11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
19 import builtins
as __builtin__
25 strthis =
"proxy of " + self.this.__repr__()
26 except __builtin__.Exception:
28 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
31 def _swig_setattr_nondynamic_instance_variable(set):
32 def set_instance_attr(self, name, value):
34 set(self, name, value)
35 elif name ==
"thisown":
37 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
38 set(self, name, value)
40 raise AttributeError(
"You cannot add instance attributes to %s" % self)
41 return set_instance_attr
44 def _swig_setattr_nondynamic_class_variable(set):
45 def set_class_attr(cls, name, value):
46 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
49 raise AttributeError(
"You cannot add class attributes to %s" % cls)
53 def _swig_add_metaclass(metaclass):
54 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
56 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
60 class _SwigNonDynamicMeta(type):
61 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
67 class IMP_PMI_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_PMI_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
72 def __init__(self, *args, **kwargs):
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_pmi.delete_IMP_PMI_SwigPyIterator
78 r"""value(IMP_PMI_SwigPyIterator self) -> PyObject *"""
79 return _IMP_pmi.IMP_PMI_SwigPyIterator_value(self)
82 r"""incr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator"""
83 return _IMP_pmi.IMP_PMI_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator"""
87 return _IMP_pmi.IMP_PMI_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_pmi.IMP_PMI_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
95 return _IMP_pmi.IMP_PMI_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_PMI_SwigPyIterator self) -> IMP_PMI_SwigPyIterator"""
99 return _IMP_pmi.IMP_PMI_SwigPyIterator_copy(self)
102 r"""next(IMP_PMI_SwigPyIterator self) -> PyObject *"""
103 return _IMP_pmi.IMP_PMI_SwigPyIterator_next(self)
106 r"""__next__(IMP_PMI_SwigPyIterator self) -> PyObject *"""
107 return _IMP_pmi.IMP_PMI_SwigPyIterator___next__(self)
110 r"""previous(IMP_PMI_SwigPyIterator self) -> PyObject *"""
111 return _IMP_pmi.IMP_PMI_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
115 return _IMP_pmi.IMP_PMI_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
119 return _IMP_pmi.IMP_PMI_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
123 return _IMP_pmi.IMP_PMI_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
127 return _IMP_pmi.IMP_PMI_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
131 return _IMP_pmi.IMP_PMI_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
135 return _IMP_pmi.IMP_PMI_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator
140 __sub__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_pmi.IMP_PMI_SwigPyIterator___sub__(self, *args)
147 _IMP_pmi.IMP_PMI_SwigPyIterator_swigregister(IMP_PMI_SwigPyIterator)
154 IMP_DEBUG = _IMP_pmi.IMP_DEBUG
156 IMP_RELEASE = _IMP_pmi.IMP_RELEASE
158 IMP_SILENT = _IMP_pmi.IMP_SILENT
160 IMP_PROGRESS = _IMP_pmi.IMP_PROGRESS
162 IMP_TERSE = _IMP_pmi.IMP_TERSE
164 IMP_VERBOSE = _IMP_pmi.IMP_VERBOSE
166 IMP_MEMORY = _IMP_pmi.IMP_MEMORY
168 IMP_NONE = _IMP_pmi.IMP_NONE
170 IMP_USAGE = _IMP_pmi.IMP_USAGE
172 IMP_INTERNAL = _IMP_pmi.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_pmi.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_pmi.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_pmi.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_pmi.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_pmi.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_pmi.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_pmi.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_pmi.IMPKERNEL_SHOW_WARNINGS
198 class _DirectorObjects(object):
199 """@internal Simple class to keep references to director objects
200 to prevent premature deletion."""
203 def register(self, obj):
204 """Take a reference to a director object; will only work for
205 refcounted C++ classes"""
206 if hasattr(obj,
'get_ref_count'):
207 self._objects.append(obj)
209 """Only drop our reference and allow cleanup by Python if no other
210 Python references exist (we hold 3 references: one in self._objects,
211 one in x, and one in the argument list for getrefcount) *and* no
212 other C++ references exist (the Python object always holds one)"""
213 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
214 or x.get_ref_count() > 1]
218 def get_object_count(self):
219 """Get number of director objects (useful for testing only)"""
220 return len(self._objects)
221 _director_objects = _DirectorObjects()
223 class _ostream(object):
224 r"""Proxy of C++ std::ostream class."""
226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
228 def __init__(self, *args, **kwargs):
229 raise AttributeError(
"No constructor defined")
230 __repr__ = _swig_repr
232 def write(self, osa_buf):
233 r"""write(_ostream self, char const * osa_buf)"""
234 return _IMP_pmi._ostream_write(self, osa_buf)
237 _IMP_pmi._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_pmi.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_pmi.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_pmi.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_pmi.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_pmi.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_pmi.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_pmi.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_pmi.IMPDISPLAY_SHOW_WARNINGS
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_CGAL
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_HDF5
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_NUMPY
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_pmi.IMPSCOREFUNCTOR_SHOW_WARNINGS
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_IMP_CGAL
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_RANDOM
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_SYSTEM
319 IMP_STATISTICS_HAS_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_CGAL
321 IMP_STATISTICS_HAS_NUMPY = _IMP_pmi.IMP_STATISTICS_HAS_NUMPY
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_pmi.IMPSTATISTICS_SHOW_WARNINGS
326 IMP_CORE_HAS_IMP_CGAL = _IMP_pmi.IMP_CORE_HAS_IMP_CGAL
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_pmi.IMP_CORE_HAS_IMP_KERNEL
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CORE_HAS_BOOST_RANDOM
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_SYSTEM
338 IMP_CORE_HAS_CGAL = _IMP_pmi.IMP_CORE_HAS_CGAL
340 IMP_CORE_HAS_HDF5 = _IMP_pmi.IMP_CORE_HAS_HDF5
342 IMP_CORE_HAS_NUMPY = _IMP_pmi.IMP_CORE_HAS_NUMPY
344 IMPCORE_SHOW_WARNINGS = _IMP_pmi.IMPCORE_SHOW_WARNINGS
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_CONTAINER_HAS_IMP_ALGEBRA
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_CGAL
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_pmi.IMP_CONTAINER_HAS_IMP_DISPLAY
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_KERNEL
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_RANDOM
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_SYSTEM
365 IMP_CONTAINER_HAS_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_CGAL
367 IMP_CONTAINER_HAS_HDF5 = _IMP_pmi.IMP_CONTAINER_HAS_HDF5
369 IMP_CONTAINER_HAS_NUMPY = _IMP_pmi.IMP_CONTAINER_HAS_NUMPY
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_pmi.IMP_CONTAINER_HAS_PYTHON_IHM
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_pmi.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_pmi.IMP_CONTAINER_HAS_ROBIN_MAP
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_pmi.IMPCONTAINER_SHOW_WARNINGS
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_pmi.IMP_ATOM_HAS_IMP_CGAL
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_pmi.IMP_ATOM_HAS_IMP_KERNEL
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ATOM_HAS_BOOST_RANDOM
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_pmi.IMP_ATOM_HAS_BOOST_REGEX
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ATOM_HAS_BOOST_SYSTEM
394 IMP_ATOM_HAS_CGAL = _IMP_pmi.IMP_ATOM_HAS_CGAL
396 IMP_ATOM_HAS_HDF5 = _IMP_pmi.IMP_ATOM_HAS_HDF5
398 IMP_ATOM_HAS_NUMPY = _IMP_pmi.IMP_ATOM_HAS_NUMPY
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_pmi.IMP_ATOM_HAS_PYTHON_IHM
402 IMPATOM_SHOW_WARNINGS = _IMP_pmi.IMPATOM_SHOW_WARNINGS
404 IMP_ATOM_TYPE_INDEX = _IMP_pmi.IMP_ATOM_TYPE_INDEX
406 IMP_RESIDUE_TYPE_INDEX = _IMP_pmi.IMP_RESIDUE_TYPE_INDEX
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_pmi.IMP_HIERARCHY_TYPE_INDEX
410 IMP_CHAIN_TYPE_INDEX = _IMP_pmi.IMP_CHAIN_TYPE_INDEX
413 IMP_EM_HAS_IMP_CGAL = _IMP_pmi.IMP_EM_HAS_IMP_CGAL
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_pmi.IMP_EM_HAS_IMP_CONTAINER
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_pmi.IMP_EM_HAS_IMP_DISPLAY
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_EM_HAS_IMP_SCORE_FUNCTOR
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_FILESYSTEM
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_EM_HAS_BOOST_RANDOM
427 IMP_EM_HAS_BOOST_REGEX = _IMP_pmi.IMP_EM_HAS_BOOST_REGEX
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_SYSTEM
431 IMP_EM_HAS_CGAL = _IMP_pmi.IMP_EM_HAS_CGAL
433 IMP_EM_HAS_HDF5 = _IMP_pmi.IMP_EM_HAS_HDF5
435 IMP_EM_HAS_NUMPY = _IMP_pmi.IMP_EM_HAS_NUMPY
437 IMP_EM_HAS_PYTHON_IHM = _IMP_pmi.IMP_EM_HAS_PYTHON_IHM
439 IMPEM_SHOW_WARNINGS = _IMP_pmi.IMPEM_SHOW_WARNINGS
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_pmi.IMP_SAXS_HAS_IMP_CGAL
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_pmi.IMP_SAXS_HAS_IMP_CONTAINER
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_pmi.IMP_SAXS_HAS_IMP_DISPLAY
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_pmi.IMP_SAXS_HAS_IMP_KERNEL
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_FILESYSTEM
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SAXS_HAS_BOOST_RANDOM
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_pmi.IMP_SAXS_HAS_BOOST_REGEX
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_SYSTEM
462 IMP_SAXS_HAS_CGAL = _IMP_pmi.IMP_SAXS_HAS_CGAL
464 IMP_SAXS_HAS_HDF5 = _IMP_pmi.IMP_SAXS_HAS_HDF5
466 IMP_SAXS_HAS_NUMPY = _IMP_pmi.IMP_SAXS_HAS_NUMPY
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_pmi.IMP_SAXS_HAS_PYTHON_IHM
470 IMPSAXS_SHOW_WARNINGS = _IMP_pmi.IMPSAXS_SHOW_WARNINGS
473 IMP_ISD_HAS_IMP_CGAL = _IMP_pmi.IMP_ISD_HAS_IMP_CGAL
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_pmi.IMP_ISD_HAS_IMP_DISPLAY
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_FILESYSTEM
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ISD_HAS_BOOST_RANDOM
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_pmi.IMP_ISD_HAS_BOOST_REGEX
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_SYSTEM
489 IMP_ISD_HAS_CGAL = _IMP_pmi.IMP_ISD_HAS_CGAL
491 IMP_ISD_HAS_HDF5 = _IMP_pmi.IMP_ISD_HAS_HDF5
493 IMP_ISD_HAS_NUMPY = _IMP_pmi.IMP_ISD_HAS_NUMPY
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_pmi.IMP_ISD_HAS_PYTHON_IHM
497 IMPISD_SHOW_WARNINGS = _IMP_pmi.IMPISD_SHOW_WARNINGS
500 IMP_PMI_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_PMI_HAS_IMP_ALGEBRA
502 IMP_PMI_HAS_IMP_ATOM = _IMP_pmi.IMP_PMI_HAS_IMP_ATOM
504 IMP_PMI_HAS_IMP_CGAL = _IMP_pmi.IMP_PMI_HAS_IMP_CGAL
506 IMP_PMI_HAS_IMP_DISPLAY = _IMP_pmi.IMP_PMI_HAS_IMP_DISPLAY
508 IMP_PMI_HAS_IMP_EM = _IMP_pmi.IMP_PMI_HAS_IMP_EM
510 IMP_PMI_HAS_IMP_KERNEL = _IMP_pmi.IMP_PMI_HAS_IMP_KERNEL
512 IMP_PMI_HAS_IMP_SAXS = _IMP_pmi.IMP_PMI_HAS_IMP_SAXS
514 IMP_PMI_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_PMI_HAS_IMP_SCORE_FUNCTOR
516 IMP_PMI_HAS_IMP_STATISTICS = _IMP_pmi.IMP_PMI_HAS_IMP_STATISTICS
518 IMP_PMI_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_FILESYSTEM
520 IMP_PMI_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_PMI_HAS_BOOST_PROGRAMOPTIONS
522 IMP_PMI_HAS_BOOST_RANDOM = _IMP_pmi.IMP_PMI_HAS_BOOST_RANDOM
524 IMP_PMI_HAS_BOOST_REGEX = _IMP_pmi.IMP_PMI_HAS_BOOST_REGEX
526 IMP_PMI_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_SYSTEM
528 IMP_PMI_HAS_CGAL = _IMP_pmi.IMP_PMI_HAS_CGAL
530 IMP_PMI_HAS_HDF5 = _IMP_pmi.IMP_PMI_HAS_HDF5
532 IMP_PMI_HAS_NUMPY = _IMP_pmi.IMP_PMI_HAS_NUMPY
534 IMP_PMI_HAS_PYTHON_IHM = _IMP_pmi.IMP_PMI_HAS_PYTHON_IHM
536 IMPPMI_SHOW_WARNINGS = _IMP_pmi.IMPPMI_SHOW_WARNINGS
539 _object_types.append(
"CompositeRestraint")
542 def _object_cast_to_CompositeRestraint(o):
543 r"""_object_cast_to_CompositeRestraint(Object o) -> CompositeRestraint"""
544 return _IMP_pmi._object_cast_to_CompositeRestraint(o)
546 _object_types.append(
"CrossLinkRestraintSet")
549 def _object_cast_to_CrossLinkRestraintSet(o):
550 r"""_object_cast_to_CrossLinkRestraintSet(Object o) -> CrossLinkRestraintSet"""
551 return _IMP_pmi._object_cast_to_CrossLinkRestraintSet(o)
553 def Uncertainties(l=[]):
554 return [Uncertainty(x)
for x
in l]
555 _plural_types.append(
"Uncertainties")
558 _value_types.append(
"Uncertainty")
561 def Resolutions(l=[]):
562 return [Resolution(x)
for x
in l]
563 _plural_types.append(
"Resolutions")
566 _value_types.append(
"Resolution")
569 def Symmetrics(l=[]):
570 return [Symmetric(x)
for x
in l]
571 _plural_types.append(
"Symmetrics")
574 _value_types.append(
"Symmetric")
577 _object_types.append(
"TransformMover")
580 def _object_cast_to_TransformMover(o):
581 r"""_object_cast_to_TransformMover(Object o) -> TransformMover"""
582 return _IMP_pmi._object_cast_to_TransformMover(o)
584 _object_types.append(
"MembraneRestraint")
587 def _object_cast_to_MembraneRestraint(o):
588 r"""_object_cast_to_MembraneRestraint(Object o) -> MembraneRestraint"""
589 return _IMP_pmi._object_cast_to_MembraneRestraint(o)
592 """Warning related to handling of structures"""
596 class ParameterWarning(UserWarning):
597 """Warning for probably incorrect input parameters"""
602 """Warning for an expected, but missing, file"""
606 r"""Proxy of C++ IMP::pmi::MembraneRestraint class."""
608 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
610 def __init__(self, m, z_nuisance, thickness, softness, plateau, linear):
611 r"""__init__(MembraneRestraint self, Model m, ParticleIndex z_nuisance, double thickness, double softness, double plateau, double linear) -> MembraneRestraint"""
612 _IMP_pmi.MembraneRestraint_swiginit(self, _IMP_pmi.new_MembraneRestraint(m, z_nuisance, thickness, softness, plateau, linear))
614 def add_particles_below(self, particles):
615 r"""add_particles_below(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
616 return _IMP_pmi.MembraneRestraint_add_particles_below(self, particles)
618 def add_particles_above(self, particles):
619 r"""add_particles_above(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
620 return _IMP_pmi.MembraneRestraint_add_particles_above(self, particles)
622 def add_particles_inside(self, particles):
623 r"""add_particles_inside(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
624 return _IMP_pmi.MembraneRestraint_add_particles_inside(self, particles)
626 def get_score(self, prob):
627 r"""get_score(MembraneRestraint self, double prob) -> double"""
628 return _IMP_pmi.MembraneRestraint_get_score(self, prob)
630 def get_probability_above(self, z, z_slope_center_upper):
631 r"""get_probability_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
632 return _IMP_pmi.MembraneRestraint_get_probability_above(self, z, z_slope_center_upper)
634 def get_score_above(self, z, z_slope_center_upper):
635 r"""get_score_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
636 return _IMP_pmi.MembraneRestraint_get_score_above(self, z, z_slope_center_upper)
638 def get_probability_below(self, z, z_slope_center_lower):
639 r"""get_probability_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
640 return _IMP_pmi.MembraneRestraint_get_probability_below(self, z, z_slope_center_lower)
642 def get_score_below(self, z, z_slope_center_lower):
643 r"""get_score_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
644 return _IMP_pmi.MembraneRestraint_get_score_below(self, z, z_slope_center_lower)
646 def get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper):
647 r"""get_score_inside(MembraneRestraint self, double z, double z_slope_center_lower, double z_slope_center_upper) -> double"""
648 return _IMP_pmi.MembraneRestraint_get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper)
649 __swig_destroy__ = _IMP_pmi.delete_MembraneRestraint
652 r"""__str__(MembraneRestraint self) -> std::string"""
653 return _IMP_pmi.MembraneRestraint___str__(self)
656 r"""__repr__(MembraneRestraint self) -> std::string"""
657 return _IMP_pmi.MembraneRestraint___repr__(self)
661 return _object_cast_to_MembraneRestraint(o)
665 _IMP_pmi.MembraneRestraint_swigregister(MembraneRestraint)
667 r"""Proxy of C++ IMP::pmi::CompositeRestraint class."""
669 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
671 def __init__(self, *args):
672 r"""__init__(CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name="CompositeRestraint%1%") -> CompositeRestraint"""
673 _IMP_pmi.CompositeRestraint_swiginit(self, _IMP_pmi.new_CompositeRestraint(*args))
675 def add_composite_particle(self, pi):
676 r"""add_composite_particle(CompositeRestraint self, _ParticleIndexesAdaptor pi)"""
677 return _IMP_pmi.CompositeRestraint_add_composite_particle(self, pi)
679 def get_number_of_elements(self):
680 r"""get_number_of_elements(CompositeRestraint self) -> unsigned int"""
681 return _IMP_pmi.CompositeRestraint_get_number_of_elements(self)
683 def do_get_inputs(self):
684 r"""do_get_inputs(CompositeRestraint self) -> IMP::ModelObjectsTemp"""
685 return _IMP_pmi.CompositeRestraint_do_get_inputs(self)
687 def get_version_info(self):
688 r"""get_version_info(CompositeRestraint self) -> VersionInfo"""
689 return _IMP_pmi.CompositeRestraint_get_version_info(self)
690 __swig_destroy__ = _IMP_pmi.delete_CompositeRestraint
692 def get_probability(self):
693 r"""get_probability(CompositeRestraint self) -> double"""
694 return _IMP_pmi.CompositeRestraint_get_probability(self)
697 r"""__str__(CompositeRestraint self) -> std::string"""
698 return _IMP_pmi.CompositeRestraint___str__(self)
701 r"""__repr__(CompositeRestraint self) -> std::string"""
702 return _IMP_pmi.CompositeRestraint___repr__(self)
706 return _object_cast_to_CompositeRestraint(o)
710 _IMP_pmi.CompositeRestraint_swigregister(CompositeRestraint)
712 r"""Proxy of C++ IMP::pmi::CrossLinkRestraintSet class."""
714 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
716 def __init__(self, *args):
718 __init__(CrossLinkRestraintSet self, Model m, std::string const & name="CrossLinkRestraintSet %1%") -> CrossLinkRestraintSet
719 __init__(CrossLinkRestraintSet self) -> CrossLinkRestraintSet
721 _IMP_pmi.CrossLinkRestraintSet_swiginit(self, _IMP_pmi.new_CrossLinkRestraintSet(*args))
723 def set_metadata(self, filename, length, slope):
724 r"""set_metadata(CrossLinkRestraintSet self, std::string filename, double length, double slope)"""
725 return _IMP_pmi.CrossLinkRestraintSet_set_metadata(self, filename, length, slope)
727 def set_linker_auth_name(self, name):
728 r"""set_linker_auth_name(CrossLinkRestraintSet self, std::string name)"""
729 return _IMP_pmi.CrossLinkRestraintSet_set_linker_auth_name(self, name)
731 def set_linker_chemical_name(self, name):
732 r"""set_linker_chemical_name(CrossLinkRestraintSet self, std::string name)"""
733 return _IMP_pmi.CrossLinkRestraintSet_set_linker_chemical_name(self, name)
735 def set_linker_smiles(self, name):
736 r"""set_linker_smiles(CrossLinkRestraintSet self, std::string name)"""
737 return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles(self, name)
739 def set_linker_smiles_canonical(self, name):
740 r"""set_linker_smiles_canonical(CrossLinkRestraintSet self, std::string name)"""
741 return _IMP_pmi.CrossLinkRestraintSet_set_linker_smiles_canonical(self, name)
743 def set_linker_inchi(self, name):
744 r"""set_linker_inchi(CrossLinkRestraintSet self, std::string name)"""
745 return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi(self, name)
747 def set_linker_inchi_key(self, name):
748 r"""set_linker_inchi_key(CrossLinkRestraintSet self, std::string name)"""
749 return _IMP_pmi.CrossLinkRestraintSet_set_linker_inchi_key(self, name)
750 __swig_destroy__ = _IMP_pmi.delete_CrossLinkRestraintSet
753 r"""__str__(CrossLinkRestraintSet self) -> std::string"""
754 return _IMP_pmi.CrossLinkRestraintSet___str__(self)
757 r"""__repr__(CrossLinkRestraintSet self) -> std::string"""
758 return _IMP_pmi.CrossLinkRestraintSet___repr__(self)
762 return _object_cast_to_CrossLinkRestraintSet(o)
765 def _get_as_binary(self):
766 r"""_get_as_binary(CrossLinkRestraintSet self) -> PyObject *"""
767 return _IMP_pmi.CrossLinkRestraintSet__get_as_binary(self)
769 def _set_from_binary(self, p):
770 r"""_set_from_binary(CrossLinkRestraintSet self, PyObject * p)"""
771 return _IMP_pmi.CrossLinkRestraintSet__set_from_binary(self, p)
773 def __getstate__(self):
774 p = self._get_as_binary()
775 if len(self.__dict__) > 1:
776 d = self.__dict__.copy()
781 def __setstate__(self, p):
782 if not hasattr(self,
'this'):
784 if isinstance(p, tuple):
786 self.__dict__.update(d)
787 return self._set_from_binary(p)
791 _IMP_pmi.CrossLinkRestraintSet_swigregister(CrossLinkRestraintSet)
793 r"""Proxy of C++ IMP::pmi::Uncertainty class."""
795 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
797 def get_uncertainty(self):
798 r"""get_uncertainty(Uncertainty self) -> IMP::Float"""
799 return _IMP_pmi.Uncertainty_get_uncertainty(self)
801 def set_uncertainty(self, d):
802 r"""set_uncertainty(Uncertainty self, IMP::Float d)"""
803 return _IMP_pmi.Uncertainty_set_uncertainty(self, d)
805 def __init__(self, *args):
807 __init__(Uncertainty self) -> Uncertainty
808 __init__(Uncertainty self, Model m, ParticleIndex id) -> Uncertainty
809 __init__(Uncertainty self, _ParticleAdaptor d) -> Uncertainty
811 _IMP_pmi.Uncertainty_swiginit(self, _IMP_pmi.new_Uncertainty(*args))
814 def get_is_setup(*args):
816 get_is_setup(Model m, ParticleIndex pi) -> bool
817 get_is_setup(_ParticleAdaptor p) -> bool
819 return _IMP_pmi.Uncertainty_get_is_setup(*args)
821 def show(self, *args):
822 r"""show(Uncertainty self, _ostream out=std::cout)"""
823 return _IMP_pmi.Uncertainty_show(self, *args)
826 def setup_particle(*args):
828 setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
829 setup_particle(_ParticleAdaptor pa, IMP::Float uncertainty) -> Uncertainty
831 return _IMP_pmi.Uncertainty_setup_particle(*args)
834 def get_uncertainty_key():
835 r"""get_uncertainty_key() -> FloatKey"""
836 return _IMP_pmi.Uncertainty_get_uncertainty_key()
838 def add_attribute(self, *args):
840 add_attribute(Uncertainty self, FloatKey k, IMP::Float v, bool opt)
841 add_attribute(Uncertainty self, FloatKey a0, IMP::Float a1)
842 add_attribute(Uncertainty self, IntKey a0, IMP::Int a1)
843 add_attribute(Uncertainty self, FloatsKey a0, IMP::Floats a1)
844 add_attribute(Uncertainty self, IntsKey a0, IMP::Ints a1)
845 add_attribute(Uncertainty self, StringKey a0, IMP::String a1)
846 add_attribute(Uncertainty self, ParticleIndexKey a0, Particle a1)
847 add_attribute(Uncertainty self, ObjectKey a0, Object a1)
849 return _IMP_pmi.Uncertainty_add_attribute(self, *args)
851 def get_value(self, *args):
853 get_value(Uncertainty self, FloatKey a0) -> IMP::Float
854 get_value(Uncertainty self, IntKey a0) -> IMP::Int
855 get_value(Uncertainty self, FloatsKey a0) -> IMP::Floats
856 get_value(Uncertainty self, IntsKey a0) -> IMP::Ints
857 get_value(Uncertainty self, StringKey a0) -> IMP::String
858 get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
859 get_value(Uncertainty self, ObjectKey a0) -> Object
861 return _IMP_pmi.Uncertainty_get_value(self, *args)
863 def set_value(self, *args):
865 set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
866 set_value(Uncertainty self, IntKey a0, IMP::Int a1)
867 set_value(Uncertainty self, FloatsKey a0, IMP::Floats a1)
868 set_value(Uncertainty self, IntsKey a0, IMP::Ints a1)
869 set_value(Uncertainty self, StringKey a0, IMP::String a1)
870 set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
871 set_value(Uncertainty self, ObjectKey a0, Object a1)
873 return _IMP_pmi.Uncertainty_set_value(self, *args)
875 def remove_attribute(self, *args):
877 remove_attribute(Uncertainty self, FloatKey a0)
878 remove_attribute(Uncertainty self, IntKey a0)
879 remove_attribute(Uncertainty self, FloatsKey a0)
880 remove_attribute(Uncertainty self, IntsKey a0)
881 remove_attribute(Uncertainty self, StringKey a0)
882 remove_attribute(Uncertainty self, ParticleIndexKey a0)
883 remove_attribute(Uncertainty self, ObjectKey a0)
885 return _IMP_pmi.Uncertainty_remove_attribute(self, *args)
887 def has_attribute(self, *args):
889 has_attribute(Uncertainty self, FloatKey a0) -> bool
890 has_attribute(Uncertainty self, IntKey a0) -> bool
891 has_attribute(Uncertainty self, FloatsKey a0) -> bool
892 has_attribute(Uncertainty self, IntsKey a0) -> bool
893 has_attribute(Uncertainty self, StringKey a0) -> bool
894 has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
895 has_attribute(Uncertainty self, ObjectKey a0) -> bool
897 return _IMP_pmi.Uncertainty_has_attribute(self, *args)
899 def get_derivative(self, a0):
900 r"""get_derivative(Uncertainty self, FloatKey a0) -> double"""
901 return _IMP_pmi.Uncertainty_get_derivative(self, a0)
904 r"""get_name(Uncertainty self) -> std::string"""
905 return _IMP_pmi.Uncertainty_get_name(self)
907 def clear_caches(self):
908 r"""clear_caches(Uncertainty self)"""
909 return _IMP_pmi.Uncertainty_clear_caches(self)
911 def set_name(self, a0):
912 r"""set_name(Uncertainty self, std::string a0)"""
913 return _IMP_pmi.Uncertainty_set_name(self, a0)
916 r"""set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
917 return _IMP_pmi.Uncertainty_set_check_level(self, a0)
919 def add_to_derivative(self, a0, a1, a2):
920 r"""add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
921 return _IMP_pmi.Uncertainty_add_to_derivative(self, a0, a1, a2)
923 def set_is_optimized(self, a0, a1):
924 r"""set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
925 return _IMP_pmi.Uncertainty_set_is_optimized(self, a0, a1)
927 def get_is_optimized(self, a0):
928 r"""get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
929 return _IMP_pmi.Uncertainty_get_is_optimized(self, a0)
932 r"""get_check_level(Uncertainty self) -> IMP::CheckLevel"""
933 return _IMP_pmi.Uncertainty_get_check_level(self)
935 def __eq__(self, *args):
937 __eq__(Uncertainty self, Uncertainty o) -> bool
938 __eq__(Uncertainty self, Particle d) -> bool
940 return _IMP_pmi.Uncertainty___eq__(self, *args)
942 def __ne__(self, *args):
944 __ne__(Uncertainty self, Uncertainty o) -> bool
945 __ne__(Uncertainty self, Particle d) -> bool
947 return _IMP_pmi.Uncertainty___ne__(self, *args)
949 def __le__(self, *args):
951 __le__(Uncertainty self, Uncertainty o) -> bool
952 __le__(Uncertainty self, Particle d) -> bool
954 return _IMP_pmi.Uncertainty___le__(self, *args)
956 def __lt__(self, *args):
958 __lt__(Uncertainty self, Uncertainty o) -> bool
959 __lt__(Uncertainty self, Particle d) -> bool
961 return _IMP_pmi.Uncertainty___lt__(self, *args)
963 def __ge__(self, *args):
965 __ge__(Uncertainty self, Uncertainty o) -> bool
966 __ge__(Uncertainty self, Particle d) -> bool
968 return _IMP_pmi.Uncertainty___ge__(self, *args)
970 def __gt__(self, *args):
972 __gt__(Uncertainty self, Uncertainty o) -> bool
973 __gt__(Uncertainty self, Particle d) -> bool
975 return _IMP_pmi.Uncertainty___gt__(self, *args)
978 r"""__hash__(Uncertainty self) -> std::size_t"""
979 return _IMP_pmi.Uncertainty___hash__(self)
982 r"""__str__(Uncertainty self) -> std::string"""
983 return _IMP_pmi.Uncertainty___str__(self)
986 r"""__repr__(Uncertainty self) -> std::string"""
987 return _IMP_pmi.Uncertainty___repr__(self)
989 def _get_as_binary(self):
990 r"""_get_as_binary(Uncertainty self) -> PyObject *"""
991 return _IMP_pmi.Uncertainty__get_as_binary(self)
993 def _set_from_binary(self, p):
994 r"""_set_from_binary(Uncertainty self, PyObject * p)"""
995 return _IMP_pmi.Uncertainty__set_from_binary(self, p)
997 def __getstate__(self):
998 p = self._get_as_binary()
999 if len(self.__dict__) > 1:
1000 d = self.__dict__.copy()
1005 def __setstate__(self, p):
1006 if not hasattr(self,
'this'):
1008 if isinstance(p, tuple):
1010 self.__dict__.update(d)
1011 return self._set_from_binary(p)
1013 __swig_destroy__ = _IMP_pmi.delete_Uncertainty
1016 _IMP_pmi.Uncertainty_swigregister(Uncertainty)
1018 r"""Proxy of C++ IMP::pmi::Resolution class."""
1020 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1023 r"""get_resolution(Resolution self) -> IMP::Float"""
1024 return _IMP_pmi.Resolution_get_resolution(self)
1026 def set_resolution(self, d):
1027 r"""set_resolution(Resolution self, IMP::Float d)"""
1028 return _IMP_pmi.Resolution_set_resolution(self, d)
1030 def __init__(self, *args):
1032 __init__(Resolution self) -> Resolution
1033 __init__(Resolution self, Model m, ParticleIndex id) -> Resolution
1034 __init__(Resolution self, _ParticleAdaptor d) -> Resolution
1036 _IMP_pmi.Resolution_swiginit(self, _IMP_pmi.new_Resolution(*args))
1039 def get_is_setup(*args):
1041 get_is_setup(Model m, ParticleIndex pi) -> bool
1042 get_is_setup(_ParticleAdaptor p) -> bool
1044 return _IMP_pmi.Resolution_get_is_setup(*args)
1046 def show(self, *args):
1047 r"""show(Resolution self, _ostream out=std::cout)"""
1048 return _IMP_pmi.Resolution_show(self, *args)
1051 def setup_particle(*args):
1053 setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
1054 setup_particle(_ParticleAdaptor pa, IMP::Float resolution) -> Resolution
1056 return _IMP_pmi.Resolution_setup_particle(*args)
1059 def get_resolution_key():
1060 r"""get_resolution_key() -> FloatKey"""
1061 return _IMP_pmi.Resolution_get_resolution_key()
1063 def add_attribute(self, *args):
1065 add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
1066 add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
1067 add_attribute(Resolution self, IntKey a0, IMP::Int a1)
1068 add_attribute(Resolution self, FloatsKey a0, IMP::Floats a1)
1069 add_attribute(Resolution self, IntsKey a0, IMP::Ints a1)
1070 add_attribute(Resolution self, StringKey a0, IMP::String a1)
1071 add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
1072 add_attribute(Resolution self, ObjectKey a0, Object a1)
1074 return _IMP_pmi.Resolution_add_attribute(self, *args)
1076 def get_value(self, *args):
1078 get_value(Resolution self, FloatKey a0) -> IMP::Float
1079 get_value(Resolution self, IntKey a0) -> IMP::Int
1080 get_value(Resolution self, FloatsKey a0) -> IMP::Floats
1081 get_value(Resolution self, IntsKey a0) -> IMP::Ints
1082 get_value(Resolution self, StringKey a0) -> IMP::String
1083 get_value(Resolution self, ParticleIndexKey a0) -> Particle
1084 get_value(Resolution self, ObjectKey a0) -> Object
1086 return _IMP_pmi.Resolution_get_value(self, *args)
1088 def set_value(self, *args):
1090 set_value(Resolution self, FloatKey a0, IMP::Float a1)
1091 set_value(Resolution self, IntKey a0, IMP::Int a1)
1092 set_value(Resolution self, FloatsKey a0, IMP::Floats a1)
1093 set_value(Resolution self, IntsKey a0, IMP::Ints a1)
1094 set_value(Resolution self, StringKey a0, IMP::String a1)
1095 set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1096 set_value(Resolution self, ObjectKey a0, Object a1)
1098 return _IMP_pmi.Resolution_set_value(self, *args)
1100 def remove_attribute(self, *args):
1102 remove_attribute(Resolution self, FloatKey a0)
1103 remove_attribute(Resolution self, IntKey a0)
1104 remove_attribute(Resolution self, FloatsKey a0)
1105 remove_attribute(Resolution self, IntsKey a0)
1106 remove_attribute(Resolution self, StringKey a0)
1107 remove_attribute(Resolution self, ParticleIndexKey a0)
1108 remove_attribute(Resolution self, ObjectKey a0)
1110 return _IMP_pmi.Resolution_remove_attribute(self, *args)
1112 def has_attribute(self, *args):
1114 has_attribute(Resolution self, FloatKey a0) -> bool
1115 has_attribute(Resolution self, IntKey a0) -> bool
1116 has_attribute(Resolution self, FloatsKey a0) -> bool
1117 has_attribute(Resolution self, IntsKey a0) -> bool
1118 has_attribute(Resolution self, StringKey a0) -> bool
1119 has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1120 has_attribute(Resolution self, ObjectKey a0) -> bool
1122 return _IMP_pmi.Resolution_has_attribute(self, *args)
1124 def get_derivative(self, a0):
1125 r"""get_derivative(Resolution self, FloatKey a0) -> double"""
1126 return _IMP_pmi.Resolution_get_derivative(self, a0)
1129 r"""get_name(Resolution self) -> std::string"""
1130 return _IMP_pmi.Resolution_get_name(self)
1132 def clear_caches(self):
1133 r"""clear_caches(Resolution self)"""
1134 return _IMP_pmi.Resolution_clear_caches(self)
1136 def set_name(self, a0):
1137 r"""set_name(Resolution self, std::string a0)"""
1138 return _IMP_pmi.Resolution_set_name(self, a0)
1141 r"""set_check_level(Resolution self, IMP::CheckLevel a0)"""
1142 return _IMP_pmi.Resolution_set_check_level(self, a0)
1144 def add_to_derivative(self, a0, a1, a2):
1145 r"""add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1146 return _IMP_pmi.Resolution_add_to_derivative(self, a0, a1, a2)
1148 def set_is_optimized(self, a0, a1):
1149 r"""set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1150 return _IMP_pmi.Resolution_set_is_optimized(self, a0, a1)
1152 def get_is_optimized(self, a0):
1153 r"""get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1154 return _IMP_pmi.Resolution_get_is_optimized(self, a0)
1157 r"""get_check_level(Resolution self) -> IMP::CheckLevel"""
1158 return _IMP_pmi.Resolution_get_check_level(self)
1160 def __eq__(self, *args):
1162 __eq__(Resolution self, Resolution o) -> bool
1163 __eq__(Resolution self, Particle d) -> bool
1165 return _IMP_pmi.Resolution___eq__(self, *args)
1167 def __ne__(self, *args):
1169 __ne__(Resolution self, Resolution o) -> bool
1170 __ne__(Resolution self, Particle d) -> bool
1172 return _IMP_pmi.Resolution___ne__(self, *args)
1174 def __le__(self, *args):
1176 __le__(Resolution self, Resolution o) -> bool
1177 __le__(Resolution self, Particle d) -> bool
1179 return _IMP_pmi.Resolution___le__(self, *args)
1181 def __lt__(self, *args):
1183 __lt__(Resolution self, Resolution o) -> bool
1184 __lt__(Resolution self, Particle d) -> bool
1186 return _IMP_pmi.Resolution___lt__(self, *args)
1188 def __ge__(self, *args):
1190 __ge__(Resolution self, Resolution o) -> bool
1191 __ge__(Resolution self, Particle d) -> bool
1193 return _IMP_pmi.Resolution___ge__(self, *args)
1195 def __gt__(self, *args):
1197 __gt__(Resolution self, Resolution o) -> bool
1198 __gt__(Resolution self, Particle d) -> bool
1200 return _IMP_pmi.Resolution___gt__(self, *args)
1203 r"""__hash__(Resolution self) -> std::size_t"""
1204 return _IMP_pmi.Resolution___hash__(self)
1207 r"""__str__(Resolution self) -> std::string"""
1208 return _IMP_pmi.Resolution___str__(self)
1211 r"""__repr__(Resolution self) -> std::string"""
1212 return _IMP_pmi.Resolution___repr__(self)
1214 def _get_as_binary(self):
1215 r"""_get_as_binary(Resolution self) -> PyObject *"""
1216 return _IMP_pmi.Resolution__get_as_binary(self)
1218 def _set_from_binary(self, p):
1219 r"""_set_from_binary(Resolution self, PyObject * p)"""
1220 return _IMP_pmi.Resolution__set_from_binary(self, p)
1222 def __getstate__(self):
1223 p = self._get_as_binary()
1224 if len(self.__dict__) > 1:
1225 d = self.__dict__.copy()
1230 def __setstate__(self, p):
1231 if not hasattr(self,
'this'):
1233 if isinstance(p, tuple):
1235 self.__dict__.update(d)
1236 return self._set_from_binary(p)
1238 __swig_destroy__ = _IMP_pmi.delete_Resolution
1241 _IMP_pmi.Resolution_swigregister(Resolution)
1243 r"""Proxy of C++ IMP::pmi::Symmetric class."""
1245 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1247 def get_symmetric(self):
1248 r"""get_symmetric(Symmetric self) -> IMP::Float"""
1249 return _IMP_pmi.Symmetric_get_symmetric(self)
1251 def set_symmetric(self, d):
1252 r"""set_symmetric(Symmetric self, IMP::Float d)"""
1253 return _IMP_pmi.Symmetric_set_symmetric(self, d)
1255 def __init__(self, *args):
1257 __init__(Symmetric self) -> Symmetric
1258 __init__(Symmetric self, Model m, ParticleIndex id) -> Symmetric
1259 __init__(Symmetric self, _ParticleAdaptor d) -> Symmetric
1261 _IMP_pmi.Symmetric_swiginit(self, _IMP_pmi.new_Symmetric(*args))
1264 def get_is_setup(*args):
1266 get_is_setup(Model m, ParticleIndex pi) -> bool
1267 get_is_setup(_ParticleAdaptor p) -> bool
1269 return _IMP_pmi.Symmetric_get_is_setup(*args)
1271 def show(self, *args):
1272 r"""show(Symmetric self, _ostream out=std::cout)"""
1273 return _IMP_pmi.Symmetric_show(self, *args)
1276 def setup_particle(*args):
1278 setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1279 setup_particle(_ParticleAdaptor pa, IMP::Float symmetric) -> Symmetric
1281 return _IMP_pmi.Symmetric_setup_particle(*args)
1284 def get_symmetric_key():
1285 r"""get_symmetric_key() -> FloatKey"""
1286 return _IMP_pmi.Symmetric_get_symmetric_key()
1288 def add_attribute(self, *args):
1290 add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1291 add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1292 add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1293 add_attribute(Symmetric self, FloatsKey a0, IMP::Floats a1)
1294 add_attribute(Symmetric self, IntsKey a0, IMP::Ints a1)
1295 add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1296 add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1297 add_attribute(Symmetric self, ObjectKey a0, Object a1)
1299 return _IMP_pmi.Symmetric_add_attribute(self, *args)
1301 def get_value(self, *args):
1303 get_value(Symmetric self, FloatKey a0) -> IMP::Float
1304 get_value(Symmetric self, IntKey a0) -> IMP::Int
1305 get_value(Symmetric self, FloatsKey a0) -> IMP::Floats
1306 get_value(Symmetric self, IntsKey a0) -> IMP::Ints
1307 get_value(Symmetric self, StringKey a0) -> IMP::String
1308 get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1309 get_value(Symmetric self, ObjectKey a0) -> Object
1311 return _IMP_pmi.Symmetric_get_value(self, *args)
1313 def set_value(self, *args):
1315 set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1316 set_value(Symmetric self, IntKey a0, IMP::Int a1)
1317 set_value(Symmetric self, FloatsKey a0, IMP::Floats a1)
1318 set_value(Symmetric self, IntsKey a0, IMP::Ints a1)
1319 set_value(Symmetric self, StringKey a0, IMP::String a1)
1320 set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1321 set_value(Symmetric self, ObjectKey a0, Object a1)
1323 return _IMP_pmi.Symmetric_set_value(self, *args)
1325 def remove_attribute(self, *args):
1327 remove_attribute(Symmetric self, FloatKey a0)
1328 remove_attribute(Symmetric self, IntKey a0)
1329 remove_attribute(Symmetric self, FloatsKey a0)
1330 remove_attribute(Symmetric self, IntsKey a0)
1331 remove_attribute(Symmetric self, StringKey a0)
1332 remove_attribute(Symmetric self, ParticleIndexKey a0)
1333 remove_attribute(Symmetric self, ObjectKey a0)
1335 return _IMP_pmi.Symmetric_remove_attribute(self, *args)
1337 def has_attribute(self, *args):
1339 has_attribute(Symmetric self, FloatKey a0) -> bool
1340 has_attribute(Symmetric self, IntKey a0) -> bool
1341 has_attribute(Symmetric self, FloatsKey a0) -> bool
1342 has_attribute(Symmetric self, IntsKey a0) -> bool
1343 has_attribute(Symmetric self, StringKey a0) -> bool
1344 has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1345 has_attribute(Symmetric self, ObjectKey a0) -> bool
1347 return _IMP_pmi.Symmetric_has_attribute(self, *args)
1349 def get_derivative(self, a0):
1350 r"""get_derivative(Symmetric self, FloatKey a0) -> double"""
1351 return _IMP_pmi.Symmetric_get_derivative(self, a0)
1354 r"""get_name(Symmetric self) -> std::string"""
1355 return _IMP_pmi.Symmetric_get_name(self)
1357 def clear_caches(self):
1358 r"""clear_caches(Symmetric self)"""
1359 return _IMP_pmi.Symmetric_clear_caches(self)
1361 def set_name(self, a0):
1362 r"""set_name(Symmetric self, std::string a0)"""
1363 return _IMP_pmi.Symmetric_set_name(self, a0)
1366 r"""set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1367 return _IMP_pmi.Symmetric_set_check_level(self, a0)
1369 def add_to_derivative(self, a0, a1, a2):
1370 r"""add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1371 return _IMP_pmi.Symmetric_add_to_derivative(self, a0, a1, a2)
1373 def set_is_optimized(self, a0, a1):
1374 r"""set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1375 return _IMP_pmi.Symmetric_set_is_optimized(self, a0, a1)
1377 def get_is_optimized(self, a0):
1378 r"""get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1379 return _IMP_pmi.Symmetric_get_is_optimized(self, a0)
1382 r"""get_check_level(Symmetric self) -> IMP::CheckLevel"""
1383 return _IMP_pmi.Symmetric_get_check_level(self)
1385 def __eq__(self, *args):
1387 __eq__(Symmetric self, Symmetric o) -> bool
1388 __eq__(Symmetric self, Particle d) -> bool
1390 return _IMP_pmi.Symmetric___eq__(self, *args)
1392 def __ne__(self, *args):
1394 __ne__(Symmetric self, Symmetric o) -> bool
1395 __ne__(Symmetric self, Particle d) -> bool
1397 return _IMP_pmi.Symmetric___ne__(self, *args)
1399 def __le__(self, *args):
1401 __le__(Symmetric self, Symmetric o) -> bool
1402 __le__(Symmetric self, Particle d) -> bool
1404 return _IMP_pmi.Symmetric___le__(self, *args)
1406 def __lt__(self, *args):
1408 __lt__(Symmetric self, Symmetric o) -> bool
1409 __lt__(Symmetric self, Particle d) -> bool
1411 return _IMP_pmi.Symmetric___lt__(self, *args)
1413 def __ge__(self, *args):
1415 __ge__(Symmetric self, Symmetric o) -> bool
1416 __ge__(Symmetric self, Particle d) -> bool
1418 return _IMP_pmi.Symmetric___ge__(self, *args)
1420 def __gt__(self, *args):
1422 __gt__(Symmetric self, Symmetric o) -> bool
1423 __gt__(Symmetric self, Particle d) -> bool
1425 return _IMP_pmi.Symmetric___gt__(self, *args)
1428 r"""__hash__(Symmetric self) -> std::size_t"""
1429 return _IMP_pmi.Symmetric___hash__(self)
1432 r"""__str__(Symmetric self) -> std::string"""
1433 return _IMP_pmi.Symmetric___str__(self)
1436 r"""__repr__(Symmetric self) -> std::string"""
1437 return _IMP_pmi.Symmetric___repr__(self)
1439 def _get_as_binary(self):
1440 r"""_get_as_binary(Symmetric self) -> PyObject *"""
1441 return _IMP_pmi.Symmetric__get_as_binary(self)
1443 def _set_from_binary(self, p):
1444 r"""_set_from_binary(Symmetric self, PyObject * p)"""
1445 return _IMP_pmi.Symmetric__set_from_binary(self, p)
1447 def __getstate__(self):
1448 p = self._get_as_binary()
1449 if len(self.__dict__) > 1:
1450 d = self.__dict__.copy()
1455 def __setstate__(self, p):
1456 if not hasattr(self,
'this'):
1458 if isinstance(p, tuple):
1460 self.__dict__.update(d)
1461 return self._set_from_binary(p)
1463 __swig_destroy__ = _IMP_pmi.delete_Symmetric
1466 _IMP_pmi.Symmetric_swigregister(Symmetric)
1468 r"""Proxy of C++ IMP::pmi::TransformMover class."""
1470 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1472 def __init__(self, *args):
1474 __init__(TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1475 __init__(TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1476 __init__(TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1477 __init__(TransformMover self) -> TransformMover
1479 _IMP_pmi.TransformMover_swiginit(self, _IMP_pmi.new_TransformMover(*args))
1481 def add_xyz_particle(self, pi):
1482 r"""add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1483 return _IMP_pmi.TransformMover_add_xyz_particle(self, pi)
1485 def add_rigid_body_particle(self, pi):
1486 r"""add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1487 return _IMP_pmi.TransformMover_add_rigid_body_particle(self, pi)
1489 def set_maximum_translation(self, mt):
1490 r"""set_maximum_translation(TransformMover self, IMP::Float mt)"""
1491 return _IMP_pmi.TransformMover_set_maximum_translation(self, mt)
1493 def set_maximum_rotation(self, mr):
1494 r"""set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1495 return _IMP_pmi.TransformMover_set_maximum_rotation(self, mr)
1497 def get_maximum_translation(self):
1498 r"""get_maximum_translation(TransformMover self) -> IMP::Float"""
1499 return _IMP_pmi.TransformMover_get_maximum_translation(self)
1501 def get_maximum_rotation(self):
1502 r"""get_maximum_rotation(TransformMover self) -> IMP::Float"""
1503 return _IMP_pmi.TransformMover_get_maximum_rotation(self)
1505 def get_last_transformation(self):
1506 r"""get_last_transformation(TransformMover self) -> Transformation3D"""
1507 return _IMP_pmi.TransformMover_get_last_transformation(self)
1509 def get_version_info(self):
1510 r"""get_version_info(TransformMover self) -> VersionInfo"""
1511 return _IMP_pmi.TransformMover_get_version_info(self)
1512 __swig_destroy__ = _IMP_pmi.delete_TransformMover
1515 r"""__str__(TransformMover self) -> std::string"""
1516 return _IMP_pmi.TransformMover___str__(self)
1519 r"""__repr__(TransformMover self) -> std::string"""
1520 return _IMP_pmi.TransformMover___repr__(self)
1524 return _object_cast_to_TransformMover(o)
1527 def _get_as_binary(self):
1528 r"""_get_as_binary(TransformMover self) -> PyObject *"""
1529 return _IMP_pmi.TransformMover__get_as_binary(self)
1531 def _set_from_binary(self, p):
1532 r"""_set_from_binary(TransformMover self, PyObject * p)"""
1533 return _IMP_pmi.TransformMover__set_from_binary(self, p)
1535 def __getstate__(self):
1536 p = self._get_as_binary()
1537 if len(self.__dict__) > 1:
1538 d = self.__dict__.copy()
1543 def __setstate__(self, p):
1544 if not hasattr(self,
'this'):
1546 if isinstance(p, tuple):
1548 self.__dict__.update(d)
1549 return self._set_from_binary(p)
1553 _IMP_pmi.TransformMover_swigregister(TransformMover)
1556 r"""create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1557 return _IMP_pmi.create_elastic_network(ps, dist_cutoff, strength)
1559 def get_dihedral_angle(p1, p2, p3, p4):
1560 r"""get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1561 return _IMP_pmi.get_dihedral_angle(p1, p2, p3, p4)
1563 def get_bipartite_minimum_sphere_distance(m1, m2):
1564 r"""get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1565 return _IMP_pmi.get_bipartite_minimum_sphere_distance(m1, m2)
1567 def get_list_of_bipartite_minimum_sphere_distance(pss):
1568 r"""get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1569 return _IMP_pmi.get_list_of_bipartite_minimum_sphere_distance(pss)
1572 r"""get_molecule_name_and_copy(Hierarchy h) -> std::string"""
1573 return _IMP_pmi.get_molecule_name_and_copy(h)
1576 r"""get_is_canonical(Hierarchy h) -> bool"""
1577 return _IMP_pmi.get_is_canonical(h)
1580 r"""get_module_version() -> std::string const"""
1581 return _IMP_pmi.get_module_version()
1584 r"""get_example_path(std::string fname) -> std::string"""
1585 return _IMP_pmi.get_example_path(fname)
1588 r"""get_data_path(std::string fname) -> std::string"""
1589 return _IMP_pmi.get_data_path(fname)
1591 from .
import _version_check
CheckLevel get_check_level()
Get the current audit mode.
A base class for ISD Restraints.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
std::string get_module_version()
Return the version of this module, as a string.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
Object used to hold a set of restraints.
Warning related to handling of structures.
std::string get_molecule_name_and_copy(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and get the "molname.copynum".
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
A base class for classes which perturb particles.
Basic utilities for handling cryo-electron microscopy 3D density maps.
Warning for an expected, but missing, file.
bool get_is_canonical(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and check if the root is named System.
Interface to specialized Particle types (e.g. atoms)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for small angle X-ray scattering (SAXS) data.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.