10706 """Proxy of C++ IMP::atom::ForceFieldParameters class"""
10707 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10709 def __init__(self):
10710 """__init__(IMP::atom::ForceFieldParameters self) -> ForceFieldParameters"""
10711 this = _IMP_atom.new_ForceFieldParameters()
10713 self.this.append(this)
10717 def get_radius(self, atom):
10718 """get_radius(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10719 return _IMP_atom.ForceFieldParameters_get_radius(self, atom)
10722 def get_epsilon(self, atom):
10723 """get_epsilon(ForceFieldParameters self, Atom atom) -> IMP::Float"""
10724 return _IMP_atom.ForceFieldParameters_get_epsilon(self, atom)
10729 add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0, FloatKey radius_key)
10730 add_radii(ForceFieldParameters self, Hierarchy mhd, double scale=1.0)
10731 add_radii(ForceFieldParameters self, Hierarchy mhd)
10733 return _IMP_atom.ForceFieldParameters_add_radii(self, *args)
10736 def add_well_depths(self, mhd):
10737 """add_well_depths(ForceFieldParameters self, Hierarchy mhd)"""
10738 return _IMP_atom.ForceFieldParameters_add_well_depths(self, mhd)
10742 """add_bonds(ForceFieldParameters self, Hierarchy mhd)"""
10743 return _IMP_atom.ForceFieldParameters_add_bonds(self, mhd)
10745 __swig_destroy__ = _IMP_atom.delete_ForceFieldParameters
10746 __del__ =
lambda self:
None
10749 """__str__(ForceFieldParameters self) -> std::string"""
10750 return _IMP_atom.ForceFieldParameters___str__(self)
10753 def __repr__(self):
10754 """__repr__(ForceFieldParameters self) -> std::string"""
10755 return _IMP_atom.ForceFieldParameters___repr__(self)
10760 return _object_cast_to_ForceFieldParameters(o)
10762 ForceFieldParameters_swigregister = _IMP_atom.ForceFieldParameters_swigregister
10763 ForceFieldParameters_swigregister(ForceFieldParameters)
10765 class CHARMMAtomTopology(object):
10766 """Proxy of C++ IMP::atom::CHARMMAtomTopology class"""
10767 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10769 def __init__(self, *args):
10771 __init__(IMP::atom::CHARMMAtomTopology self, std::string name) -> CHARMMAtomTopology
10772 __init__(IMP::atom::CHARMMAtomTopology self, std::string name, CHARMMAtomTopology other) -> CHARMMAtomTopology
10774 this = _IMP_atom.new_CHARMMAtomTopology(*args)
10776 self.this.append(this)
10780 def get_name(self):
10781 """get_name(CHARMMAtomTopology self) -> std::string"""
10782 return _IMP_atom.CHARMMAtomTopology_get_name(self)
10785 def get_charmm_type(self):
10786 """get_charmm_type(CHARMMAtomTopology self) -> std::string"""
10787 return _IMP_atom.CHARMMAtomTopology_get_charmm_type(self)
10790 def get_charge(self):
10791 """get_charge(CHARMMAtomTopology self) -> double"""
10792 return _IMP_atom.CHARMMAtomTopology_get_charge(self)
10795 def set_charmm_type(self, charmm_type):
10796 """set_charmm_type(CHARMMAtomTopology self, std::string charmm_type)"""
10797 return _IMP_atom.CHARMMAtomTopology_set_charmm_type(self, charmm_type)
10800 def set_charge(self, charge):
10801 """set_charge(CHARMMAtomTopology self, double charge)"""
10802 return _IMP_atom.CHARMMAtomTopology_set_charge(self, charge)
10805 def show(self, *args):
10807 show(CHARMMAtomTopology self, _ostream out)
10808 show(CHARMMAtomTopology self)
10810 return _IMP_atom.CHARMMAtomTopology_show(self, *args)
10814 """__str__(CHARMMAtomTopology self) -> std::string"""
10815 return _IMP_atom.CHARMMAtomTopology___str__(self)
10818 def __repr__(self):
10819 """__repr__(CHARMMAtomTopology self) -> std::string"""
10820 return _IMP_atom.CHARMMAtomTopology___repr__(self)
10822 __swig_destroy__ = _IMP_atom.delete_CHARMMAtomTopology
10823 __del__ =
lambda self:
None
10824 CHARMMAtomTopology_swigregister = _IMP_atom.CHARMMAtomTopology_swigregister
10825 CHARMMAtomTopology_swigregister(CHARMMAtomTopology)
10827 class CHARMMBondEndpoint(object):
10828 """Proxy of C++ IMP::atom::CHARMMBondEndpoint class"""
10829 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10831 def __init__(self, atom_name, residue=None):
10833 __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name, CHARMMResidueTopology residue=None) -> CHARMMBondEndpoint
10834 __init__(IMP::atom::CHARMMBondEndpoint self, std::string atom_name) -> CHARMMBondEndpoint
10836 this = _IMP_atom.new_CHARMMBondEndpoint(atom_name, residue)
10838 self.this.append(this)
10842 def get_atom_name(self):
10843 """get_atom_name(CHARMMBondEndpoint self) -> std::string"""
10844 return _IMP_atom.CHARMMBondEndpoint_get_atom_name(self)
10847 def get_atom(self, current_residue, previous_residue, next_residue, resmap):
10848 """get_atom(CHARMMBondEndpoint self, CHARMMResidueTopology current_residue, CHARMMResidueTopology previous_residue, CHARMMResidueTopology next_residue, std::map< IMP::atom::CHARMMResidueTopology const *,IMP::atom::Hierarchy > const & resmap) -> Atom"""
10849 return _IMP_atom.CHARMMBondEndpoint_get_atom(self, current_residue, previous_residue, next_residue, resmap)
10852 def show(self, *args):
10854 show(CHARMMBondEndpoint self, _ostream out)
10855 show(CHARMMBondEndpoint self)
10857 return _IMP_atom.CHARMMBondEndpoint_show(self, *args)
10861 """__str__(CHARMMBondEndpoint self) -> std::string"""
10862 return _IMP_atom.CHARMMBondEndpoint___str__(self)
10865 def __repr__(self):
10866 """__repr__(CHARMMBondEndpoint self) -> std::string"""
10867 return _IMP_atom.CHARMMBondEndpoint___repr__(self)
10869 __swig_destroy__ = _IMP_atom.delete_CHARMMBondEndpoint
10870 __del__ =
lambda self:
None
10871 CHARMMBondEndpoint_swigregister = _IMP_atom.CHARMMBondEndpoint_swigregister
10872 CHARMMBondEndpoint_swigregister(CHARMMBondEndpoint)
10874 class CHARMMDihedral(object):
10875 """Proxy of C++ IMP::atom::CHARMMConnection<(4)> class"""
10876 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10877 __repr__ = _swig_repr
10879 def __init__(self, atoms):
10880 """__init__(IMP::atom::CHARMMConnection<(4)> self, IMP::Strings const & atoms) -> CHARMMDihedral"""
10881 this = _IMP_atom.new_CHARMMDihedral(atoms)
10883 self.this.append(this)
10887 def get_endpoint(self, i):
10888 """get_endpoint(CHARMMDihedral self, unsigned int i) -> CHARMMBondEndpoint"""
10889 return _IMP_atom.CHARMMDihedral_get_endpoint(self, i)
10892 def get_contains_atom(self, name):
10893 """get_contains_atom(CHARMMDihedral self, std::string name) -> bool"""
10894 return _IMP_atom.CHARMMDihedral_get_contains_atom(self, name)
10897 def show(self, *args):
10899 show(CHARMMDihedral self, _ostream out)
10900 show(CHARMMDihedral self)
10902 return _IMP_atom.CHARMMDihedral_show(self, *args)
10904 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedral
10905 __del__ =
lambda self:
None
10906 CHARMMDihedral_swigregister = _IMP_atom.CHARMMDihedral_swigregister
10907 CHARMMDihedral_swigregister(CHARMMDihedral)
10909 class CHARMMInternalCoordinate(CHARMMDihedral):
10910 """Proxy of C++ IMP::atom::CHARMMInternalCoordinate class"""
10911 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10913 def __init__(self, *args):
10915 __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Strings const & atoms, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10916 __init__(IMP::atom::CHARMMInternalCoordinate self, IMP::Vector< IMP::atom::CHARMMBondEndpoint > const endpoints, float first_distance, float first_angle, float dihedral, float second_angle, float second_distance, bool improper) -> CHARMMInternalCoordinate
10918 this = _IMP_atom.new_CHARMMInternalCoordinate(*args)
10920 self.this.append(this)
10924 def get_first_distance(self):
10925 """get_first_distance(CHARMMInternalCoordinate self) -> float"""
10926 return _IMP_atom.CHARMMInternalCoordinate_get_first_distance(self)
10929 def get_second_distance(self):
10930 """get_second_distance(CHARMMInternalCoordinate self) -> float"""
10931 return _IMP_atom.CHARMMInternalCoordinate_get_second_distance(self)
10934 def get_first_angle(self):
10935 """get_first_angle(CHARMMInternalCoordinate self) -> float"""
10936 return _IMP_atom.CHARMMInternalCoordinate_get_first_angle(self)
10939 def get_second_angle(self):
10940 """get_second_angle(CHARMMInternalCoordinate self) -> float"""
10941 return _IMP_atom.CHARMMInternalCoordinate_get_second_angle(self)
10945 """get_dihedral(CHARMMInternalCoordinate self) -> float"""
10946 return _IMP_atom.CHARMMInternalCoordinate_get_dihedral(self)
10949 def get_improper(self):
10950 """get_improper(CHARMMInternalCoordinate self) -> bool"""
10951 return _IMP_atom.CHARMMInternalCoordinate_get_improper(self)
10954 def show(self, *args):
10956 show(CHARMMInternalCoordinate self, _ostream out)
10957 show(CHARMMInternalCoordinate self)
10959 return _IMP_atom.CHARMMInternalCoordinate_show(self, *args)
10963 """__str__(CHARMMInternalCoordinate self) -> std::string"""
10964 return _IMP_atom.CHARMMInternalCoordinate___str__(self)
10967 def __repr__(self):
10968 """__repr__(CHARMMInternalCoordinate self) -> std::string"""
10969 return _IMP_atom.CHARMMInternalCoordinate___repr__(self)
10971 __swig_destroy__ = _IMP_atom.delete_CHARMMInternalCoordinate
10972 __del__ =
lambda self:
None
10973 CHARMMInternalCoordinate_swigregister = _IMP_atom.CHARMMInternalCoordinate_swigregister
10974 CHARMMInternalCoordinate_swigregister(CHARMMInternalCoordinate)
10976 class CHARMMResidueTopologyBase(
IMP.Object):
10977 """Proxy of C++ IMP::atom::CHARMMResidueTopologyBase class"""
10978 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
10980 def __init__(self, *args, **kwargs):
10981 raise AttributeError(
"No constructor defined")
10983 def get_type(self):
10984 """get_type(CHARMMResidueTopologyBase self) -> std::string"""
10985 return _IMP_atom.CHARMMResidueTopologyBase_get_type(self)
10988 def get_number_of_atoms(self):
10989 """get_number_of_atoms(CHARMMResidueTopologyBase self) -> unsigned int"""
10990 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_atoms(self)
10993 def add_atom(self, atom):
10994 """add_atom(CHARMMResidueTopologyBase self, CHARMMAtomTopology atom)"""
10995 return _IMP_atom.CHARMMResidueTopologyBase_add_atom(self, atom)
11000 get_atom(CHARMMResidueTopologyBase self, unsigned int i) -> CHARMMAtomTopology
11001 get_atom(CHARMMResidueTopologyBase self, AtomType type) -> CHARMMAtomTopology
11002 get_atom(CHARMMResidueTopologyBase self, std::string name) -> CHARMMAtomTopology
11004 return _IMP_atom.CHARMMResidueTopologyBase_get_atom(self, *args)
11007 def get_number_of_bonds(self):
11008 """get_number_of_bonds(CHARMMResidueTopologyBase self) -> unsigned int"""
11009 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_bonds(self)
11012 def add_bond(self, bond):
11013 """add_bond(CHARMMResidueTopologyBase self, IMP::atom::CHARMMBond const & bond)"""
11014 return _IMP_atom.CHARMMResidueTopologyBase_add_bond(self, bond)
11017 def get_number_of_angles(self):
11018 """get_number_of_angles(CHARMMResidueTopologyBase self) -> unsigned int"""
11019 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_angles(self)
11022 def add_angle(self, bond):
11023 """add_angle(CHARMMResidueTopologyBase self, IMP::atom::CHARMMAngle const & bond)"""
11024 return _IMP_atom.CHARMMResidueTopologyBase_add_angle(self, bond)
11027 def get_number_of_dihedrals(self):
11028 """get_number_of_dihedrals(CHARMMResidueTopologyBase self) -> unsigned int"""
11029 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_dihedrals(self)
11032 def add_dihedral(self, bond):
11033 """add_dihedral(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11034 return _IMP_atom.CHARMMResidueTopologyBase_add_dihedral(self, bond)
11037 def get_number_of_impropers(self):
11038 """get_number_of_impropers(CHARMMResidueTopologyBase self) -> unsigned int"""
11039 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_impropers(self)
11042 def add_improper(self, bond):
11043 """add_improper(CHARMMResidueTopologyBase self, CHARMMDihedral bond)"""
11044 return _IMP_atom.CHARMMResidueTopologyBase_add_improper(self, bond)
11047 def get_number_of_internal_coordinates(self):
11048 """get_number_of_internal_coordinates(CHARMMResidueTopologyBase self) -> unsigned int"""
11049 return _IMP_atom.CHARMMResidueTopologyBase_get_number_of_internal_coordinates(self)
11052 def add_internal_coordinate(self, ic):
11053 """add_internal_coordinate(CHARMMResidueTopologyBase self, CHARMMInternalCoordinate ic)"""
11054 return _IMP_atom.CHARMMResidueTopologyBase_add_internal_coordinate(self, ic)
11057 def get_internal_coordinate(self, index):
11058 """get_internal_coordinate(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMInternalCoordinate"""
11059 return _IMP_atom.CHARMMResidueTopologyBase_get_internal_coordinate(self, index)
11063 """get_bond(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMBond const &"""
11064 return _IMP_atom.CHARMMResidueTopologyBase_get_bond(self, index)
11067 def get_angle(self, index):
11068 """get_angle(CHARMMResidueTopologyBase self, unsigned int index) -> IMP::atom::CHARMMAngle const &"""
11069 return _IMP_atom.CHARMMResidueTopologyBase_get_angle(self, index)
11073 """get_dihedral(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11074 return _IMP_atom.CHARMMResidueTopologyBase_get_dihedral(self, index)
11077 def get_improper(self, index):
11078 """get_improper(CHARMMResidueTopologyBase self, unsigned int index) -> CHARMMDihedral"""
11079 return _IMP_atom.CHARMMResidueTopologyBase_get_improper(self, index)
11082 def get_version_info(self):
11083 """get_version_info(CHARMMResidueTopologyBase self) -> VersionInfo"""
11084 return _IMP_atom.CHARMMResidueTopologyBase_get_version_info(self)
11088 """__str__(CHARMMResidueTopologyBase self) -> std::string"""
11089 return _IMP_atom.CHARMMResidueTopologyBase___str__(self)
11092 def __repr__(self):
11093 """__repr__(CHARMMResidueTopologyBase self) -> std::string"""
11094 return _IMP_atom.CHARMMResidueTopologyBase___repr__(self)
11099 return _object_cast_to_CHARMMResidueTopologyBase(o)
11101 CHARMMResidueTopologyBase_swigregister = _IMP_atom.CHARMMResidueTopologyBase_swigregister
11102 CHARMMResidueTopologyBase_swigregister(CHARMMResidueTopologyBase)
11104 class CHARMMIdealResidueTopology(CHARMMResidueTopologyBase):
11105 """Proxy of C++ IMP::atom::CHARMMIdealResidueTopology class"""
11106 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11108 def __init__(self, *args):
11110 __init__(IMP::atom::CHARMMIdealResidueTopology self, std::string type) -> CHARMMIdealResidueTopology
11111 __init__(IMP::atom::CHARMMIdealResidueTopology self, ResidueType type) -> CHARMMIdealResidueTopology
11113 this = _IMP_atom.new_CHARMMIdealResidueTopology(*args)
11115 self.this.append(this)
11119 def remove_atom(self, name):
11120 """remove_atom(CHARMMIdealResidueTopology self, std::string name)"""
11121 return _IMP_atom.CHARMMIdealResidueTopology_remove_atom(self, name)
11124 def set_default_first_patch(self, patch):
11125 """set_default_first_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11126 return _IMP_atom.CHARMMIdealResidueTopology_set_default_first_patch(self, patch)
11129 def set_default_last_patch(self, patch):
11130 """set_default_last_patch(CHARMMIdealResidueTopology self, std::string patch)"""
11131 return _IMP_atom.CHARMMIdealResidueTopology_set_default_last_patch(self, patch)
11134 def get_default_first_patch(self):
11135 """get_default_first_patch(CHARMMIdealResidueTopology self) -> std::string"""
11136 return _IMP_atom.CHARMMIdealResidueTopology_get_default_first_patch(self)
11139 def get_default_last_patch(self):
11140 """get_default_last_patch(CHARMMIdealResidueTopology self) -> std::string"""
11141 return _IMP_atom.CHARMMIdealResidueTopology_get_default_last_patch(self)
11145 """__str__(CHARMMIdealResidueTopology self) -> std::string"""
11146 return _IMP_atom.CHARMMIdealResidueTopology___str__(self)
11149 def __repr__(self):
11150 """__repr__(CHARMMIdealResidueTopology self) -> std::string"""
11151 return _IMP_atom.CHARMMIdealResidueTopology___repr__(self)
11156 return _object_cast_to_CHARMMIdealResidueTopology(o)
11158 CHARMMIdealResidueTopology_swigregister = _IMP_atom.CHARMMIdealResidueTopology_swigregister
11159 CHARMMIdealResidueTopology_swigregister(CHARMMIdealResidueTopology)
11161 class CHARMMPatch(CHARMMResidueTopologyBase):
11162 """Proxy of C++ IMP::atom::CHARMMPatch class"""
11163 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11165 def __init__(self, type):
11166 """__init__(IMP::atom::CHARMMPatch self, std::string type) -> CHARMMPatch"""
11167 this = _IMP_atom.new_CHARMMPatch(type)
11169 self.this.append(this)
11173 def add_removed_atom(self, name):
11174 """add_removed_atom(CHARMMPatch self, std::string name)"""
11175 return _IMP_atom.CHARMMPatch_add_removed_atom(self, name)
11178 def get_number_of_removed_atoms(self):
11179 """get_number_of_removed_atoms(CHARMMPatch self) -> unsigned int"""
11180 return _IMP_atom.CHARMMPatch_get_number_of_removed_atoms(self)
11183 def get_removed_atom(self, i):
11184 """get_removed_atom(CHARMMPatch self, unsigned int i) -> std::string"""
11185 return _IMP_atom.CHARMMPatch_get_removed_atom(self, i)
11188 def apply(self, *args):
11190 apply(CHARMMPatch self, CHARMMResidueTopology res)
11191 apply(CHARMMPatch self, CHARMMResidueTopology res1, CHARMMResidueTopology res2)
11193 return _IMP_atom.CHARMMPatch_apply(self, *args)
11197 """__str__(CHARMMPatch self) -> std::string"""
11198 return _IMP_atom.CHARMMPatch___str__(self)
11201 def __repr__(self):
11202 """__repr__(CHARMMPatch self) -> std::string"""
11203 return _IMP_atom.CHARMMPatch___repr__(self)
11208 return _object_cast_to_CHARMMPatch(o)
11210 CHARMMPatch_swigregister = _IMP_atom.CHARMMPatch_swigregister
11211 CHARMMPatch_swigregister(CHARMMPatch)
11213 class CHARMMResidueTopology(CHARMMIdealResidueTopology):
11214 """Proxy of C++ IMP::atom::CHARMMResidueTopology class"""
11215 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11217 def __init__(self, *args):
11219 __init__(IMP::atom::CHARMMResidueTopology self, ResidueType type) -> CHARMMResidueTopology
11220 __init__(IMP::atom::CHARMMResidueTopology self, CHARMMIdealResidueTopology ideal) -> CHARMMResidueTopology
11222 this = _IMP_atom.new_CHARMMResidueTopology(*args)
11224 self.this.append(this)
11228 def get_patched(self):
11229 """get_patched(CHARMMResidueTopology self) -> bool"""
11230 return _IMP_atom.CHARMMResidueTopology_get_patched(self)
11233 def set_patched(self, patched):
11234 """set_patched(CHARMMResidueTopology self, bool patched)"""
11235 return _IMP_atom.CHARMMResidueTopology_set_patched(self, patched)
11239 """__str__(CHARMMResidueTopology self) -> std::string"""
11240 return _IMP_atom.CHARMMResidueTopology___str__(self)
11243 def __repr__(self):
11244 """__repr__(CHARMMResidueTopology self) -> std::string"""
11245 return _IMP_atom.CHARMMResidueTopology___repr__(self)
11250 return _object_cast_to_CHARMMResidueTopology(o)
11252 CHARMMResidueTopology_swigregister = _IMP_atom.CHARMMResidueTopology_swigregister
11253 CHARMMResidueTopology_swigregister(CHARMMResidueTopology)
11255 class CHARMMAtom(Atom):
11256 """Proxy of C++ IMP::atom::CHARMMAtom class"""
11257 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11259 def __init__(self, *args):
11261 __init__(IMP::atom::CHARMMAtom self) -> CHARMMAtom
11262 __init__(IMP::atom::CHARMMAtom self, Model m, ParticleIndex id) -> CHARMMAtom
11263 __init__(IMP::atom::CHARMMAtom self, _ParticleAdaptor d) -> CHARMMAtom
11265 this = _IMP_atom.new_CHARMMAtom(*args)
11267 self.this.append(this)
11271 def show(self, *args):
11273 show(CHARMMAtom self, _ostream out)
11274 show(CHARMMAtom self)
11276 return _IMP_atom.CHARMMAtom_show(self, *args)
11279 def setup_particle(*args):
11281 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11282 setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11284 return _IMP_atom.CHARMMAtom_setup_particle(*args)
11286 setup_particle = staticmethod(setup_particle)
11288 def get_charmm_type(self):
11289 """get_charmm_type(CHARMMAtom self) -> IMP::String"""
11290 return _IMP_atom.CHARMMAtom_get_charmm_type(self)
11293 def set_charmm_type(self, t):
11294 """set_charmm_type(CHARMMAtom self, IMP::String t)"""
11295 return _IMP_atom.CHARMMAtom_set_charmm_type(self, t)
11298 def get_is_setup(*args):
11300 get_is_setup(_ParticleAdaptor p) -> bool
11301 get_is_setup(Model m, ParticleIndex pi) -> bool
11303 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11305 get_is_setup = staticmethod(get_is_setup)
11307 def get_charmm_type_key():
11308 """get_charmm_type_key() -> StringKey"""
11309 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11311 get_charmm_type_key = staticmethod(get_charmm_type_key)
11313 def add_attribute(self, *args):
11315 add_attribute(CHARMMAtom self, FloatKey k, IMP::Float v, bool opt)
11316 add_attribute(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11317 add_attribute(CHARMMAtom self, IntKey a0, IMP::Int a1)
11318 add_attribute(CHARMMAtom self, StringKey a0, IMP::String a1)
11319 add_attribute(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11320 add_attribute(CHARMMAtom self, ObjectKey a0, Object a1)
11322 return _IMP_atom.CHARMMAtom_add_attribute(self, *args)
11325 def get_value(self, *args):
11327 get_value(CHARMMAtom self, FloatKey a0) -> IMP::Float
11328 get_value(CHARMMAtom self, IntKey a0) -> IMP::Int
11329 get_value(CHARMMAtom self, StringKey a0) -> IMP::String
11330 get_value(CHARMMAtom self, ParticleIndexKey a0) -> Particle
11331 get_value(CHARMMAtom self, ObjectKey a0) -> Object
11333 return _IMP_atom.CHARMMAtom_get_value(self, *args)
11336 def set_value(self, *args):
11338 set_value(CHARMMAtom self, FloatKey a0, IMP::Float a1)
11339 set_value(CHARMMAtom self, IntKey a0, IMP::Int a1)
11340 set_value(CHARMMAtom self, StringKey a0, IMP::String a1)
11341 set_value(CHARMMAtom self, ParticleIndexKey a0, Particle a1)
11342 set_value(CHARMMAtom self, ObjectKey a0, Object a1)
11344 return _IMP_atom.CHARMMAtom_set_value(self, *args)
11347 def remove_attribute(self, *args):
11349 remove_attribute(CHARMMAtom self, FloatKey a0)
11350 remove_attribute(CHARMMAtom self, IntKey a0)
11351 remove_attribute(CHARMMAtom self, StringKey a0)
11352 remove_attribute(CHARMMAtom self, ParticleIndexKey a0)
11353 remove_attribute(CHARMMAtom self, ObjectKey a0)
11355 return _IMP_atom.CHARMMAtom_remove_attribute(self, *args)
11358 def has_attribute(self, *args):
11360 has_attribute(CHARMMAtom self, FloatKey a0) -> bool
11361 has_attribute(CHARMMAtom self, IntKey a0) -> bool
11362 has_attribute(CHARMMAtom self, StringKey a0) -> bool
11363 has_attribute(CHARMMAtom self, ParticleIndexKey a0) -> bool
11364 has_attribute(CHARMMAtom self, ObjectKey a0) -> bool
11366 return _IMP_atom.CHARMMAtom_has_attribute(self, *args)
11369 def get_derivative(self, a0):
11370 """get_derivative(CHARMMAtom self, FloatKey a0) -> double"""
11371 return _IMP_atom.CHARMMAtom_get_derivative(self, a0)
11374 def get_name(self):
11375 """get_name(CHARMMAtom self) -> std::string"""
11376 return _IMP_atom.CHARMMAtom_get_name(self)
11379 def clear_caches(self):
11380 """clear_caches(CHARMMAtom self)"""
11381 return _IMP_atom.CHARMMAtom_clear_caches(self)
11384 def set_name(self, a0):
11385 """set_name(CHARMMAtom self, std::string a0)"""
11386 return _IMP_atom.CHARMMAtom_set_name(self, a0)
11390 """set_check_level(CHARMMAtom self, IMP::CheckLevel a0)"""
11391 return _IMP_atom.CHARMMAtom_set_check_level(self, a0)
11394 def add_to_derivative(self, a0, a1, a2):
11395 """add_to_derivative(CHARMMAtom self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
11396 return _IMP_atom.CHARMMAtom_add_to_derivative(self, a0, a1, a2)
11399 def set_is_optimized(self, a0, a1):
11400 """set_is_optimized(CHARMMAtom self, FloatKey a0, bool a1)"""
11401 return _IMP_atom.CHARMMAtom_set_is_optimized(self, a0, a1)
11404 def get_is_optimized(self, a0):
11405 """get_is_optimized(CHARMMAtom self, FloatKey a0) -> bool"""
11406 return _IMP_atom.CHARMMAtom_get_is_optimized(self, a0)
11410 """get_check_level(CHARMMAtom self) -> IMP::CheckLevel"""
11411 return _IMP_atom.CHARMMAtom_get_check_level(self)
11414 def __eq__(self, *args):
11416 __eq__(CHARMMAtom self, CHARMMAtom o) -> bool
11417 __eq__(CHARMMAtom self, Particle d) -> bool
11419 return _IMP_atom.CHARMMAtom___eq__(self, *args)
11422 def __ne__(self, *args):
11424 __ne__(CHARMMAtom self, CHARMMAtom o) -> bool
11425 __ne__(CHARMMAtom self, Particle d) -> bool
11427 return _IMP_atom.CHARMMAtom___ne__(self, *args)
11430 def __le__(self, *args):
11432 __le__(CHARMMAtom self, CHARMMAtom o) -> bool
11433 __le__(CHARMMAtom self, Particle d) -> bool
11435 return _IMP_atom.CHARMMAtom___le__(self, *args)
11438 def __lt__(self, *args):
11440 __lt__(CHARMMAtom self, CHARMMAtom o) -> bool
11441 __lt__(CHARMMAtom self, Particle d) -> bool
11443 return _IMP_atom.CHARMMAtom___lt__(self, *args)
11446 def __ge__(self, *args):
11448 __ge__(CHARMMAtom self, CHARMMAtom o) -> bool
11449 __ge__(CHARMMAtom self, Particle d) -> bool
11451 return _IMP_atom.CHARMMAtom___ge__(self, *args)
11454 def __gt__(self, *args):
11456 __gt__(CHARMMAtom self, CHARMMAtom o) -> bool
11457 __gt__(CHARMMAtom self, Particle d) -> bool
11459 return _IMP_atom.CHARMMAtom___gt__(self, *args)
11462 def __hash__(self):
11463 """__hash__(CHARMMAtom self) -> std::size_t"""
11464 return _IMP_atom.CHARMMAtom___hash__(self)
11468 """__str__(CHARMMAtom self) -> std::string"""
11469 return _IMP_atom.CHARMMAtom___str__(self)
11472 def __repr__(self):
11473 """__repr__(CHARMMAtom self) -> std::string"""
11474 return _IMP_atom.CHARMMAtom___repr__(self)
11476 __swig_destroy__ = _IMP_atom.delete_CHARMMAtom
11477 __del__ =
lambda self:
None
11478 CHARMMAtom_swigregister = _IMP_atom.CHARMMAtom_swigregister
11479 CHARMMAtom_swigregister(CHARMMAtom)
11481 def CHARMMAtom_setup_particle(*args):
11483 setup_particle(Model m, ParticleIndex pi, IMP::String charmm_type) -> CHARMMAtom
11484 CHARMMAtom_setup_particle(_ParticleAdaptor decorator, IMP::String charmm_type) -> CHARMMAtom
11486 return _IMP_atom.CHARMMAtom_setup_particle(*args)
11488 def CHARMMAtom_get_is_setup(*args):
11490 get_is_setup(_ParticleAdaptor p) -> bool
11491 CHARMMAtom_get_is_setup(Model m, ParticleIndex pi) -> bool
11493 return _IMP_atom.CHARMMAtom_get_is_setup(*args)
11495 def CHARMMAtom_get_charmm_type_key():
11496 """CHARMMAtom_get_charmm_type_key() -> StringKey"""
11497 return _IMP_atom.CHARMMAtom_get_charmm_type_key()
11501 """get_charmm_untyped_atoms(Hierarchy hierarchy) -> IMP::atom::Atoms"""
11502 return _IMP_atom.get_charmm_untyped_atoms(hierarchy)
11505 """remove_charmm_untyped_atoms(Hierarchy hierarchy)"""
11506 return _IMP_atom.remove_charmm_untyped_atoms(hierarchy)
11507 class CHARMMBondParameters(object):
11508 """Proxy of C++ IMP::atom::CHARMMBondParameters class"""
11509 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11510 force_constant = _swig_property(_IMP_atom.CHARMMBondParameters_force_constant_get, _IMP_atom.CHARMMBondParameters_force_constant_set)
11511 ideal = _swig_property(_IMP_atom.CHARMMBondParameters_ideal_get, _IMP_atom.CHARMMBondParameters_ideal_set)
11513 def __init__(self):
11514 """__init__(IMP::atom::CHARMMBondParameters self) -> CHARMMBondParameters"""
11515 this = _IMP_atom.new_CHARMMBondParameters()
11517 self.this.append(this)
11521 def show(self, *args):
11523 show(CHARMMBondParameters self, _ostream out)
11524 show(CHARMMBondParameters self)
11526 return _IMP_atom.CHARMMBondParameters_show(self, *args)
11530 """__str__(CHARMMBondParameters self) -> std::string"""
11531 return _IMP_atom.CHARMMBondParameters___str__(self)
11534 def __repr__(self):
11535 """__repr__(CHARMMBondParameters self) -> std::string"""
11536 return _IMP_atom.CHARMMBondParameters___repr__(self)
11538 __swig_destroy__ = _IMP_atom.delete_CHARMMBondParameters
11539 __del__ =
lambda self:
None
11540 CHARMMBondParameters_swigregister = _IMP_atom.CHARMMBondParameters_swigregister
11541 CHARMMBondParameters_swigregister(CHARMMBondParameters)
11543 class CHARMMDihedralParameters(object):
11544 """Proxy of C++ IMP::atom::CHARMMDihedralParameters class"""
11545 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11546 force_constant = _swig_property(_IMP_atom.CHARMMDihedralParameters_force_constant_get, _IMP_atom.CHARMMDihedralParameters_force_constant_set)
11547 multiplicity = _swig_property(_IMP_atom.CHARMMDihedralParameters_multiplicity_get, _IMP_atom.CHARMMDihedralParameters_multiplicity_set)
11548 ideal = _swig_property(_IMP_atom.CHARMMDihedralParameters_ideal_get, _IMP_atom.CHARMMDihedralParameters_ideal_set)
11550 def __init__(self):
11551 """__init__(IMP::atom::CHARMMDihedralParameters self) -> CHARMMDihedralParameters"""
11552 this = _IMP_atom.new_CHARMMDihedralParameters()
11554 self.this.append(this)
11558 def show(self, *args):
11560 show(CHARMMDihedralParameters self, _ostream out)
11561 show(CHARMMDihedralParameters self)
11563 return _IMP_atom.CHARMMDihedralParameters_show(self, *args)
11567 """__str__(CHARMMDihedralParameters self) -> std::string"""
11568 return _IMP_atom.CHARMMDihedralParameters___str__(self)
11571 def __repr__(self):
11572 """__repr__(CHARMMDihedralParameters self) -> std::string"""
11573 return _IMP_atom.CHARMMDihedralParameters___repr__(self)
11575 __swig_destroy__ = _IMP_atom.delete_CHARMMDihedralParameters
11576 __del__ =
lambda self:
None
11577 CHARMMDihedralParameters_swigregister = _IMP_atom.CHARMMDihedralParameters_swigregister
11578 CHARMMDihedralParameters_swigregister(CHARMMDihedralParameters)
11580 class CHARMMParameters(ForceFieldParameters):
11581 """Proxy of C++ IMP::atom::CHARMMParameters class"""
11582 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11584 def __init__(self, *args):
11586 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name, bool translate_names_to_pdb=False) -> CHARMMParameters
11587 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name, TextInput par_file_name) -> CHARMMParameters
11588 __init__(IMP::atom::CHARMMParameters self, TextInput topology_file_name) -> CHARMMParameters
11590 this = _IMP_atom.new_CHARMMParameters(*args)
11592 self.this.append(this)
11596 def add_residue_topology(self, res):
11597 """add_residue_topology(CHARMMParameters self, CHARMMIdealResidueTopology res)"""
11598 return _IMP_atom.CHARMMParameters_add_residue_topology(self, res)
11601 def get_residue_topology(self, type):
11602 """get_residue_topology(CHARMMParameters self, ResidueType type) -> CHARMMIdealResidueTopology"""
11603 return _IMP_atom.CHARMMParameters_get_residue_topology(self, type)
11606 def add_patch(self, patch):
11607 """add_patch(CHARMMParameters self, CHARMMPatch patch)"""
11608 return _IMP_atom.CHARMMParameters_add_patch(self, patch)
11611 def get_patch(self, name):
11612 """get_patch(CHARMMParameters self, std::string name) -> CHARMMPatch"""
11613 return _IMP_atom.CHARMMParameters_get_patch(self, name)
11616 def create_topology(self, hierarchy):
11617 """create_topology(CHARMMParameters self, Hierarchy hierarchy) -> CHARMMTopology"""
11618 return _IMP_atom.CHARMMParameters_create_topology(self, hierarchy)
11621 def get_bond_parameters(self, type1, type2):
11622 """get_bond_parameters(CHARMMParameters self, std::string type1, std::string type2) -> CHARMMBondParameters"""
11623 return _IMP_atom.CHARMMParameters_get_bond_parameters(self, type1, type2)
11626 def get_angle_parameters(self, type1, type2, type3):
11627 """get_angle_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3) -> CHARMMBondParameters"""
11628 return _IMP_atom.CHARMMParameters_get_angle_parameters(self, type1, type2, type3)
11631 def get_dihedral_parameters(self, type1, type2, type3, type4):
11632 """get_dihedral_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> IMP::atom::CHARMMDihedralParametersList"""
11633 return _IMP_atom.CHARMMParameters_get_dihedral_parameters(self, type1, type2, type3, type4)
11636 def get_improper_parameters(self, type1, type2, type3, type4):
11637 """get_improper_parameters(CHARMMParameters self, std::string type1, std::string type2, std::string type3, std::string type4) -> CHARMMDihedralParameters"""
11638 return _IMP_atom.CHARMMParameters_get_improper_parameters(self, type1, type2, type3, type4)
11641 def create_angles(self, bonds):
11642 """create_angles(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11643 return _IMP_atom.CHARMMParameters_create_angles(self, bonds)
11646 def create_dihedrals(self, bonds):
11647 """create_dihedrals(CHARMMParameters self, IMP::Particles bonds) -> IMP::Particles"""
11648 return _IMP_atom.CHARMMParameters_create_dihedrals(self, bonds)
11651 def get_version_info(self):
11652 """get_version_info(CHARMMParameters self) -> VersionInfo"""
11653 return _IMP_atom.CHARMMParameters_get_version_info(self)
11657 """__str__(CHARMMParameters self) -> std::string"""
11658 return _IMP_atom.CHARMMParameters___str__(self)
11661 def __repr__(self):
11662 """__repr__(CHARMMParameters self) -> std::string"""
11663 return _IMP_atom.CHARMMParameters___repr__(self)
11668 return _object_cast_to_CHARMMParameters(o)
11670 CHARMMParameters_swigregister = _IMP_atom.CHARMMParameters_swigregister
11671 CHARMMParameters_swigregister(CHARMMParameters)
11675 """get_heavy_atom_CHARMM_parameters() -> CHARMMParameters"""
11676 return _IMP_atom.get_heavy_atom_CHARMM_parameters()
11679 """get_all_atom_CHARMM_parameters() -> CHARMMParameters"""
11680 return _IMP_atom.get_all_atom_CHARMM_parameters()
11682 """Proxy of C++ IMP::atom::CHARMMSegmentTopology class"""
11683 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11685 def remove_residue(self, d):
11686 """remove_residue(CHARMMSegmentTopology self, CHARMMResidueTopology d)"""
11687 return _IMP_atom.CHARMMSegmentTopology_remove_residue(self, d)
11690 def remove_residues(self, d):
11691 """remove_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & d)"""
11692 return _IMP_atom.CHARMMSegmentTopology_remove_residues(self, d)
11695 def set_residues(self, ps):
11696 """set_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & ps)"""
11697 return _IMP_atom.CHARMMSegmentTopology_set_residues(self, ps)
11700 def set_residues_order(self, objs):
11701 """set_residues_order(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11702 return _IMP_atom.CHARMMSegmentTopology_set_residues_order(self, objs)
11705 def add_residue(self, obj):
11706 """add_residue(CHARMMSegmentTopology self, CHARMMResidueTopology obj) -> unsigned int"""
11707 return _IMP_atom.CHARMMSegmentTopology_add_residue(self, obj)
11710 def add_residues(self, objs):
11711 """add_residues(CHARMMSegmentTopology self, IMP::atom::CHARMMResidueTopologies const & objs)"""
11712 return _IMP_atom.CHARMMSegmentTopology_add_residues(self, objs)
11715 def clear_residues(self):
11716 """clear_residues(CHARMMSegmentTopology self)"""
11717 return _IMP_atom.CHARMMSegmentTopology_clear_residues(self)
11720 def get_number_of_residues(self):
11721 """get_number_of_residues(CHARMMSegmentTopology self) -> unsigned int"""
11722 return _IMP_atom.CHARMMSegmentTopology_get_number_of_residues(self)
11725 def get_has_residues(self):
11726 """get_has_residues(CHARMMSegmentTopology self) -> bool"""
11727 return _IMP_atom.CHARMMSegmentTopology_get_has_residues(self)
11731 """get_residue(CHARMMSegmentTopology self, unsigned int i) -> CHARMMResidueTopology"""
11732 return _IMP_atom.CHARMMSegmentTopology_get_residue(self, i)
11735 def get_residues(self):
11736 """get_residues(CHARMMSegmentTopology self) -> IMP::atom::CHARMMResidueTopologies"""
11737 return _IMP_atom.CHARMMSegmentTopology_get_residues(self)
11740 def reserve_residues(self, sz):
11741 """reserve_residues(CHARMMSegmentTopology self, unsigned int sz)"""
11742 return _IMP_atom.CHARMMSegmentTopology_reserve_residues(self, sz)
11745 def get_version_info(self):
11746 """get_version_info(CHARMMSegmentTopology self) -> VersionInfo"""
11747 return _IMP_atom.CHARMMSegmentTopology_get_version_info(self)
11750 def __init__(self, *args):
11752 __init__(IMP::atom::CHARMMSegmentTopology self, std::string name) -> CHARMMSegmentTopology
11753 __init__(IMP::atom::CHARMMSegmentTopology self) -> CHARMMSegmentTopology
11755 this = _IMP_atom.new_CHARMMSegmentTopology(*args)
11757 self.this.append(this)
11761 def apply_default_patches(self, ff):
11762 """apply_default_patches(CHARMMSegmentTopology self, CHARMMParameters ff)"""
11763 return _IMP_atom.CHARMMSegmentTopology_apply_default_patches(self, ff)
11767 """__str__(CHARMMSegmentTopology self) -> std::string"""
11768 return _IMP_atom.CHARMMSegmentTopology___str__(self)
11771 def __repr__(self):
11772 """__repr__(CHARMMSegmentTopology self) -> std::string"""
11773 return _IMP_atom.CHARMMSegmentTopology___repr__(self)
11778 return _object_cast_to_CHARMMSegmentTopology(o)
11780 CHARMMSegmentTopology_swigregister = _IMP_atom.CHARMMSegmentTopology_swigregister
11781 CHARMMSegmentTopology_swigregister(CHARMMSegmentTopology)
11784 """Proxy of C++ IMP::atom::CHARMMTopology class"""
11785 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11787 def __init__(self, *args):
11789 __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field, std::string name) -> CHARMMTopology
11790 __init__(IMP::atom::CHARMMTopology self, CHARMMParameters force_field) -> CHARMMTopology
11792 this = _IMP_atom.new_CHARMMTopology(*args)
11794 self.this.append(this)
11798 def get_parameters(self):
11799 """get_parameters(CHARMMTopology self) -> CHARMMParameters"""
11800 return _IMP_atom.CHARMMTopology_get_parameters(self)
11803 def add_sequence(self, sequence):
11804 """add_sequence(CHARMMTopology self, std::string sequence)"""
11805 return _IMP_atom.CHARMMTopology_add_sequence(self, sequence)
11808 def apply_default_patches(self):
11809 """apply_default_patches(CHARMMTopology self)"""
11810 return _IMP_atom.CHARMMTopology_apply_default_patches(self)
11813 def create_hierarchy(self, model):
11814 """create_hierarchy(CHARMMTopology self, Model model) -> Hierarchy"""
11815 return _IMP_atom.CHARMMTopology_create_hierarchy(self, model)
11818 def add_atom_types(self, hierarchy):
11819 """add_atom_types(CHARMMTopology self, Hierarchy hierarchy)"""
11820 return _IMP_atom.CHARMMTopology_add_atom_types(self, hierarchy)
11823 def add_coordinates(self, hierarchy):
11824 """add_coordinates(CHARMMTopology self, Hierarchy hierarchy)"""
11825 return _IMP_atom.CHARMMTopology_add_coordinates(self, hierarchy)
11828 def add_missing_atoms(self, hierarchy):
11829 """add_missing_atoms(CHARMMTopology self, Hierarchy hierarchy)"""
11830 return _IMP_atom.CHARMMTopology_add_missing_atoms(self, hierarchy)
11833 def setup_hierarchy(self, hierarchy):
11834 """setup_hierarchy(CHARMMTopology self, Hierarchy hierarchy)"""
11835 return _IMP_atom.CHARMMTopology_setup_hierarchy(self, hierarchy)
11838 def add_charges(self, hierarchy):
11839 """add_charges(CHARMMTopology self, Hierarchy hierarchy)"""
11840 return _IMP_atom.CHARMMTopology_add_charges(self, hierarchy)
11844 """add_bonds(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11845 return _IMP_atom.CHARMMTopology_add_bonds(self, hierarchy)
11848 def add_dihedrals(self, hierarchy):
11849 """add_dihedrals(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11850 return _IMP_atom.CHARMMTopology_add_dihedrals(self, hierarchy)
11853 def add_impropers(self, hierarchy):
11854 """add_impropers(CHARMMTopology self, Hierarchy hierarchy) -> IMP::Particles"""
11855 return _IMP_atom.CHARMMTopology_add_impropers(self, hierarchy)
11858 def remove_segment(self, d):
11859 """remove_segment(CHARMMTopology self, CHARMMSegmentTopology d)"""
11860 return _IMP_atom.CHARMMTopology_remove_segment(self, d)
11863 def remove_segments(self, d):
11864 """remove_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & d)"""
11865 return _IMP_atom.CHARMMTopology_remove_segments(self, d)
11868 def set_segments(self, ps):
11869 """set_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & ps)"""
11870 return _IMP_atom.CHARMMTopology_set_segments(self, ps)
11873 def set_segments_order(self, objs):
11874 """set_segments_order(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11875 return _IMP_atom.CHARMMTopology_set_segments_order(self, objs)
11878 def add_segment(self, obj):
11879 """add_segment(CHARMMTopology self, CHARMMSegmentTopology obj) -> unsigned int"""
11880 return _IMP_atom.CHARMMTopology_add_segment(self, obj)
11883 def add_segments(self, objs):
11884 """add_segments(CHARMMTopology self, IMP::atom::CHARMMSegmentTopologies const & objs)"""
11885 return _IMP_atom.CHARMMTopology_add_segments(self, objs)
11888 def clear_segments(self):
11889 """clear_segments(CHARMMTopology self)"""
11890 return _IMP_atom.CHARMMTopology_clear_segments(self)
11893 def get_number_of_segments(self):
11894 """get_number_of_segments(CHARMMTopology self) -> unsigned int"""
11895 return _IMP_atom.CHARMMTopology_get_number_of_segments(self)
11898 def get_has_segments(self):
11899 """get_has_segments(CHARMMTopology self) -> bool"""
11900 return _IMP_atom.CHARMMTopology_get_has_segments(self)
11904 """get_segment(CHARMMTopology self, unsigned int i) -> CHARMMSegmentTopology"""
11905 return _IMP_atom.CHARMMTopology_get_segment(self, i)
11908 def get_segments(self):
11909 """get_segments(CHARMMTopology self) -> IMP::atom::CHARMMSegmentTopologies"""
11910 return _IMP_atom.CHARMMTopology_get_segments(self)
11913 def reserve_segments(self, sz):
11914 """reserve_segments(CHARMMTopology self, unsigned int sz)"""
11915 return _IMP_atom.CHARMMTopology_reserve_segments(self, sz)
11918 def get_version_info(self):
11919 """get_version_info(CHARMMTopology self) -> VersionInfo"""
11920 return _IMP_atom.CHARMMTopology_get_version_info(self)
11924 """__str__(CHARMMTopology self) -> std::string"""
11925 return _IMP_atom.CHARMMTopology___str__(self)
11928 def __repr__(self):
11929 """__repr__(CHARMMTopology self) -> std::string"""
11930 return _IMP_atom.CHARMMTopology___repr__(self)
11935 return _object_cast_to_CHARMMTopology(o)
11937 CHARMMTopology_swigregister = _IMP_atom.CHARMMTopology_swigregister
11938 CHARMMTopology_swigregister(CHARMMTopology)
11941 """Proxy of C++ IMP::atom::CHARMMStereochemistryRestraint class"""
11942 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
11944 def __init__(self, *args):
11946 __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology) -> CHARMMStereochemistryRestraint
11947 __init__(IMP::atom::CHARMMStereochemistryRestraint self, Hierarchy h, CHARMMTopology topology, IMP::ParticlesTemp limit_to_these_particles) -> CHARMMStereochemistryRestraint
11949 this = _IMP_atom.new_CHARMMStereochemistryRestraint(*args)
11951 self.this.append(this)
11955 def get_pair_filter(self):
11956 """get_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11957 return _IMP_atom.CHARMMStereochemistryRestraint_get_pair_filter(self)
11960 def get_full_pair_filter(self):
11961 """get_full_pair_filter(CHARMMStereochemistryRestraint self) -> StereochemistryPairFilter"""
11962 return _IMP_atom.CHARMMStereochemistryRestraint_get_full_pair_filter(self)
11965 def do_get_inputs(self):
11966 """do_get_inputs(CHARMMStereochemistryRestraint self) -> IMP::ModelObjectsTemp"""
11967 return _IMP_atom.CHARMMStereochemistryRestraint_do_get_inputs(self)
11970 def get_version_info(self):
11971 """get_version_info(CHARMMStereochemistryRestraint self) -> VersionInfo"""
11972 return _IMP_atom.CHARMMStereochemistryRestraint_get_version_info(self)
11976 """__str__(CHARMMStereochemistryRestraint self) -> std::string"""
11977 return _IMP_atom.CHARMMStereochemistryRestraint___str__(self)
11980 def __repr__(self):
11981 """__repr__(CHARMMStereochemistryRestraint self) -> std::string"""
11982 return _IMP_atom.CHARMMStereochemistryRestraint___repr__(self)
11987 return _object_cast_to_CHARMMStereochemistryRestraint(o)
11989 CHARMMStereochemistryRestraint_swigregister = _IMP_atom.CHARMMStereochemistryRestraint_swigregister
11990 CHARMMStereochemistryRestraint_swigregister(CHARMMStereochemistryRestraint)
11995 add_bonds(Hierarchy d, ForceFieldParameters ffp)
11996 add_bonds(Hierarchy d)
11998 return _IMP_atom.add_bonds(*args)
12002 add_radii(Hierarchy d, ForceFieldParameters ffp, FloatKey radius_key)
12003 add_radii(Hierarchy d, ForceFieldParameters ffp)
12004 add_radii(Hierarchy d)
12006 return _IMP_atom.add_radii(*args)
12008 _IMP_atom.ALBER_swigconstant(_IMP_atom)
12009 ALBER = _IMP_atom.ALBER
12011 _IMP_atom.HARPAZ_swigconstant(_IMP_atom)
12012 HARPAZ = _IMP_atom.HARPAZ
12014 _IMP_atom.ANDERSSON_swigconstant(_IMP_atom)
12015 ANDERSSON = _IMP_atom.ANDERSSON
12017 _IMP_atom.TSAI_swigconstant(_IMP_atom)
12018 TSAI = _IMP_atom.TSAI
12020 _IMP_atom.QUILLIN_swigconstant(_IMP_atom)
12021 QUILLIN = _IMP_atom.QUILLIN
12023 _IMP_atom.SQUIRE_swigconstant(_IMP_atom)
12024 SQUIRE = _IMP_atom.SQUIRE
12027 """get_protein_density_from_reference(IMP::atom::ProteinDensityReference densityReference) -> double"""
12028 return _IMP_atom.get_protein_density_from_reference(densityReference)
12032 get_volume_from_mass(double m, IMP::atom::ProteinDensityReference ref) -> double
12033 get_volume_from_mass(double m) -> double
12035 return _IMP_atom.get_volume_from_mass(*args)
12039 get_mass_from_volume(double v, IMP::atom::ProteinDensityReference ref) -> double
12040 get_mass_from_volume(double v) -> double
12042 return _IMP_atom.get_mass_from_volume(*args)
12045 """get_mass_from_number_of_residues(unsigned int num_aa) -> double"""
12046 return _IMP_atom.get_mass_from_number_of_residues(num_aa)
12049 """get_volume_from_residue_type(ResidueType rt) -> double"""
12050 return _IMP_atom.get_volume_from_residue_type(rt)
12053 """get_molarity(double n, double volume) -> double"""
12054 return _IMP_atom.get_molarity(n, volume)
12056 def get_kd(na, nb, nab, volume):
12057 """get_kd(double na, double nb, double nab, double volume) -> double"""
12058 return _IMP_atom.get_kd(na, nb, nab, volume)
12061 """get_einstein_diffusion_coefficient(double r) -> double"""
12062 return _IMP_atom.get_einstein_diffusion_coefficient(r)
12065 """get_einstein_rotational_diffusion_coefficient(double r) -> double"""
12066 return _IMP_atom.get_einstein_rotational_diffusion_coefficient(r)
12070 get_diffusion_length(double D, double t) -> double
12071 get_diffusion_length(double D, double force, double t, double temp=273) -> double
12072 get_diffusion_length(double D, double force, double t) -> double
12074 return _IMP_atom.get_diffusion_length(*args)
12077 """get_diffusion_angle(double D, double dtfs) -> double"""
12078 return _IMP_atom.get_diffusion_angle(D, dtfs)
12081 """get_diffusion_coefficient(IMP::algebra::Vector3Ds const & displacements, double dt) -> double"""
12082 return _IMP_atom.get_diffusion_coefficient(displacements, dt)
12085 """get_rotational_diffusion_coefficient(IMP::algebra::Rotation3Ds const & displacements, double dt) -> double"""
12086 return _IMP_atom.get_rotational_diffusion_coefficient(displacements, dt)
12088 """Proxy of C++ IMP::atom::EzRestraint class"""
12089 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12091 def __init__(self, m, ps):
12092 """__init__(IMP::atom::EzRestraint self, Model m, _ParticleIndexesAdaptor ps) -> EzRestraint"""
12093 this = _IMP_atom.new_EzRestraint(m, ps)
12095 self.this.append(this)
12099 def get_version_info(self):
12100 """get_version_info(EzRestraint self) -> VersionInfo"""
12101 return _IMP_atom.EzRestraint_get_version_info(self)
12105 """__str__(EzRestraint self) -> std::string"""
12106 return _IMP_atom.EzRestraint___str__(self)
12109 def __repr__(self):
12110 """__repr__(EzRestraint self) -> std::string"""
12111 return _IMP_atom.EzRestraint___repr__(self)
12116 return _object_cast_to_EzRestraint(o)
12118 EzRestraint_swigregister = _IMP_atom.EzRestraint_swigregister
12119 EzRestraint_swigregister(EzRestraint)
12124 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1, bool ismol=True) -> Hierarchy
12125 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1) -> Hierarchy
12126 create_protein(Model m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0) -> Hierarchy
12127 create_protein(Model m, std::string name, double target_radius, int number_of_residues) -> Hierarchy
12128 create_protein(Model m, std::string name, double target_radius, IMP::Ints const domain_boundaries) -> Hierarchy
12130 return _IMP_atom.create_protein(*args)
12134 create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=False) -> Hierarchy
12135 create_simplified_along_backbone(Hierarchy input, int num_res) -> Hierarchy
12136 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments, bool keep_detailed=False) -> Hierarchy
12137 create_simplified_along_backbone(Chain input, IMP::IntRanges const & residue_segments) -> Hierarchy
12139 return _IMP_atom.create_simplified_along_backbone(*args)
12142 """create_simplified_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12143 return _IMP_atom.create_simplified_from_volume(h, resolution)
12146 """create_simplified_assembly_from_volume(Hierarchy h, double resolution) -> Hierarchy"""
12147 return _IMP_atom.create_simplified_assembly_from_volume(h, resolution)
12149 def get_residue_indexes(h):
12150 """get_residue_indexes(Hierarchy h) -> IMP::Ints"""
12151 return _IMP_atom.get_residue_indexes(h)
12153 def get_residue_type(*args):
12155 get_residue_type(char c) -> ResidueType
12156 get_residue_type(Hierarchy h) -> ResidueType
12158 return _IMP_atom.get_residue_type(*args)
12160 def get_atom_type(h):
12161 """get_atom_type(Hierarchy h) -> AtomType"""
12162 return _IMP_atom.get_atom_type(h)
12164 def get_domain_name(h):
12165 """get_domain_name(Hierarchy h) -> std::string"""
12166 return _IMP_atom.get_domain_name(h)
12170 create_excluded_volume_restraint(IMP::atom::Selections const & s) -> Restraint
12171 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs, double resolution=-1) -> Restraint
12172 create_excluded_volume_restraint(IMP::atom::Hierarchies const & hs) -> Restraint
12174 return _IMP_atom.create_excluded_volume_restraint(*args)
12178 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other, double resolution=-1)
12179 setup_as_approximation(Particle h, IMP::ParticlesTemp const & other)
12180 setup_as_approximation(Hierarchy h, double resolution=-1)
12181 setup_as_approximation(Hierarchy h)
12183 return _IMP_atom.setup_as_approximation(*args)
12184 class _HierarchyTreeVertexIndex(object):
12185 """Proxy of C++ IMP::atom::HierarchyTreeVertexIndex class"""
12186 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12187 __repr__ = _swig_repr
12189 def __init__(self):
12190 """__init__(IMP::atom::HierarchyTreeVertexIndex self) -> _HierarchyTreeVertexIndex"""
12191 this = _IMP_atom.new__HierarchyTreeVertexIndex()
12193 self.this.append(this)
12196 __swig_destroy__ = _IMP_atom.delete__HierarchyTreeVertexIndex
12197 __del__ =
lambda self:
None
12198 _HierarchyTreeVertexIndex_swigregister = _IMP_atom._HierarchyTreeVertexIndex_swigregister
12199 _HierarchyTreeVertexIndex_swigregister(_HierarchyTreeVertexIndex)
12202 def show_as_graphviz(name, out):
12203 """show_as_graphviz(IMP::atom::HierarchyTree const & name, TextOutput out)"""
12204 return _IMP_atom.show_as_graphviz(name, out)
12206 def get_vertex_index(g):
12207 """get_vertex_index(IMP::atom::HierarchyTree const & g) -> _HierarchyTreeVertexIndex"""
12208 return _IMP_atom.get_vertex_index(g)
12211 """get_hierarchy_tree(Hierarchy h) -> IMP::atom::HierarchyTree"""
12212 return _IMP_atom.get_hierarchy_tree(h)
12214 """Proxy of C++ IMP::atom::HierarchyGeometry class"""
12215 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12217 def __init__(self, d, resolution=0):
12219 __init__(IMP::atom::HierarchyGeometry self, Hierarchy d, double resolution=0) -> HierarchyGeometry
12220 __init__(IMP::atom::HierarchyGeometry self, Hierarchy d) -> HierarchyGeometry
12222 this = _IMP_atom.new_HierarchyGeometry(d, resolution)
12224 self.this.append(this)
12228 def get_version_info(self):
12229 """get_version_info(HierarchyGeometry self) -> VersionInfo"""
12230 return _IMP_atom.HierarchyGeometry_get_version_info(self)
12234 """__str__(HierarchyGeometry self) -> std::string"""
12235 return _IMP_atom.HierarchyGeometry___str__(self)
12238 def __repr__(self):
12239 """__repr__(HierarchyGeometry self) -> std::string"""
12240 return _IMP_atom.HierarchyGeometry___repr__(self)
12245 return _object_cast_to_HierarchyGeometry(o)
12247 HierarchyGeometry_swigregister = _IMP_atom.HierarchyGeometry_swigregister
12248 HierarchyGeometry_swigregister(HierarchyGeometry)
12251 """Proxy of C++ IMP::atom::HierarchiesGeometry class"""
12252 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12254 def __init__(self, sc, resolution=-1):
12256 __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc, double resolution=-1) -> HierarchiesGeometry
12257 __init__(IMP::atom::HierarchiesGeometry self, SingletonContainer sc) -> HierarchiesGeometry
12259 this = _IMP_atom.new_HierarchiesGeometry(sc, resolution)
12261 self.this.append(this)
12265 def get_version_info(self):
12266 """get_version_info(HierarchiesGeometry self) -> VersionInfo"""
12267 return _IMP_atom.HierarchiesGeometry_get_version_info(self)
12271 """__str__(HierarchiesGeometry self) -> std::string"""
12272 return _IMP_atom.HierarchiesGeometry___str__(self)
12275 def __repr__(self):
12276 """__repr__(HierarchiesGeometry self) -> std::string"""
12277 return _IMP_atom.HierarchiesGeometry___repr__(self)
12282 return _object_cast_to_HierarchiesGeometry(o)
12284 HierarchiesGeometry_swigregister = _IMP_atom.HierarchiesGeometry_swigregister
12285 HierarchiesGeometry_swigregister(HierarchiesGeometry)
12290 transform(Hierarchy h, Transformation3D tr)
12291 transform(Hierarchy h, Transformation3D tr)
12293 return _IMP_atom.transform(*args)
12294 class DopePairScore(_ADopeBase):
12295 """Proxy of C++ IMP::atom::DopePairScore class"""
12296 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12298 def __init__(self, *args):
12300 __init__(IMP::atom::DopePairScore self, double threshold) -> DopePairScore
12301 __init__(IMP::atom::DopePairScore self) -> DopePairScore
12302 __init__(IMP::atom::DopePairScore self, double threshold, TextInput data_file) -> DopePairScore
12304 this = _IMP_atom.new_DopePairScore(*args)
12306 self.this.append(this)
12311 """__str__(DopePairScore self) -> std::string"""
12312 return _IMP_atom.DopePairScore___str__(self)
12315 def __repr__(self):
12316 """__repr__(DopePairScore self) -> std::string"""
12317 return _IMP_atom.DopePairScore___repr__(self)
12322 return _object_cast_to_DopePairScore(o)
12324 __swig_destroy__ = _IMP_atom.delete_DopePairScore
12325 __del__ =
lambda self:
None
12326 DopePairScore_swigregister = _IMP_atom.DopePairScore_swigregister
12327 DopePairScore_swigregister(DopePairScore)
12331 """add_dope_score_data(Hierarchy h)"""
12332 return _IMP_atom.add_dope_score_data(h)
12333 class OrientedSoapPairScore(_OrientedSoapBase):
12334 """Proxy of C++ IMP::atom::OrientedSoapPairScore class"""
12335 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12337 def __init__(self, library):
12338 """__init__(IMP::atom::OrientedSoapPairScore self, std::string library) -> OrientedSoapPairScore"""
12339 this = _IMP_atom.new_OrientedSoapPairScore(library)
12341 self.this.append(this)
12345 def get_pair_filter(self):
12346 """get_pair_filter(OrientedSoapPairScore self) -> SoapPairFilter"""
12347 return _IMP_atom.OrientedSoapPairScore_get_pair_filter(self)
12351 """__str__(OrientedSoapPairScore self) -> std::string"""
12352 return _IMP_atom.OrientedSoapPairScore___str__(self)
12355 def __repr__(self):
12356 """__repr__(OrientedSoapPairScore self) -> std::string"""
12357 return _IMP_atom.OrientedSoapPairScore___repr__(self)
12362 return _object_cast_to_OrientedSoapPairScore(o)
12364 __swig_destroy__ = _IMP_atom.delete_OrientedSoapPairScore
12365 __del__ =
lambda self:
None
12366 OrientedSoapPairScore_swigregister = _IMP_atom.OrientedSoapPairScore_swigregister
12367 OrientedSoapPairScore_swigregister(OrientedSoapPairScore)
12370 """Proxy of C++ IMP::atom::SameResiduePairFilter class"""
12371 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12373 def __init__(self):
12374 """__init__(IMP::atom::SameResiduePairFilter self) -> SameResiduePairFilter"""
12375 this = _IMP_atom.new_SameResiduePairFilter()
12377 self.this.append(this)
12381 def do_get_inputs(self, m, pis):
12382 """do_get_inputs(SameResiduePairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
12383 return _IMP_atom.SameResiduePairFilter_do_get_inputs(self, m, pis)
12386 def get_value(self, *args):
12388 get_value(SameResiduePairFilter self, IMP::ParticlePair const & a) -> int
12389 get_value(SameResiduePairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
12391 return _IMP_atom.SameResiduePairFilter_get_value(self, *args)
12394 def get_value_index(self, *args):
12396 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
12397 get_value_index(SameResiduePairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
12399 return _IMP_atom.SameResiduePairFilter_get_value_index(self, *args)
12402 def get_version_info(self):
12403 """get_version_info(SameResiduePairFilter self) -> VersionInfo"""
12404 return _IMP_atom.SameResiduePairFilter_get_version_info(self)
12408 """__str__(SameResiduePairFilter self) -> std::string"""
12409 return _IMP_atom.SameResiduePairFilter___str__(self)
12412 def __repr__(self):
12413 """__repr__(SameResiduePairFilter self) -> std::string"""
12414 return _IMP_atom.SameResiduePairFilter___repr__(self)
12419 return _object_cast_to_SameResiduePairFilter(o)
12421 SameResiduePairFilter_swigregister = _IMP_atom.SameResiduePairFilter_swigregister
12422 SameResiduePairFilter_swigregister(SameResiduePairFilter)
12425 """Proxy of C++ IMP::atom::RemoveRigidMotionOptimizerState class"""
12426 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12428 def __init__(self, m, pis):
12429 """__init__(IMP::atom::RemoveRigidMotionOptimizerState self, Model m, _ParticleIndexesAdaptor pis) -> RemoveRigidMotionOptimizerState"""
12430 this = _IMP_atom.new_RemoveRigidMotionOptimizerState(m, pis)
12432 self.this.append(this)
12436 def set_particles(self, pis):
12437 """set_particles(RemoveRigidMotionOptimizerState self, IMP::Particles const & pis)"""
12438 return _IMP_atom.RemoveRigidMotionOptimizerState_set_particles(self, pis)
12441 def remove_rigid_motion(self):
12442 """remove_rigid_motion(RemoveRigidMotionOptimizerState self)"""
12443 return _IMP_atom.RemoveRigidMotionOptimizerState_remove_rigid_motion(self)
12446 def get_version_info(self):
12447 """get_version_info(RemoveRigidMotionOptimizerState self) -> VersionInfo"""
12448 return _IMP_atom.RemoveRigidMotionOptimizerState_get_version_info(self)
12452 """__str__(RemoveRigidMotionOptimizerState self) -> std::string"""
12453 return _IMP_atom.RemoveRigidMotionOptimizerState___str__(self)
12456 def __repr__(self):
12457 """__repr__(RemoveRigidMotionOptimizerState self) -> std::string"""
12458 return _IMP_atom.RemoveRigidMotionOptimizerState___repr__(self)
12463 return _object_cast_to_RemoveRigidMotionOptimizerState(o)
12465 RemoveRigidMotionOptimizerState_swigregister = _IMP_atom.RemoveRigidMotionOptimizerState_swigregister
12466 RemoveRigidMotionOptimizerState_swigregister(RemoveRigidMotionOptimizerState)
12469 """Proxy of C++ IMP::atom::BerendsenThermostatOptimizerState class"""
12470 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12472 def __init__(self, pis, temperature, tau):
12473 """__init__(IMP::atom::BerendsenThermostatOptimizerState self, IMP::Particles const & pis, double temperature, double tau) -> BerendsenThermostatOptimizerState"""
12474 this = _IMP_atom.new_BerendsenThermostatOptimizerState(pis, temperature, tau)
12476 self.this.append(this)
12480 def set_particles(self, pis):
12481 """set_particles(BerendsenThermostatOptimizerState self, IMP::Particles const & pis)"""
12482 return _IMP_atom.BerendsenThermostatOptimizerState_set_particles(self, pis)
12485 def get_temperature(self):
12486 """get_temperature(BerendsenThermostatOptimizerState self) -> double"""
12487 return _IMP_atom.BerendsenThermostatOptimizerState_get_temperature(self)
12491 """get_tau(BerendsenThermostatOptimizerState self) -> double"""
12492 return _IMP_atom.BerendsenThermostatOptimizerState_get_tau(self)
12495 def set_temperature(self, temperature):
12496 """set_temperature(BerendsenThermostatOptimizerState self, double temperature)"""
12497 return _IMP_atom.BerendsenThermostatOptimizerState_set_temperature(self, temperature)
12500 def set_tau(self, tau):
12501 """set_tau(BerendsenThermostatOptimizerState self, double tau)"""
12502 return _IMP_atom.BerendsenThermostatOptimizerState_set_tau(self, tau)
12505 def rescale_velocities(self):
12506 """rescale_velocities(BerendsenThermostatOptimizerState self)"""
12507 return _IMP_atom.BerendsenThermostatOptimizerState_rescale_velocities(self)
12510 def get_version_info(self):
12511 """get_version_info(BerendsenThermostatOptimizerState self) -> VersionInfo"""
12512 return _IMP_atom.BerendsenThermostatOptimizerState_get_version_info(self)
12516 """__str__(BerendsenThermostatOptimizerState self) -> std::string"""
12517 return _IMP_atom.BerendsenThermostatOptimizerState___str__(self)
12520 def __repr__(self):
12521 """__repr__(BerendsenThermostatOptimizerState self) -> std::string"""
12522 return _IMP_atom.BerendsenThermostatOptimizerState___repr__(self)
12527 return _object_cast_to_BerendsenThermostatOptimizerState(o)
12529 BerendsenThermostatOptimizerState_swigregister = _IMP_atom.BerendsenThermostatOptimizerState_swigregister
12530 BerendsenThermostatOptimizerState_swigregister(BerendsenThermostatOptimizerState)
12533 """Proxy of C++ IMP::atom::LangevinThermostatOptimizerState class"""
12534 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12536 def __init__(self, m, pis, temperature, gamma):
12537 """__init__(IMP::atom::LangevinThermostatOptimizerState self, Model m, _ParticleIndexesAdaptor pis, double temperature, double gamma) -> LangevinThermostatOptimizerState"""
12538 this = _IMP_atom.new_LangevinThermostatOptimizerState(m, pis, temperature, gamma)
12540 self.this.append(this)
12544 def set_particles(self, pis):
12545 """set_particles(LangevinThermostatOptimizerState self, IMP::Particles const & pis)"""
12546 return _IMP_atom.LangevinThermostatOptimizerState_set_particles(self, pis)
12549 def get_temperature(self):
12550 """get_temperature(LangevinThermostatOptimizerState self) -> double"""
12551 return _IMP_atom.LangevinThermostatOptimizerState_get_temperature(self)
12554 def get_gamma(self):
12555 """get_gamma(LangevinThermostatOptimizerState self) -> double"""
12556 return _IMP_atom.LangevinThermostatOptimizerState_get_gamma(self)
12559 def set_temperature(self, temperature):
12560 """set_temperature(LangevinThermostatOptimizerState self, double temperature)"""
12561 return _IMP_atom.LangevinThermostatOptimizerState_set_temperature(self, temperature)
12564 def set_gamma(self, gamma):
12565 """set_gamma(LangevinThermostatOptimizerState self, double gamma)"""
12566 return _IMP_atom.LangevinThermostatOptimizerState_set_gamma(self, gamma)
12569 def rescale_velocities(self):
12570 """rescale_velocities(LangevinThermostatOptimizerState self)"""
12571 return _IMP_atom.LangevinThermostatOptimizerState_rescale_velocities(self)
12574 def get_version_info(self):
12575 """get_version_info(LangevinThermostatOptimizerState self) -> VersionInfo"""
12576 return _IMP_atom.LangevinThermostatOptimizerState_get_version_info(self)
12580 """__str__(LangevinThermostatOptimizerState self) -> std::string"""
12581 return _IMP_atom.LangevinThermostatOptimizerState___str__(self)
12584 def __repr__(self):
12585 """__repr__(LangevinThermostatOptimizerState self) -> std::string"""
12586 return _IMP_atom.LangevinThermostatOptimizerState___repr__(self)
12591 return _object_cast_to_LangevinThermostatOptimizerState(o)
12593 LangevinThermostatOptimizerState_swigregister = _IMP_atom.LangevinThermostatOptimizerState_swigregister
12594 LangevinThermostatOptimizerState_swigregister(LangevinThermostatOptimizerState)
12597 """Proxy of C++ IMP::atom::PDBSelector class"""
12598 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12600 def __init__(self, name):
12601 """__init__(IMP::atom::PDBSelector self, std::string name) -> PDBSelector"""
12602 if self.__class__ == PDBSelector:
12606 this = _IMP_atom.new_PDBSelector(_self, name)
12608 self.this.append(this)
12612 if self.__class__ != PDBSelector:
12613 _director_objects.register(self)
12618 def get_is_selected(self, pdb_line):
12619 """get_is_selected(PDBSelector self, std::string const & pdb_line) -> bool"""
12620 return _IMP_atom.PDBSelector_get_is_selected(self, pdb_line)
12622 __swig_destroy__ = _IMP_atom.delete_PDBSelector
12623 __del__ =
lambda self:
None
12626 """__str__(PDBSelector self) -> std::string"""
12627 return _IMP_atom.PDBSelector___str__(self)
12630 def __repr__(self):
12631 """__repr__(PDBSelector self) -> std::string"""
12632 return _IMP_atom.PDBSelector___repr__(self)
12637 return _object_cast_to_PDBSelector(o)
12640 def get_type_name(self):
12641 return self.__class__.__name__
12642 def do_show(self, out):
12644 def get_version_info(self):
12645 if"IMP::atom" ==
"IMP":
12646 return VersionInfo(self.__module__,
12647 __import__(self.__module__).get_module_version())
12650 __import__(self.__module__).get_module_version())
12653 return _object_cast_to_PDBSelector(o)
12656 def __and__(self, s):
12657 return AndPDBSelector(self, s)
12658 def __or__(self, s):
12659 return OrPDBSelector(self, s)
12660 def __xor__(self, s):
12661 return XorPDBSelector(self, s)
12662 def __invert__(self):
12663 return NotPDBSelector(self)
12664 def __sub__(self, s):
12665 return AndPDBSelector(self, NotPDBSelector(s))
12667 def __disown__(self):
12669 _IMP_atom.disown_PDBSelector(self)
12670 return weakref_proxy(self)
12672 def do_destroy(self):
12673 """do_destroy(PDBSelector self)"""
12674 return _IMP_atom.PDBSelector_do_destroy(self)
12676 PDBSelector_swigregister = _IMP_atom.PDBSelector_swigregister
12677 PDBSelector_swigregister(PDBSelector)
12679 class NonAlternativePDBSelector(PDBSelector):
12680 """Proxy of C++ IMP::atom::NonAlternativePDBSelector class"""
12681 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12683 def __init__(self, *args):
12685 __init__(IMP::atom::NonAlternativePDBSelector self, std::string name) -> NonAlternativePDBSelector
12686 __init__(IMP::atom::NonAlternativePDBSelector self) -> NonAlternativePDBSelector
12688 this = _IMP_atom.new_NonAlternativePDBSelector(*args)
12690 self.this.append(this)
12694 def get_version_info(self):
12695 """get_version_info(NonAlternativePDBSelector self) -> VersionInfo"""
12696 return _IMP_atom.NonAlternativePDBSelector_get_version_info(self)
12700 """__str__(NonAlternativePDBSelector self) -> std::string"""
12701 return _IMP_atom.NonAlternativePDBSelector___str__(self)
12704 def __repr__(self):
12705 """__repr__(NonAlternativePDBSelector self) -> std::string"""
12706 return _IMP_atom.NonAlternativePDBSelector___repr__(self)
12711 return _object_cast_to_NonAlternativePDBSelector(o)
12713 NonAlternativePDBSelector_swigregister = _IMP_atom.NonAlternativePDBSelector_swigregister
12714 NonAlternativePDBSelector_swigregister(NonAlternativePDBSelector)
12716 class ATOMPDBSelector(NonAlternativePDBSelector):
12717 """Proxy of C++ IMP::atom::ATOMPDBSelector class"""
12718 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12720 def __init__(self, *args):
12722 __init__(IMP::atom::ATOMPDBSelector self, std::string name) -> ATOMPDBSelector
12723 __init__(IMP::atom::ATOMPDBSelector self) -> ATOMPDBSelector
12725 this = _IMP_atom.new_ATOMPDBSelector(*args)
12727 self.this.append(this)
12732 """__str__(ATOMPDBSelector self) -> std::string"""
12733 return _IMP_atom.ATOMPDBSelector___str__(self)
12736 def __repr__(self):
12737 """__repr__(ATOMPDBSelector self) -> std::string"""
12738 return _IMP_atom.ATOMPDBSelector___repr__(self)
12743 return _object_cast_to_ATOMPDBSelector(o)
12745 ATOMPDBSelector_swigregister = _IMP_atom.ATOMPDBSelector_swigregister
12746 ATOMPDBSelector_swigregister(ATOMPDBSelector)
12748 class CAlphaPDBSelector(NonAlternativePDBSelector):
12749 """Proxy of C++ IMP::atom::CAlphaPDBSelector class"""
12750 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12752 def __init__(self, *args):
12754 __init__(IMP::atom::CAlphaPDBSelector self, std::string name) -> CAlphaPDBSelector
12755 __init__(IMP::atom::CAlphaPDBSelector self) -> CAlphaPDBSelector
12757 this = _IMP_atom.new_CAlphaPDBSelector(*args)
12759 self.this.append(this)
12764 """__str__(CAlphaPDBSelector self) -> std::string"""
12765 return _IMP_atom.CAlphaPDBSelector___str__(self)
12768 def __repr__(self):
12769 """__repr__(CAlphaPDBSelector self) -> std::string"""
12770 return _IMP_atom.CAlphaPDBSelector___repr__(self)
12775 return _object_cast_to_CAlphaPDBSelector(o)
12777 CAlphaPDBSelector_swigregister = _IMP_atom.CAlphaPDBSelector_swigregister
12778 CAlphaPDBSelector_swigregister(CAlphaPDBSelector)
12780 class CBetaPDBSelector(NonAlternativePDBSelector):
12781 """Proxy of C++ IMP::atom::CBetaPDBSelector class"""
12782 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12784 def __init__(self, *args):
12786 __init__(IMP::atom::CBetaPDBSelector self, std::string name) -> CBetaPDBSelector
12787 __init__(IMP::atom::CBetaPDBSelector self) -> CBetaPDBSelector
12789 this = _IMP_atom.new_CBetaPDBSelector(*args)
12791 self.this.append(this)
12796 """__str__(CBetaPDBSelector self) -> std::string"""
12797 return _IMP_atom.CBetaPDBSelector___str__(self)
12800 def __repr__(self):
12801 """__repr__(CBetaPDBSelector self) -> std::string"""
12802 return _IMP_atom.CBetaPDBSelector___repr__(self)
12807 return _object_cast_to_CBetaPDBSelector(o)
12809 CBetaPDBSelector_swigregister = _IMP_atom.CBetaPDBSelector_swigregister
12810 CBetaPDBSelector_swigregister(CBetaPDBSelector)
12812 class AtomTypePDBSelector(PDBSelector):
12813 """Proxy of C++ IMP::atom::AtomTypePDBSelector class"""
12814 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12816 def __init__(self, *args):
12818 __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types, std::string name) -> AtomTypePDBSelector
12819 __init__(IMP::atom::AtomTypePDBSelector self, IMP::Strings atom_types) -> AtomTypePDBSelector
12821 this = _IMP_atom.new_AtomTypePDBSelector(*args)
12823 self.this.append(this)
12827 def get_version_info(self):
12828 """get_version_info(AtomTypePDBSelector self) -> VersionInfo"""
12829 return _IMP_atom.AtomTypePDBSelector_get_version_info(self)
12833 """__str__(AtomTypePDBSelector self) -> std::string"""
12834 return _IMP_atom.AtomTypePDBSelector___str__(self)
12837 def __repr__(self):
12838 """__repr__(AtomTypePDBSelector self) -> std::string"""
12839 return _IMP_atom.AtomTypePDBSelector___repr__(self)
12844 return _object_cast_to_AtomTypePDBSelector(o)
12846 AtomTypePDBSelector_swigregister = _IMP_atom.AtomTypePDBSelector_swigregister
12847 AtomTypePDBSelector_swigregister(AtomTypePDBSelector)
12849 class ResidueTypePDBSelector(PDBSelector):
12850 """Proxy of C++ IMP::atom::ResidueTypePDBSelector class"""
12851 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12853 def __init__(self, *args):
12855 __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types, std::string name) -> ResidueTypePDBSelector
12856 __init__(IMP::atom::ResidueTypePDBSelector self, IMP::Strings residue_types) -> ResidueTypePDBSelector
12858 this = _IMP_atom.new_ResidueTypePDBSelector(*args)
12860 self.this.append(this)
12864 def get_version_info(self):
12865 """get_version_info(ResidueTypePDBSelector self) -> VersionInfo"""
12866 return _IMP_atom.ResidueTypePDBSelector_get_version_info(self)
12870 """__str__(ResidueTypePDBSelector self) -> std::string"""
12871 return _IMP_atom.ResidueTypePDBSelector___str__(self)
12874 def __repr__(self):
12875 """__repr__(ResidueTypePDBSelector self) -> std::string"""
12876 return _IMP_atom.ResidueTypePDBSelector___repr__(self)
12881 return _object_cast_to_ResidueTypePDBSelector(o)
12883 ResidueTypePDBSelector_swigregister = _IMP_atom.ResidueTypePDBSelector_swigregister
12884 ResidueTypePDBSelector_swigregister(ResidueTypePDBSelector)
12886 class CPDBSelector(NonAlternativePDBSelector):
12887 """Proxy of C++ IMP::atom::CPDBSelector class"""
12888 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12890 def __init__(self, *args):
12892 __init__(IMP::atom::CPDBSelector self, std::string name) -> CPDBSelector
12893 __init__(IMP::atom::CPDBSelector self) -> CPDBSelector
12895 this = _IMP_atom.new_CPDBSelector(*args)
12897 self.this.append(this)
12902 """__str__(CPDBSelector self) -> std::string"""
12903 return _IMP_atom.CPDBSelector___str__(self)
12906 def __repr__(self):
12907 """__repr__(CPDBSelector self) -> std::string"""
12908 return _IMP_atom.CPDBSelector___repr__(self)
12913 return _object_cast_to_CPDBSelector(o)
12915 CPDBSelector_swigregister = _IMP_atom.CPDBSelector_swigregister
12916 CPDBSelector_swigregister(CPDBSelector)
12918 class NPDBSelector(NonAlternativePDBSelector):
12919 """Proxy of C++ IMP::atom::NPDBSelector class"""
12920 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12922 def __init__(self, *args):
12924 __init__(IMP::atom::NPDBSelector self, std::string name) -> NPDBSelector
12925 __init__(IMP::atom::NPDBSelector self) -> NPDBSelector
12927 this = _IMP_atom.new_NPDBSelector(*args)
12929 self.this.append(this)
12934 """__str__(NPDBSelector self) -> std::string"""
12935 return _IMP_atom.NPDBSelector___str__(self)
12938 def __repr__(self):
12939 """__repr__(NPDBSelector self) -> std::string"""
12940 return _IMP_atom.NPDBSelector___repr__(self)
12945 return _object_cast_to_NPDBSelector(o)
12947 NPDBSelector_swigregister = _IMP_atom.NPDBSelector_swigregister
12948 NPDBSelector_swigregister(NPDBSelector)
12950 class AllPDBSelector(PDBSelector):
12951 """Proxy of C++ IMP::atom::AllPDBSelector class"""
12952 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12954 def __init__(self, *args):
12956 __init__(IMP::atom::AllPDBSelector self, std::string name) -> AllPDBSelector
12957 __init__(IMP::atom::AllPDBSelector self) -> AllPDBSelector
12959 this = _IMP_atom.new_AllPDBSelector(*args)
12961 self.this.append(this)
12965 def get_version_info(self):
12966 """get_version_info(AllPDBSelector self) -> VersionInfo"""
12967 return _IMP_atom.AllPDBSelector_get_version_info(self)
12971 """__str__(AllPDBSelector self) -> std::string"""
12972 return _IMP_atom.AllPDBSelector___str__(self)
12975 def __repr__(self):
12976 """__repr__(AllPDBSelector self) -> std::string"""
12977 return _IMP_atom.AllPDBSelector___repr__(self)
12982 return _object_cast_to_AllPDBSelector(o)
12984 AllPDBSelector_swigregister = _IMP_atom.AllPDBSelector_swigregister
12985 AllPDBSelector_swigregister(AllPDBSelector)
12987 class ChainPDBSelector(NonAlternativePDBSelector):
12988 """Proxy of C++ IMP::atom::ChainPDBSelector class"""
12989 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
12991 def __init__(self, *args):
12993 __init__(IMP::atom::ChainPDBSelector self, std::string const & chains, std::string name) -> ChainPDBSelector
12994 __init__(IMP::atom::ChainPDBSelector self, std::string const & chains) -> ChainPDBSelector
12996 this = _IMP_atom.new_ChainPDBSelector(*args)
12998 self.this.append(this)
13003 """__str__(ChainPDBSelector self) -> std::string"""
13004 return _IMP_atom.ChainPDBSelector___str__(self)
13007 def __repr__(self):
13008 """__repr__(ChainPDBSelector self) -> std::string"""
13009 return _IMP_atom.ChainPDBSelector___repr__(self)
13014 return _object_cast_to_ChainPDBSelector(o)
13016 ChainPDBSelector_swigregister = _IMP_atom.ChainPDBSelector_swigregister
13017 ChainPDBSelector_swigregister(ChainPDBSelector)
13019 class WaterPDBSelector(NonAlternativePDBSelector):
13020 """Proxy of C++ IMP::atom::WaterPDBSelector class"""
13021 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13023 def __init__(self, *args):
13025 __init__(IMP::atom::WaterPDBSelector self, std::string name) -> WaterPDBSelector
13026 __init__(IMP::atom::WaterPDBSelector self) -> WaterPDBSelector
13028 this = _IMP_atom.new_WaterPDBSelector(*args)
13030 self.this.append(this)
13035 """__str__(WaterPDBSelector self) -> std::string"""
13036 return _IMP_atom.WaterPDBSelector___str__(self)
13039 def __repr__(self):
13040 """__repr__(WaterPDBSelector self) -> std::string"""
13041 return _IMP_atom.WaterPDBSelector___repr__(self)
13046 return _object_cast_to_WaterPDBSelector(o)
13048 WaterPDBSelector_swigregister = _IMP_atom.WaterPDBSelector_swigregister
13049 WaterPDBSelector_swigregister(WaterPDBSelector)
13051 class HydrogenPDBSelector(NonAlternativePDBSelector):
13052 """Proxy of C++ IMP::atom::HydrogenPDBSelector class"""
13053 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13055 def __init__(self, *args):
13057 __init__(IMP::atom::HydrogenPDBSelector self, std::string name) -> HydrogenPDBSelector
13058 __init__(IMP::atom::HydrogenPDBSelector self) -> HydrogenPDBSelector
13060 this = _IMP_atom.new_HydrogenPDBSelector(*args)
13062 self.this.append(this)
13067 """__str__(HydrogenPDBSelector self) -> std::string"""
13068 return _IMP_atom.HydrogenPDBSelector___str__(self)
13071 def __repr__(self):
13072 """__repr__(HydrogenPDBSelector self) -> std::string"""
13073 return _IMP_atom.HydrogenPDBSelector___repr__(self)
13078 return _object_cast_to_HydrogenPDBSelector(o)
13080 HydrogenPDBSelector_swigregister = _IMP_atom.HydrogenPDBSelector_swigregister
13081 HydrogenPDBSelector_swigregister(HydrogenPDBSelector)
13083 class NonWaterNonHydrogenPDBSelector(NonAlternativePDBSelector):
13084 """Proxy of C++ IMP::atom::NonWaterNonHydrogenPDBSelector class"""
13085 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13087 def __init__(self, *args):
13089 __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self, std::string name) -> NonWaterNonHydrogenPDBSelector
13090 __init__(IMP::atom::NonWaterNonHydrogenPDBSelector self) -> NonWaterNonHydrogenPDBSelector
13092 this = _IMP_atom.new_NonWaterNonHydrogenPDBSelector(*args)
13094 self.this.append(this)
13099 """__str__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13100 return _IMP_atom.NonWaterNonHydrogenPDBSelector___str__(self)
13103 def __repr__(self):
13104 """__repr__(NonWaterNonHydrogenPDBSelector self) -> std::string"""
13105 return _IMP_atom.NonWaterNonHydrogenPDBSelector___repr__(self)
13110 return _object_cast_to_NonWaterNonHydrogenPDBSelector(o)
13112 NonWaterNonHydrogenPDBSelector_swigregister = _IMP_atom.NonWaterNonHydrogenPDBSelector_swigregister
13113 NonWaterNonHydrogenPDBSelector_swigregister(NonWaterNonHydrogenPDBSelector)
13115 class NonWaterPDBSelector(NonAlternativePDBSelector):
13116 """Proxy of C++ IMP::atom::NonWaterPDBSelector class"""
13117 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13119 def __init__(self, *args):
13121 __init__(IMP::atom::NonWaterPDBSelector self, std::string name) -> NonWaterPDBSelector
13122 __init__(IMP::atom::NonWaterPDBSelector self) -> NonWaterPDBSelector
13124 this = _IMP_atom.new_NonWaterPDBSelector(*args)
13126 self.this.append(this)
13131 """__str__(NonWaterPDBSelector self) -> std::string"""
13132 return _IMP_atom.NonWaterPDBSelector___str__(self)
13135 def __repr__(self):
13136 """__repr__(NonWaterPDBSelector self) -> std::string"""
13137 return _IMP_atom.NonWaterPDBSelector___repr__(self)
13142 return _object_cast_to_NonWaterPDBSelector(o)
13144 NonWaterPDBSelector_swigregister = _IMP_atom.NonWaterPDBSelector_swigregister
13145 NonWaterPDBSelector_swigregister(NonWaterPDBSelector)
13147 class BackbonePDBSelector(NonWaterNonHydrogenPDBSelector):
13148 """Proxy of C++ IMP::atom::BackbonePDBSelector class"""
13149 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13151 def __init__(self, *args):
13153 __init__(IMP::atom::BackbonePDBSelector self, std::string name) -> BackbonePDBSelector
13154 __init__(IMP::atom::BackbonePDBSelector self) -> BackbonePDBSelector
13156 this = _IMP_atom.new_BackbonePDBSelector(*args)
13158 self.this.append(this)
13163 """__str__(BackbonePDBSelector self) -> std::string"""
13164 return _IMP_atom.BackbonePDBSelector___str__(self)
13167 def __repr__(self):
13168 """__repr__(BackbonePDBSelector self) -> std::string"""
13169 return _IMP_atom.BackbonePDBSelector___repr__(self)
13174 return _object_cast_to_BackbonePDBSelector(o)
13176 BackbonePDBSelector_swigregister = _IMP_atom.BackbonePDBSelector_swigregister
13177 BackbonePDBSelector_swigregister(BackbonePDBSelector)
13179 class PPDBSelector(NonAlternativePDBSelector):
13180 """Proxy of C++ IMP::atom::PPDBSelector class"""
13181 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13183 def __init__(self, *args):
13185 __init__(IMP::atom::PPDBSelector self, std::string name) -> PPDBSelector
13186 __init__(IMP::atom::PPDBSelector self) -> PPDBSelector
13188 this = _IMP_atom.new_PPDBSelector(*args)
13190 self.this.append(this)
13195 """__str__(PPDBSelector self) -> std::string"""
13196 return _IMP_atom.PPDBSelector___str__(self)
13199 def __repr__(self):
13200 """__repr__(PPDBSelector self) -> std::string"""
13201 return _IMP_atom.PPDBSelector___repr__(self)
13206 return _object_cast_to_PPDBSelector(o)
13208 PPDBSelector_swigregister = _IMP_atom.PPDBSelector_swigregister
13209 PPDBSelector_swigregister(PPDBSelector)
13211 class AndPDBSelector(PDBSelector):
13212 """Proxy of C++ IMP::atom::AndPDBSelector class"""
13213 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13215 def get_version_info(self):
13216 """get_version_info(AndPDBSelector self) -> VersionInfo"""
13217 return _IMP_atom.AndPDBSelector_get_version_info(self)
13220 def __init__(self, a, b):
13221 """__init__(IMP::atom::AndPDBSelector self, PDBSelector a, PDBSelector b) -> AndPDBSelector"""
13222 this = _IMP_atom.new_AndPDBSelector(a, b)
13224 self.this.append(this)
13229 """__str__(AndPDBSelector self) -> std::string"""
13230 return _IMP_atom.AndPDBSelector___str__(self)
13233 def __repr__(self):
13234 """__repr__(AndPDBSelector self) -> std::string"""
13235 return _IMP_atom.AndPDBSelector___repr__(self)
13240 return _object_cast_to_AndPDBSelector(o)
13242 AndPDBSelector_swigregister = _IMP_atom.AndPDBSelector_swigregister
13243 AndPDBSelector_swigregister(AndPDBSelector)
13245 class OrPDBSelector(PDBSelector):
13246 """Proxy of C++ IMP::atom::OrPDBSelector class"""
13247 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13249 def get_version_info(self):
13250 """get_version_info(OrPDBSelector self) -> VersionInfo"""
13251 return _IMP_atom.OrPDBSelector_get_version_info(self)
13254 def __init__(self, a, b):
13255 """__init__(IMP::atom::OrPDBSelector self, PDBSelector a, PDBSelector b) -> OrPDBSelector"""
13256 this = _IMP_atom.new_OrPDBSelector(a, b)
13258 self.this.append(this)
13263 """__str__(OrPDBSelector self) -> std::string"""
13264 return _IMP_atom.OrPDBSelector___str__(self)
13267 def __repr__(self):
13268 """__repr__(OrPDBSelector self) -> std::string"""
13269 return _IMP_atom.OrPDBSelector___repr__(self)
13274 return _object_cast_to_OrPDBSelector(o)
13276 OrPDBSelector_swigregister = _IMP_atom.OrPDBSelector_swigregister
13277 OrPDBSelector_swigregister(OrPDBSelector)
13279 class XorPDBSelector(PDBSelector):
13280 """Proxy of C++ IMP::atom::XorPDBSelector class"""
13281 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13283 def get_version_info(self):
13284 """get_version_info(XorPDBSelector self) -> VersionInfo"""
13285 return _IMP_atom.XorPDBSelector_get_version_info(self)
13288 def __init__(self, a, b):
13289 """__init__(IMP::atom::XorPDBSelector self, PDBSelector a, PDBSelector b) -> XorPDBSelector"""
13290 this = _IMP_atom.new_XorPDBSelector(a, b)
13292 self.this.append(this)
13297 """__str__(XorPDBSelector self) -> std::string"""
13298 return _IMP_atom.XorPDBSelector___str__(self)
13301 def __repr__(self):
13302 """__repr__(XorPDBSelector self) -> std::string"""
13303 return _IMP_atom.XorPDBSelector___repr__(self)
13308 return _object_cast_to_XorPDBSelector(o)
13310 XorPDBSelector_swigregister = _IMP_atom.XorPDBSelector_swigregister
13311 XorPDBSelector_swigregister(XorPDBSelector)
13313 class NotPDBSelector(PDBSelector):
13314 """Proxy of C++ IMP::atom::NotPDBSelector class"""
13315 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13317 def get_version_info(self):
13318 """get_version_info(NotPDBSelector self) -> VersionInfo"""
13319 return _IMP_atom.NotPDBSelector_get_version_info(self)
13322 def __init__(self, a):
13323 """__init__(IMP::atom::NotPDBSelector self, PDBSelector a) -> NotPDBSelector"""
13324 this = _IMP_atom.new_NotPDBSelector(a)
13326 self.this.append(this)
13331 """__str__(NotPDBSelector self) -> std::string"""
13332 return _IMP_atom.NotPDBSelector___str__(self)
13335 def __repr__(self):
13336 """__repr__(NotPDBSelector self) -> std::string"""
13337 return _IMP_atom.NotPDBSelector___repr__(self)
13342 return _object_cast_to_NotPDBSelector(o)
13344 NotPDBSelector_swigregister = _IMP_atom.NotPDBSelector_swigregister
13345 NotPDBSelector_swigregister(NotPDBSelector)
13348 def get_default_pdb_selector():
13349 """get_default_pdb_selector() -> PDBSelector"""
13350 return _IMP_atom.get_default_pdb_selector()
13354 read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True, bool no_radii=False) -> Hierarchy
13355 read_pdb(TextInput input, Model model, PDBSelector selector, bool select_first_model=True) -> Hierarchy
13356 read_pdb(TextInput input, Model model, PDBSelector selector) -> Hierarchy
13357 read_pdb(TextInput input, Model model) -> Hierarchy
13358 read_pdb(TextInput input, int model, Hierarchy h)
13360 return _IMP_atom.read_pdb(*args)
13364 read_multimodel_pdb(TextInput input, Model model, PDBSelector selector, bool noradii=False) -> IMP::atom::Hierarchies
13365 read_multimodel_pdb(TextInput input, Model model, PDBSelector selector) -> IMP::atom::Hierarchies
13366 read_multimodel_pdb(TextInput input, Model model) -> IMP::atom::Hierarchies
13368 return _IMP_atom.read_multimodel_pdb(*args)
13372 write_pdb(Selection mhd, TextOutput out, unsigned int model=1)
13373 write_pdb(Selection mhd, TextOutput out)
13375 return _IMP_atom.write_pdb(mhd, out, model)
13379 write_pdb_of_c_alphas(Selection mhd, TextOutput out, unsigned int model=1)
13380 write_pdb_of_c_alphas(Selection mhd, TextOutput out)
13382 return _IMP_atom.write_pdb_of_c_alphas(mhd, out, model)
13385 """write_multimodel_pdb(IMP::atom::Hierarchies const & mhd, TextOutput out)"""
13386 return _IMP_atom.write_multimodel_pdb(mhd, out)
13388 def get_pdb_string(*args):
13390 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occpancy=1.00, double tempFactor=0.00, IMP::atom::Element e) -> std::string
13391 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occpancy=1.00, double tempFactor=0.00) -> std::string
13392 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode, double occpancy=1.00) -> std::string
13393 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1, char res_icode) -> std::string
13394 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain, int res_index=1) -> std::string
13395 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt, char chain) -> std::string
13396 get_pdb_string(Vector3D v, int index=-1, AtomType at, ResidueType rt) -> std::string
13397 get_pdb_string(Vector3D v, int index=-1, AtomType at) -> std::string
13398 get_pdb_string(Vector3D v, int index=-1) -> std::string
13399 get_pdb_string(Vector3D v) -> std::string
13401 return _IMP_atom.get_pdb_string(*args)
13403 def get_pdb_conect_record_string(arg1, arg2):
13404 """get_pdb_conect_record_string(int arg1, int arg2) -> std::string"""
13405 return _IMP_atom.get_pdb_conect_record_string(arg1, arg2)
13407 """Proxy of C++ IMP::atom::WritePDBOptimizerState class"""
13408 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13410 def __init__(self, *args):
13412 __init__(IMP::atom::WritePDBOptimizerState self, Model m, _ParticleIndexesAdaptor pis, std::string filename) -> WritePDBOptimizerState
13413 __init__(IMP::atom::WritePDBOptimizerState self, IMP::atom::Hierarchies const mh, std::string filename) -> WritePDBOptimizerState
13415 this = _IMP_atom.new_WritePDBOptimizerState(*args)
13417 self.this.append(this)
13421 def get_version_info(self):
13422 """get_version_info(WritePDBOptimizerState self) -> VersionInfo"""
13423 return _IMP_atom.WritePDBOptimizerState_get_version_info(self)
13427 """__str__(WritePDBOptimizerState self) -> std::string"""
13428 return _IMP_atom.WritePDBOptimizerState___str__(self)
13431 def __repr__(self):
13432 """__repr__(WritePDBOptimizerState self) -> std::string"""
13433 return _IMP_atom.WritePDBOptimizerState___repr__(self)
13438 return _object_cast_to_WritePDBOptimizerState(o)
13440 WritePDBOptimizerState_swigregister = _IMP_atom.WritePDBOptimizerState_swigregister
13441 WritePDBOptimizerState_swigregister(WritePDBOptimizerState)
13445 """get_kt(double T) -> double"""
13446 return _IMP_atom.get_kt(T)
13448 """Proxy of C++ IMP::atom::CAAngleRestraint class"""
13449 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13451 def __init__(self, m, p1, p2, p3, phi0, score):
13452 """__init__(IMP::atom::CAAngleRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, IMP::Floats phi0, IMP::Floats score) -> CAAngleRestraint"""
13453 this = _IMP_atom.new_CAAngleRestraint(m, p1, p2, p3, phi0, score)
13455 self.this.append(this)
13459 def do_get_inputs(self):
13460 """do_get_inputs(CAAngleRestraint self) -> IMP::ModelObjectsTemp"""
13461 return _IMP_atom.CAAngleRestraint_do_get_inputs(self)
13464 def get_version_info(self):
13465 """get_version_info(CAAngleRestraint self) -> VersionInfo"""
13466 return _IMP_atom.CAAngleRestraint_get_version_info(self)
13470 """__str__(CAAngleRestraint self) -> std::string"""
13471 return _IMP_atom.CAAngleRestraint___str__(self)
13474 def __repr__(self):
13475 """__repr__(CAAngleRestraint self) -> std::string"""
13476 return _IMP_atom.CAAngleRestraint___repr__(self)
13481 return _object_cast_to_CAAngleRestraint(o)
13483 CAAngleRestraint_swigregister = _IMP_atom.CAAngleRestraint_swigregister
13484 CAAngleRestraint_swigregister(CAAngleRestraint)
13487 """Proxy of C++ IMP::atom::CADihedralRestraint class"""
13488 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13490 def __init__(self, m, p1, p2, p3, p4, p5, phi0, phi1, score):
13491 """__init__(IMP::atom::CADihedralRestraint self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, _ParticleIndexAdaptor p3, _ParticleIndexAdaptor p4, _ParticleIndexAdaptor p5, IMP::Floats phi0, IMP::Floats phi1, IMP::Floats score) -> CADihedralRestraint"""
13492 this = _IMP_atom.new_CADihedralRestraint(m, p1, p2, p3, p4, p5, phi0, phi1, score)
13494 self.this.append(this)
13498 def do_get_inputs(self):
13499 """do_get_inputs(CADihedralRestraint self) -> IMP::ModelObjectsTemp"""
13500 return _IMP_atom.CADihedralRestraint_do_get_inputs(self)
13503 def get_version_info(self):
13504 """get_version_info(CADihedralRestraint self) -> VersionInfo"""
13505 return _IMP_atom.CADihedralRestraint_get_version_info(self)
13509 """__str__(CADihedralRestraint self) -> std::string"""
13510 return _IMP_atom.CADihedralRestraint___str__(self)
13513 def __repr__(self):
13514 """__repr__(CADihedralRestraint self) -> std::string"""
13515 return _IMP_atom.CADihedralRestraint___repr__(self)
13520 return _object_cast_to_CADihedralRestraint(o)
13522 CADihedralRestraint_swigregister = _IMP_atom.CADihedralRestraint_swigregister
13523 CADihedralRestraint_swigregister(CADihedralRestraint)
13526 """Proxy of C++ IMP::atom::StructureSource class"""
13527 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13529 def get_source_id(self):
13530 """get_source_id(StructureSource self) -> std::string"""
13531 return _IMP_atom.StructureSource_get_source_id(self)
13534 def get_source_chain_id(self):
13535 """get_source_chain_id(StructureSource self) -> std::string"""
13536 return _IMP_atom.StructureSource_get_source_chain_id(self)
13539 def set_source_id(self, source_id):
13540 """set_source_id(StructureSource self, std::string source_id)"""
13541 return _IMP_atom.StructureSource_set_source_id(self, source_id)
13544 def set_source_chain_id(self, source_chain_id):
13545 """set_source_chain_id(StructureSource self, std::string source_chain_id)"""
13546 return _IMP_atom.StructureSource_set_source_chain_id(self, source_chain_id)
13549 def __init__(self, *args):
13551 __init__(IMP::atom::StructureSource self) -> StructureSource
13552 __init__(IMP::atom::StructureSource self, Model m, ParticleIndex id) -> StructureSource
13553 __init__(IMP::atom::StructureSource self, _ParticleAdaptor d) -> StructureSource
13555 this = _IMP_atom.new_StructureSource(*args)
13557 self.this.append(this)
13561 def get_is_setup(*args):
13563 get_is_setup(Model m, ParticleIndex pi) -> bool
13564 get_is_setup(_ParticleAdaptor p) -> bool
13566 return _IMP_atom.StructureSource_get_is_setup(*args)
13568 get_is_setup = staticmethod(get_is_setup)
13570 def show(self, *args):
13572 show(StructureSource self, _ostream out)
13573 show(StructureSource self)
13575 return _IMP_atom.StructureSource_show(self, *args)
13578 def setup_particle(*args):
13580 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13581 setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13583 return _IMP_atom.StructureSource_setup_particle(*args)
13585 setup_particle = staticmethod(setup_particle)
13587 def add_attribute(self, *args):
13589 add_attribute(StructureSource self, FloatKey k, IMP::Float v, bool opt)
13590 add_attribute(StructureSource self, FloatKey a0, IMP::Float a1)
13591 add_attribute(StructureSource self, IntKey a0, IMP::Int a1)
13592 add_attribute(StructureSource self, StringKey a0, IMP::String a1)
13593 add_attribute(StructureSource self, ParticleIndexKey a0, Particle a1)
13594 add_attribute(StructureSource self, ObjectKey a0, Object a1)
13596 return _IMP_atom.StructureSource_add_attribute(self, *args)
13599 def get_value(self, *args):
13601 get_value(StructureSource self, FloatKey a0) -> IMP::Float
13602 get_value(StructureSource self, IntKey a0) -> IMP::Int
13603 get_value(StructureSource self, StringKey a0) -> IMP::String
13604 get_value(StructureSource self, ParticleIndexKey a0) -> Particle
13605 get_value(StructureSource self, ObjectKey a0) -> Object
13607 return _IMP_atom.StructureSource_get_value(self, *args)
13610 def set_value(self, *args):
13612 set_value(StructureSource self, FloatKey a0, IMP::Float a1)
13613 set_value(StructureSource self, IntKey a0, IMP::Int a1)
13614 set_value(StructureSource self, StringKey a0, IMP::String a1)
13615 set_value(StructureSource self, ParticleIndexKey a0, Particle a1)
13616 set_value(StructureSource self, ObjectKey a0, Object a1)
13618 return _IMP_atom.StructureSource_set_value(self, *args)
13621 def remove_attribute(self, *args):
13623 remove_attribute(StructureSource self, FloatKey a0)
13624 remove_attribute(StructureSource self, IntKey a0)
13625 remove_attribute(StructureSource self, StringKey a0)
13626 remove_attribute(StructureSource self, ParticleIndexKey a0)
13627 remove_attribute(StructureSource self, ObjectKey a0)
13629 return _IMP_atom.StructureSource_remove_attribute(self, *args)
13632 def has_attribute(self, *args):
13634 has_attribute(StructureSource self, FloatKey a0) -> bool
13635 has_attribute(StructureSource self, IntKey a0) -> bool
13636 has_attribute(StructureSource self, StringKey a0) -> bool
13637 has_attribute(StructureSource self, ParticleIndexKey a0) -> bool
13638 has_attribute(StructureSource self, ObjectKey a0) -> bool
13640 return _IMP_atom.StructureSource_has_attribute(self, *args)
13643 def get_derivative(self, a0):
13644 """get_derivative(StructureSource self, FloatKey a0) -> double"""
13645 return _IMP_atom.StructureSource_get_derivative(self, a0)
13648 def get_name(self):
13649 """get_name(StructureSource self) -> std::string"""
13650 return _IMP_atom.StructureSource_get_name(self)
13653 def clear_caches(self):
13654 """clear_caches(StructureSource self)"""
13655 return _IMP_atom.StructureSource_clear_caches(self)
13658 def set_name(self, a0):
13659 """set_name(StructureSource self, std::string a0)"""
13660 return _IMP_atom.StructureSource_set_name(self, a0)
13664 """set_check_level(StructureSource self, IMP::CheckLevel a0)"""
13665 return _IMP_atom.StructureSource_set_check_level(self, a0)
13668 def add_to_derivative(self, a0, a1, a2):
13669 """add_to_derivative(StructureSource self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
13670 return _IMP_atom.StructureSource_add_to_derivative(self, a0, a1, a2)
13673 def set_is_optimized(self, a0, a1):
13674 """set_is_optimized(StructureSource self, FloatKey a0, bool a1)"""
13675 return _IMP_atom.StructureSource_set_is_optimized(self, a0, a1)
13678 def get_is_optimized(self, a0):
13679 """get_is_optimized(StructureSource self, FloatKey a0) -> bool"""
13680 return _IMP_atom.StructureSource_get_is_optimized(self, a0)
13684 """get_check_level(StructureSource self) -> IMP::CheckLevel"""
13685 return _IMP_atom.StructureSource_get_check_level(self)
13688 def __eq__(self, *args):
13690 __eq__(StructureSource self, StructureSource o) -> bool
13691 __eq__(StructureSource self, Particle d) -> bool
13693 return _IMP_atom.StructureSource___eq__(self, *args)
13696 def __ne__(self, *args):
13698 __ne__(StructureSource self, StructureSource o) -> bool
13699 __ne__(StructureSource self, Particle d) -> bool
13701 return _IMP_atom.StructureSource___ne__(self, *args)
13704 def __le__(self, *args):
13706 __le__(StructureSource self, StructureSource o) -> bool
13707 __le__(StructureSource self, Particle d) -> bool
13709 return _IMP_atom.StructureSource___le__(self, *args)
13712 def __lt__(self, *args):
13714 __lt__(StructureSource self, StructureSource o) -> bool
13715 __lt__(StructureSource self, Particle d) -> bool
13717 return _IMP_atom.StructureSource___lt__(self, *args)
13720 def __ge__(self, *args):
13722 __ge__(StructureSource self, StructureSource o) -> bool
13723 __ge__(StructureSource self, Particle d) -> bool
13725 return _IMP_atom.StructureSource___ge__(self, *args)
13728 def __gt__(self, *args):
13730 __gt__(StructureSource self, StructureSource o) -> bool
13731 __gt__(StructureSource self, Particle d) -> bool
13733 return _IMP_atom.StructureSource___gt__(self, *args)
13736 def __hash__(self):
13737 """__hash__(StructureSource self) -> std::size_t"""
13738 return _IMP_atom.StructureSource___hash__(self)
13742 """__str__(StructureSource self) -> std::string"""
13743 return _IMP_atom.StructureSource___str__(self)
13746 def __repr__(self):
13747 """__repr__(StructureSource self) -> std::string"""
13748 return _IMP_atom.StructureSource___repr__(self)
13750 __swig_destroy__ = _IMP_atom.delete_StructureSource
13751 __del__ =
lambda self:
None
13752 StructureSource_swigregister = _IMP_atom.StructureSource_swigregister
13753 StructureSource_swigregister(StructureSource)
13755 def StructureSource_get_is_setup(*args):
13757 get_is_setup(Model m, ParticleIndex pi) -> bool
13758 StructureSource_get_is_setup(_ParticleAdaptor p) -> bool
13760 return _IMP_atom.StructureSource_get_is_setup(*args)
13762 def StructureSource_setup_particle(*args):
13764 setup_particle(Model m, ParticleIndex pi, std::string source_id, std::string source_chain_id) -> StructureSource
13765 StructureSource_setup_particle(_ParticleAdaptor decorator, std::string source_id, std::string source_chain_id) -> StructureSource
13767 return _IMP_atom.StructureSource_setup_particle(*args)
13770 def __lshift__(*args):
13772 __lshift__(_ostream out, Bonded n) -> _ostream
13773 __lshift__(_ostream out, Bond n) -> _ostream
13774 __lshift__(_ostream out, Hierarchy n) -> _ostream
13775 __lshift__(_ostream out, Angle n) -> _ostream
13776 __lshift__(_ostream out, Dihedral n) -> _ostream
13777 __lshift__(_ostream out, CenterOfMass n) -> _ostream
13778 __lshift__(_ostream out, Diffusion n) -> _ostream
13779 __lshift__(_ostream out, RigidBodyDiffusion n) -> _ostream
13780 __lshift__(_ostream out, TAMDParticle n) -> _ostream
13781 __lshift__(_ostream out, Chain n) -> _ostream
13782 __lshift__(_ostream out, Charged n) -> _ostream
13783 __lshift__(_ostream out, Domain n) -> _ostream
13784 __lshift__(_ostream out, LennardJones n) -> _ostream
13785 __lshift__(_ostream out, Fragment n) -> _ostream
13786 __lshift__(_ostream out, SecondaryStructureResidue n) -> _ostream
13787 __lshift__(_ostream out, Atom n) -> _ostream
13788 __lshift__(_ostream out, Residue n) -> _ostream
13789 __lshift__(_ostream out, Representation n) -> _ostream
13790 __lshift__(_ostream out, State n) -> _ostream
13791 __lshift__(_ostream out, Molecule n) -> _ostream
13792 __lshift__(_ostream out, Copy n) -> _ostream
13793 __lshift__(_ostream out, StructureSource n) -> _ostream
13795 return _IMP_atom.__lshift__(*args)
13799 show_molecular_hierarchy(Hierarchy h, _ostream out) -> _ostream
13800 show_molecular_hierarchy(Hierarchy h) -> _ostream
13802 return _IMP_atom.show_molecular_hierarchy(*args)
13803 class CHARMMBond(object):
13804 """Proxy of C++ IMP::atom::CHARMMConnection<(2)> class"""
13805 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13806 __repr__ = _swig_repr
13808 def __init__(self, atoms):
13809 """__init__(IMP::atom::CHARMMConnection<(2)> self, IMP::Strings const & atoms) -> CHARMMBond"""
13810 this = _IMP_atom.new_CHARMMBond(atoms)
13812 self.this.append(this)
13816 def get_endpoint(self, i):
13817 """get_endpoint(CHARMMBond self, unsigned int i) -> CHARMMBondEndpoint"""
13818 return _IMP_atom.CHARMMBond_get_endpoint(self, i)
13821 def get_contains_atom(self, name):
13822 """get_contains_atom(CHARMMBond self, std::string name) -> bool"""
13823 return _IMP_atom.CHARMMBond_get_contains_atom(self, name)
13826 def show(self, *args):
13828 show(CHARMMBond self, _ostream out)
13829 show(CHARMMBond self)
13831 return _IMP_atom.CHARMMBond_show(self, *args)
13833 __swig_destroy__ = _IMP_atom.delete_CHARMMBond
13834 __del__ =
lambda self:
None
13835 CHARMMBond_swigregister = _IMP_atom.CHARMMBond_swigregister
13836 CHARMMBond_swigregister(CHARMMBond)
13838 class CHARMMAngle(object):
13839 """Proxy of C++ IMP::atom::CHARMMConnection<(3)> class"""
13840 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
13841 __repr__ = _swig_repr
13843 def __init__(self, atoms):
13844 """__init__(IMP::atom::CHARMMConnection<(3)> self, IMP::Strings const & atoms) -> CHARMMAngle"""
13845 this = _IMP_atom.new_CHARMMAngle(atoms)
13847 self.this.append(this)
13851 def get_endpoint(self, i):
13852 """get_endpoint(CHARMMAngle self, unsigned int i) -> CHARMMBondEndpoint"""
13853 return _IMP_atom.CHARMMAngle_get_endpoint(self, i)
13856 def get_contains_atom(self, name):
13857 """get_contains_atom(CHARMMAngle self, std::string name) -> bool"""
13858 return _IMP_atom.CHARMMAngle_get_contains_atom(self, name)
13861 def show(self, *args):
13863 show(CHARMMAngle self, _ostream out)
13864 show(CHARMMAngle self)
13866 return _IMP_atom.CHARMMAngle_show(self, *args)
13868 __swig_destroy__ = _IMP_atom.delete_CHARMMAngle
13869 __del__ =
lambda self:
None
13870 CHARMMAngle_swigregister = _IMP_atom.CHARMMAngle_swigregister
13871 CHARMMAngle_swigregister(CHARMMAngle)
13874 def _get_native_overlap_cpp(m1, m2, threshold):
13875 """_get_native_overlap_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, double threshold) -> double"""
13876 return _IMP_atom._get_native_overlap_cpp(m1, m2, threshold)
13878 def _get_drmsd_cpp(m0, m1):
13879 """_get_drmsd_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1) -> double"""
13880 return _IMP_atom._get_drmsd_cpp(m0, m1)
13882 def _get_drmsd_Q_cpp(m0, m1, threshold):
13883 """_get_drmsd_Q_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m0, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, double threshold) -> double"""
13884 return _IMP_atom._get_drmsd_Q_cpp(m0, m1, threshold)
13886 def _get_drms_cpp(m1, m2):
13887 """_get_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2) -> double"""
13888 return _IMP_atom._get_drms_cpp(m1, m2)
13890 def _get_rigid_bodies_drms_cpp(m1, m2, ranges):
13891 """_get_rigid_bodies_drms_cpp(IMP::Vector< IMP::algebra::VectorD< 3 > > const & m1, IMP::Vector< IMP::algebra::VectorD< 3 > > const & m2, IMP::IntRanges const & ranges) -> double"""
13892 return _IMP_atom._get_rigid_bodies_drms_cpp(m1, m2, ranges)
13895 va= [IMP.algebra.get_vector(x)
for x
in a]
13896 vb= [IMP.algebra.get_vector(x)
for x
in b]
13897 return _get_native_overlap_cpp(va, vb, d)
13900 va= [IMP.algebra.get_vector(x)
for x
in a]
13901 vb= [IMP.algebra.get_vector(x)
for x
in b]
13902 return _get_drmsd_cpp(va, vb)
13905 va= [IMP.algebra.get_vector(x)
for x
in a]
13906 vb= [IMP.algebra.get_vector(x)
for x
in b]
13907 return _get_drms_cpp(va, vb)
13910 va= [IMP.algebra.get_vector(x)
for x
in a]
13911 vb= [IMP.algebra.get_vector(x)
for x
in b]
13912 return _get_drmsd_Q_cpp(va, vb, t)
13915 va= [IMP.algebra.get_vector(x)
for x
in a]
13916 vb= [IMP.algebra.get_vector(x)
for x
in b]
13918 return _get_rigid_bodies_drms_cpp(va, vb, ranges)
13922 def get_module_version():
13923 """get_module_version() -> std::string const"""
13924 return _IMP_atom.get_module_version()
13927 """get_example_path(std::string fname) -> std::string"""
13928 return _IMP_atom.get_example_path(fname)
13931 """get_data_path(std::string fname) -> std::string"""
13932 return _IMP_atom.get_data_path(fname)
13934 from .
import _version_check
13935 _version_check.check_version(get_module_version())
13936 __version__ = get_module_version()
A base class for geometry contained in particles.
A base class for modifiers of ParticlesTemp.
AtomType add_atom_type(std::string name, Element e)
Create a new AtomType.
double get_kt(double T)
Return kT for a given temperature.
double get_volume_from_residue_type(ResidueType rt)
Return an estimate for the volume of a given residue.
Abstract class for scoring object(s) of type ParticleIndexPair.
A shared container for Pairs.
CHARMMParameters * get_heavy_atom_CHARMM_parameters()
Float get_secondary_structure_match_score(SecondaryStructureResidue ssr1, SecondaryStructureResidue ssr2)
Compares the secondary structure probabilities of two residues.
double get_rigid_bodies_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, const IMP::IntRanges &ranges)
DRMS between two sets of rigid bodies.
Chain get_chain(Hierarchy h)
CheckLevel get_check_level()
Get the current audit mode.
Atoms get_phi_dihedral_atoms(Residue rd)
Return the atoms comprising the phi dihedral.
void show_molecular_hierarchy(Hierarchy h)
Print out the molecular hierarchy.
double get_drms(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
double get_einstein_rotational_diffusion_coefficient(double r)
void remove_charmm_untyped_atoms(Hierarchy hierarchy)
Remove any atom from the Hierarchy that does not have a CHARMM type.
double get_protein_density_from_reference(ProteinDensityReference densityReference)
void show_with_representations(Hierarchy h, std::ostream &out=std::cout)
Traverse through the tree and show atom info, including representations.
Hierarchy create_simplified_from_volume(Hierarchy h, double resolution)
void add_particles(RMF::FileHandle fh, const ParticlesTemp &hs)
double get_native_overlap(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2, double threshold)
Computes the native overlap between two sets of 3D points.
Various classes to hold sets of particles.
The base class for geometry.
IMP::core::RigidBody create_compatible_rigid_body(Hierarchy h, Hierarchy reference)
Rigidify a molecule or collection of molecules.
Hierarchy create_simplified_along_backbone(Hierarchy input, int num_res, bool keep_detailed=false)
double get_drmsd(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1)
Calculate distance the root mean square deviation between two sets of 3D points.
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
double get_mass(ResidueType c)
Get the mass from the residue type.
void add_radii(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters(), FloatKey radius_key=FloatKey("radius"))
A base class for geometry from a set of particles.
double get_dihedral(XYZ a, XYZ b, XYZ c, XYZ d)
Compute the dihedral angle (in radians) between the four particles.
double get_mass_from_number_of_residues(unsigned int num_aa)
Estimate the mass of a protein from the number of amino acids.
Make CGAL functionality available to IMP.
void write_pdb(const Selection &mhd, TextOutput out, unsigned int model=1)
void setup_as_approximation(Particle *h, const ParticlesTemp &other)
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
double get_mass_from_volume(double v, ProteinDensityReference ref=ALBER)
Estimate the mass of a protein from its volume.
void destroy_bond(Bond b)
Destroy the bond connecting two particles.
HierarchyTree get_hierarchy_tree(Hierarchy h)
Get a graph for the passed Hierarchy.
void add_particle(RMF::FileHandle fh, Particle *hs)
Atoms get_charmm_untyped_atoms(Hierarchy hierarchy)
Get all atoms in the Hierarchy that do not have CHARMM types.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
char get_one_letter_code(ResidueType c)
Get the 1-letter amino acid code from the residue type.
Atom get_atom(Residue rd, AtomType at)
Return a particle atom from the residue.
Composable functors to implement scores via compile-time composition.
Restraint * create_excluded_volume_restraint(const Hierarchies &hs, double resolution=-1)
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
void write_pdb_of_c_alphas(const Selection &mhd, TextOutput out, unsigned int model=1)
Write a hierarchy to a PDB as C_alpha atoms.
double get_kd(double na, double nb, double nab, double volume)
double get_diffusion_angle(double D, double dtfs)
bool get_atom_type_exists(std::string name)
Return true if that atom type already exists.
double get_volume(const BoundingBoxD< D > &bb)
See BoundingBoxD.
double get_rotational_diffusion_coefficient(const algebra::Rotation3Ds &displacements, double dt)
FloatPair get_component_placement_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the difference between two placements of the same set of points.
void transform(Hierarchy h, const algebra::Transformation3D &tr)
Transform a hierarchy. This is aware of rigid bodies.
core::XYZR create_cover(const Selection &s, std::string name=std::string())
double get_volume_from_mass(double m, ProteinDensityReference ref=ALBER)
Estimate the volume of a protein from its mass.
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
Common base class for heavy weight IMP objects.
Hierarchy create_protein(Model *m, std::string name, double target_radius, int number_of_residues, int first_residue_index=0, double volume=-1)
Create a coarse grained molecule.
Atoms get_psi_dihedral_atoms(Residue rd)
Return the atoms comprising the psi dihedral.
Abstract class for scoring object(s) of type ParticleIndex.
ParticlesTemp get_order(const Subset &s, const SubsetFilterTables &sft)
Bond create_bond(Bonded a, Bonded b, Int t)
Connect the two wrapped particles by a bond.
Base class for all optimizers.
double get_rmsd(const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Hierarchy get_previous_residue(Residue rd)
Return the residue from the same chain with one lower index.
SecondaryStructureResidue setup_coarse_secondary_structure_residue(const Particles &ssr_ps, Model *mdl, bool winner_takes_all_per_res=false)
Coarsen some SecondaryStructureResidues.
double get_molarity(double n, double volume)
boost::graph HierarchyTree
A graph for representing a Hierarchy so you can view it nicely.
Hierarchy read_mol2(TextInput mol2_file, Model *model, Mol2Selector *mol2sel=nullptr)
Create a hierarchy from a Mol2 file.
Version and module information for Objects.
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
A decorator for a particle with x,y,z coordinates.
Restraint * create_internal_connectivity_restraint(const Selection &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selection.
void write_mol2(Hierarchy rhd, TextOutput file_name)
Write a ligand hierarchy as a mol2 file.
Hierarchy read_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector(), bool select_first_model=true)
int get_state_index(Hierarchy h)
Walk up the hierarchy to find the current state.
SecondaryStructureResidues setup_coarse_secondary_structure_residues(const Particles &ssr_ps, Model *mdl, int coarse_factor, int start_res_num, bool winner_takes_all_per_res=false)
void add_protein_ligand_score_data(Hierarchy h)
Interface to specialized Particle types (e.g. atoms)
std::string get_molecule_name(Hierarchy h)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
double get_pairwise_rmsd_score(const core::XYZs &ref1, const core::XYZs &ref2, const core::XYZs &mdl1, const core::XYZs &mdl2)
Measure the RMSD between two placements of the same set of points.
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
Hierarchies read_multimodel_pdb(TextInput input, Model *model, PDBSelector *selector=get_default_pdb_selector())
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Residue get_residue(Atom d, bool nothrow=false)
Return the Residue containing this atom.
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Abstract class to implement hierarchical methods.
void add_dope_score_data(atom::Hierarchy h)
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
std::string show_graphviz(Graph g)
Restraint * create_distance_restraint(const Selection &n0, const Selection &n1, double x0, double k, std::string name="Distance%1%")
Representation get_representation(Hierarchy h, bool nothrow=false)
Return the Representation object containing this hierarchy.
FloatPair get_placement_score(const core::XYZs &source, const core::XYZs &target)
Measure the difference between two placements of the same set of points.
void write_multimodel_pdb(const Hierarchies &mhd, TextOutput out)
int get_copy_index(Hierarchy h)
Walk up the hierarchy to find the current copy index.
A decorator for helping deal with a generalized hierarchy.
double get_maximum_time_step_estimate(BrownianDynamics *bd)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
double get_surface_area(const Geometry &)
Compute the surface area of any volumetric object.
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
double get_rmsd_transforming_first(const Transformation3D &tr, const Vector3DsOrXYZs0 &m1, const Vector3DsOrXYZs1 &m2)
Calculate the root mean square deviation between two sets of 3D points.
Hierarchy create_simplified_assembly_from_volume(Hierarchy h, double resolution)
Output IMP model data in various file formats.
std::string get_chain_id(Hierarchy h)
IMP::core::RigidBody create_rigid_body(const Hierarchies &h, std::string name=std::string("created rigid body"))
Rigidify a molecule or collection of molecules.
CHARMMParameters * get_all_atom_CHARMM_parameters()
Hierarchies get_leaves(const Selection &h)
double get_drmsd_Q(const Vector3DsOrXYZs0 &m0, const Vector3DsOrXYZs1 &m1, double threshold)
DensityMap * get_segment(DensityMap *map_to_segment, int nx_start, int nx_end, int ny_start, int ny_end, int nz_start, int nz_end)
Get a segment of the map according to xyz indexes.
Applies a PairScore to each Pair in a list.
Hierarchy get_next_residue(Residue rd)
Return the residue from the same chain with one higher index.
Restraint * create_connectivity_restraint(const Selections &s, double k, std::string name="Connectivity%1%")
Create a restraint connecting the selections.
void add_bonds(Hierarchy d, const ForceFieldParameters *ffp=get_all_atom_CHARMM_parameters())
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
double get_diffusion_length(double D, double t)
double get_einstein_diffusion_coefficient(double r)
A restraint is a term in an IMP ScoringFunction.
A decorator for a particle with x,y,z coordinates and a radius.