10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_npctransport')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_npctransport')
25 _IMP_npctransport = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_npctransport', [dirname(__file__)])
35 import _IMP_npctransport
36 return _IMP_npctransport
39 _mod = imp.load_module(
'_IMP_npctransport', fp, pathname, description)
43 _IMP_npctransport = swig_import_helper()
44 del swig_import_helper
46 import _IMP_npctransport
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_NPCTRANSPORT_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_NPCTRANSPORT_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_npctransport.delete_IMP_NPCTRANSPORT_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
126 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_value(self)
131 incr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
132 incr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
134 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_incr(self, n)
139 decr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
140 decr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
142 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_distance(self, x)
151 """equal(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
152 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_equal(self, x)
156 """copy(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator"""
157 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_copy(self)
161 """next(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
162 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_next(self)
166 """__next__(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
167 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___next__(self)
171 """previous(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
172 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
177 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
182 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
187 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
192 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
197 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
202 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator
208 __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___sub__(self, *args)
214 IMP_NPCTRANSPORT_SwigPyIterator_swigregister = _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_swigregister
215 IMP_NPCTRANSPORT_SwigPyIterator_swigregister(IMP_NPCTRANSPORT_SwigPyIterator)
223 IMP_DEBUG = _IMP_npctransport.IMP_DEBUG
224 IMP_RELEASE = _IMP_npctransport.IMP_RELEASE
225 IMP_SILENT = _IMP_npctransport.IMP_SILENT
226 IMP_PROGRESS = _IMP_npctransport.IMP_PROGRESS
227 IMP_TERSE = _IMP_npctransport.IMP_TERSE
228 IMP_VERBOSE = _IMP_npctransport.IMP_VERBOSE
229 IMP_MEMORY = _IMP_npctransport.IMP_MEMORY
230 IMP_NONE = _IMP_npctransport.IMP_NONE
231 IMP_USAGE = _IMP_npctransport.IMP_USAGE
232 IMP_INTERNAL = _IMP_npctransport.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_npctransport.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_npctransport.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_npctransport._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_npctransport._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_npctransport.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_npctransport.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_npctransport.IMP_HAS_NOEXCEPT
288 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
290 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
291 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
292 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
293 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
294 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
296 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
297 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
298 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
299 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
300 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
302 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
303 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
304 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
305 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
306 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
307 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
308 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
309 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
311 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
312 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
313 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
314 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
315 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
316 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
317 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
319 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
320 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
322 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
323 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
324 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
325 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
326 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
328 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
329 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
330 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
331 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
332 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
333 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
336 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
344 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
346 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
347 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
348 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
349 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
350 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
351 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
352 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
353 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
354 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
355 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
356 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
357 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
358 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
359 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
362 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
363 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
364 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
365 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
366 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
367 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
368 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
369 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
370 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
371 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
372 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
373 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
374 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
375 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
376 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
378 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
379 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
380 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
381 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
382 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
383 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
384 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
385 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
386 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
387 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
388 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
391 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
392 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
393 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
394 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
395 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
396 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
397 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
398 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
399 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
400 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
402 _object_types.append(
"SitesPairScore")
405 def _object_cast_to_SitesPairScore(o):
406 """_object_cast_to_SitesPairScore(Object o) -> SitesPairScore"""
407 return _IMP_npctransport._object_cast_to_SitesPairScore(o)
409 _object_types.append(
"Scoring")
412 def _object_cast_to_Scoring(o):
413 """_object_cast_to_Scoring(Object o) -> Scoring"""
414 return _IMP_npctransport._object_cast_to_Scoring(o)
416 _object_types.append(
"BrownianDynamicsTAMDWithSlabSupport")
419 def _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o):
420 """_object_cast_to_BrownianDynamicsTAMDWithSlabSupport(Object o) -> BrownianDynamicsTAMDWithSlabSupport"""
421 return _IMP_npctransport._object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
423 _object_types.append(
"Statistics")
426 def _object_cast_to_Statistics(o):
427 """_object_cast_to_Statistics(Object o) -> Statistics"""
428 return _IMP_npctransport._object_cast_to_Statistics(o)
430 _object_types.append(
"SimulationData")
433 def _object_cast_to_SimulationData(o):
434 """_object_cast_to_SimulationData(Object o) -> SimulationData"""
435 return _IMP_npctransport._object_cast_to_SimulationData(o)
437 _object_types.append(
"SitesGeometry")
440 def _object_cast_to_SitesGeometry(o):
441 """_object_cast_to_SitesGeometry(Object o) -> SitesGeometry"""
442 return _IMP_npctransport._object_cast_to_SitesGeometry(o)
444 _object_types.append(
"TypedSitesGeometry")
447 def _object_cast_to_TypedSitesGeometry(o):
448 """_object_cast_to_TypedSitesGeometry(Object o) -> TypedSitesGeometry"""
449 return _IMP_npctransport._object_cast_to_TypedSitesGeometry(o)
451 _object_types.append(
"SlabWithCylindricalPorePairScore")
454 def _object_cast_to_SlabWithCylindricalPorePairScore(o):
455 """_object_cast_to_SlabWithCylindricalPorePairScore(Object o) -> SlabWithCylindricalPorePairScore"""
456 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPorePairScore(o)
458 _object_types.append(
"SlabWithToroidalPorePairScore")
461 def _object_cast_to_SlabWithToroidalPorePairScore(o):
462 """_object_cast_to_SlabWithToroidalPorePairScore(Object o) -> SlabWithToroidalPorePairScore"""
463 return _IMP_npctransport._object_cast_to_SlabWithToroidalPorePairScore(o)
465 _object_types.append(
"PoreRadiusSingletonScore")
468 def _object_cast_to_PoreRadiusSingletonScore(o):
469 """_object_cast_to_PoreRadiusSingletonScore(Object o) -> PoreRadiusSingletonScore"""
470 return _IMP_npctransport._object_cast_to_PoreRadiusSingletonScore(o)
472 _object_types.append(
"ExcludeZRangeSingletonScore")
475 def _object_cast_to_ExcludeZRangeSingletonScore(o):
476 """_object_cast_to_ExcludeZRangeSingletonScore(Object o) -> ExcludeZRangeSingletonScore"""
477 return _IMP_npctransport._object_cast_to_ExcludeZRangeSingletonScore(o)
479 _object_types.append(
"ZBiasSingletonScore")
482 def _object_cast_to_ZBiasSingletonScore(o):
483 """_object_cast_to_ZBiasSingletonScore(Object o) -> ZBiasSingletonScore"""
484 return _IMP_npctransport._object_cast_to_ZBiasSingletonScore(o)
486 _object_types.append(
"SlabWithCylindricalPoreWireGeometry")
489 def _object_cast_to_SlabWithCylindricalPoreWireGeometry(o):
490 """_object_cast_to_SlabWithCylindricalPoreWireGeometry(Object o) -> SlabWithCylindricalPoreWireGeometry"""
491 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
493 _object_types.append(
"SlabWithCylindricalPoreSurfaceGeometry")
496 def _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o):
497 """_object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(Object o) -> SlabWithCylindricalPoreSurfaceGeometry"""
498 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
500 _object_types.append(
"SlabWithToroidalPoreWireGeometry")
503 def _object_cast_to_SlabWithToroidalPoreWireGeometry(o):
504 """_object_cast_to_SlabWithToroidalPoreWireGeometry(Object o) -> SlabWithToroidalPoreWireGeometry"""
505 return _IMP_npctransport._object_cast_to_SlabWithToroidalPoreWireGeometry(o)
507 _object_types.append(
"LinearSoftSpherePairScore")
510 def _object_cast_to_LinearSoftSpherePairScore(o):
511 """_object_cast_to_LinearSoftSpherePairScore(Object o) -> LinearSoftSpherePairScore"""
512 return _IMP_npctransport._object_cast_to_LinearSoftSpherePairScore(o)
514 _object_types.append(
"FunctorLinearSoftSpherePairScore")
517 def _object_cast_to_FunctorLinearSoftSpherePairScore(o):
518 """_object_cast_to_FunctorLinearSoftSpherePairScore(Object o) -> FunctorLinearSoftSpherePairScore"""
519 return _IMP_npctransport._object_cast_to_FunctorLinearSoftSpherePairScore(o)
521 _object_types.append(
"LinearInteractionPairScore")
524 def _object_cast_to_LinearInteractionPairScore(o):
525 """_object_cast_to_LinearInteractionPairScore(Object o) -> LinearInteractionPairScore"""
526 return _IMP_npctransport._object_cast_to_LinearInteractionPairScore(o)
528 _object_types.append(
"FunctorLinearInteractionPairScore")
531 def _object_cast_to_FunctorLinearInteractionPairScore(o):
532 """_object_cast_to_FunctorLinearInteractionPairScore(Object o) -> FunctorLinearInteractionPairScore"""
533 return _IMP_npctransport._object_cast_to_FunctorLinearInteractionPairScore(o)
535 _object_types.append(
"LinearWellPairScore")
538 def _object_cast_to_LinearWellPairScore(o):
539 """_object_cast_to_LinearWellPairScore(Object o) -> LinearWellPairScore"""
540 return _IMP_npctransport._object_cast_to_LinearWellPairScore(o)
542 _object_types.append(
"HarmonicSpringSingletonScore")
545 def _object_cast_to_HarmonicSpringSingletonScore(o):
546 """_object_cast_to_HarmonicSpringSingletonScore(Object o) -> HarmonicSpringSingletonScore"""
547 return _IMP_npctransport._object_cast_to_HarmonicSpringSingletonScore(o)
549 _object_types.append(
"HierarchyWithSitesSaveLink")
552 def _object_cast_to_HierarchyWithSitesSaveLink(o):
553 """_object_cast_to_HierarchyWithSitesSaveLink(Object o) -> HierarchyWithSitesSaveLink"""
554 return _IMP_npctransport._object_cast_to_HierarchyWithSitesSaveLink(o)
556 _object_types.append(
"HierarchyWithSitesLoadLink")
559 def _object_cast_to_HierarchyWithSitesLoadLink(o):
560 """_object_cast_to_HierarchyWithSitesLoadLink(Object o) -> HierarchyWithSitesLoadLink"""
561 return _IMP_npctransport._object_cast_to_HierarchyWithSitesLoadLink(o)
563 _object_types.append(
"ChainStatisticsOptimizerState")
566 def _object_cast_to_ChainStatisticsOptimizerState(o):
567 """_object_cast_to_ChainStatisticsOptimizerState(Object o) -> ChainStatisticsOptimizerState"""
568 return _IMP_npctransport._object_cast_to_ChainStatisticsOptimizerState(o)
570 _object_types.append(
"BodyStatisticsOptimizerState")
573 def _object_cast_to_BodyStatisticsOptimizerState(o):
574 """_object_cast_to_BodyStatisticsOptimizerState(Object o) -> BodyStatisticsOptimizerState"""
575 return _IMP_npctransport._object_cast_to_BodyStatisticsOptimizerState(o)
577 _object_types.append(
"BipartitePairsStatisticsOptimizerState")
580 def _object_cast_to_BipartitePairsStatisticsOptimizerState(o):
581 """_object_cast_to_BipartitePairsStatisticsOptimizerState(Object o) -> BipartitePairsStatisticsOptimizerState"""
582 return _IMP_npctransport._object_cast_to_BipartitePairsStatisticsOptimizerState(o)
584 _object_types.append(
"ParticleTransportStatisticsOptimizerState")
587 def _object_cast_to_ParticleTransportStatisticsOptimizerState(o):
588 """_object_cast_to_ParticleTransportStatisticsOptimizerState(Object o) -> ParticleTransportStatisticsOptimizerState"""
589 return _IMP_npctransport._object_cast_to_ParticleTransportStatisticsOptimizerState(o)
591 _object_types.append(
"FGChain")
594 def _object_cast_to_FGChain(o):
595 """_object_cast_to_FGChain(Object o) -> FGChain"""
596 return _IMP_npctransport._object_cast_to_FGChain(o)
598 _object_types.append(
"ParticleFactory")
601 def _object_cast_to_ParticleFactory(o):
602 """_object_cast_to_ParticleFactory(Object o) -> ParticleFactory"""
603 return _IMP_npctransport._object_cast_to_ParticleFactory(o)
606 _plural_types.append(
"Avro2PBReaders")
607 _value_types.append(
"Avro2PBReader")
610 SitesPairScoreParametersList=list
611 _plural_types.append(
"SitesPairScoreParametersList")
612 _value_types.append(
"SitesPairScoreParameters")
615 def Transportings(l=[]):
616 return [Transporting(x)
for x
in l]
617 _plural_types.append(
"Transportings")
620 _value_types.append(
"Transporting")
623 def SlabWithPores(l=[]):
624 return [SlabWithPore(x)
for x
in l]
625 _plural_types.append(
"SlabWithPores")
628 _value_types.append(
"SlabWithPore")
631 def SlabWithCylindricalPores(l=[]):
632 return [SlabWithCylindricalPore(x)
for x
in l]
633 _plural_types.append(
"SlabWithCylindricalPores")
636 _value_types.append(
"SlabWithCylindricalPore")
639 def RelaxingSprings(l=[]):
640 return [RelaxingSpring(x)
for x
in l]
641 _plural_types.append(
"RelaxingSprings")
644 _value_types.append(
"RelaxingSpring")
647 def SlabWithToroidalPores(l=[]):
648 return [SlabWithToroidalPore(x)
for x
in l]
649 _plural_types.append(
"SlabWithToroidalPores")
652 _value_types.append(
"SlabWithToroidalPore")
654 class _DoubleParameter(object):
655 """Proxy of C++ IMP::npctransport::Parameter<(double)> class."""
657 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
658 __repr__ = _swig_repr
662 __init__(IMP::npctransport::Parameter<(double)> self) -> _DoubleParameter
663 __init__(IMP::npctransport::Parameter<(double)> self, double t) -> _DoubleParameter
665 this = _IMP_npctransport.new__DoubleParameter(*args)
667 self.this.append(this)
668 except __builtin__.Exception:
672 """get_value(_DoubleParameter self) -> double"""
673 return _IMP_npctransport._DoubleParameter_get_value(self)
677 """is_init(_DoubleParameter self) -> bool"""
678 return _IMP_npctransport._DoubleParameter_is_init(self)
680 __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
681 __del__ =
lambda self:
None
682 _DoubleParameter_swigregister = _IMP_npctransport._DoubleParameter_swigregister
683 _DoubleParameter_swigregister(_DoubleParameter)
685 class _IntParameter(object):
686 """Proxy of C++ IMP::npctransport::Parameter<(int)> class."""
688 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
689 __repr__ = _swig_repr
693 __init__(IMP::npctransport::Parameter<(int)> self) -> _IntParameter
694 __init__(IMP::npctransport::Parameter<(int)> self, int t) -> _IntParameter
696 this = _IMP_npctransport.new__IntParameter(*args)
698 self.this.append(this)
699 except __builtin__.Exception:
703 """get_value(_IntParameter self) -> int"""
704 return _IMP_npctransport._IntParameter_get_value(self)
708 """is_init(_IntParameter self) -> bool"""
709 return _IMP_npctransport._IntParameter_is_init(self)
711 __swig_destroy__ = _IMP_npctransport.delete__IntParameter
712 __del__ =
lambda self:
None
713 _IntParameter_swigregister = _IMP_npctransport._IntParameter_swigregister
714 _IntParameter_swigregister(_IntParameter)
716 class _BoolParameter(object):
717 """Proxy of C++ IMP::npctransport::Parameter<(bool)> class."""
719 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
720 __repr__ = _swig_repr
724 __init__(IMP::npctransport::Parameter<(bool)> self) -> _BoolParameter
725 __init__(IMP::npctransport::Parameter<(bool)> self, bool t) -> _BoolParameter
727 this = _IMP_npctransport.new__BoolParameter(*args)
729 self.this.append(this)
730 except __builtin__.Exception:
734 """get_value(_BoolParameter self) -> bool"""
735 return _IMP_npctransport._BoolParameter_get_value(self)
739 """is_init(_BoolParameter self) -> bool"""
740 return _IMP_npctransport._BoolParameter_is_init(self)
742 __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
743 __del__ =
lambda self:
None
744 _BoolParameter_swigregister = _IMP_npctransport._BoolParameter_swigregister
745 _BoolParameter_swigregister(_BoolParameter)
749 """make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
750 return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
753 """make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
754 return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
758 make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
759 make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
761 return _IMP_npctransport.make_unordered_particle_index_pair(*args)
763 """Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class."""
765 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
769 __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k, std::string name) -> LinearSoftSpherePairScore
770 __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k) -> LinearSoftSpherePairScore
772 this = _IMP_npctransport.new_LinearSoftSpherePairScore(*args)
774 self.this.append(this)
775 except __builtin__.Exception:
778 def do_get_inputs(self, m, pis):
779 """do_get_inputs(LinearSoftSpherePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
780 return _IMP_npctransport.LinearSoftSpherePairScore_do_get_inputs(self, m, pis)
784 """get_k(LinearSoftSpherePairScore self) -> double"""
785 return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
788 def get_version_info(self):
789 """get_version_info(LinearSoftSpherePairScore self) -> VersionInfo"""
790 return _IMP_npctransport.LinearSoftSpherePairScore_get_version_info(self)
794 """__str__(LinearSoftSpherePairScore self) -> std::string"""
795 return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
799 """__repr__(LinearSoftSpherePairScore self) -> std::string"""
800 return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
805 return _object_cast_to_LinearSoftSpherePairScore(o)
807 LinearSoftSpherePairScore_swigregister = _IMP_npctransport.LinearSoftSpherePairScore_swigregister
808 LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
811 """Proxy of C++ IMP::npctransport::LinearInteractionPairScore class."""
813 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
817 __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr, std::string name) -> LinearInteractionPairScore
818 __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr) -> LinearInteractionPairScore
820 this = _IMP_npctransport.new_LinearInteractionPairScore(*args)
822 self.this.append(this)
823 except __builtin__.Exception:
826 def evaluate_if_good_index(self, *args):
828 evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPair const & p, DerivativeAccumulator da, double max) -> double
829 evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound) -> double
831 return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
834 def do_get_inputs(self, m, pis):
835 """do_get_inputs(LinearInteractionPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
836 return _IMP_npctransport.LinearInteractionPairScore_do_get_inputs(self, m, pis)
839 def get_range_attraction(self):
840 """get_range_attraction(LinearInteractionPairScore self) -> double"""
841 return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
844 def get_k_attraction(self):
845 """get_k_attraction(LinearInteractionPairScore self) -> double"""
846 return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
849 def set_k_attraction(self, k_attr):
850 """set_k_attraction(LinearInteractionPairScore self, double k_attr)"""
851 return _IMP_npctransport.LinearInteractionPairScore_set_k_attraction(self, k_attr)
854 def get_k_repulsion(self):
855 """get_k_repulsion(LinearInteractionPairScore self) -> double"""
856 return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
859 def set_k_repulsion(self, k_rep):
860 """set_k_repulsion(LinearInteractionPairScore self, double k_rep)"""
861 return _IMP_npctransport.LinearInteractionPairScore_set_k_repulsion(self, k_rep)
864 def get_version_info(self):
865 """get_version_info(LinearInteractionPairScore self) -> VersionInfo"""
866 return _IMP_npctransport.LinearInteractionPairScore_get_version_info(self)
870 """__str__(LinearInteractionPairScore self) -> std::string"""
871 return _IMP_npctransport.LinearInteractionPairScore___str__(self)
875 """__repr__(LinearInteractionPairScore self) -> std::string"""
876 return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
881 return _object_cast_to_LinearInteractionPairScore(o)
883 LinearInteractionPairScore_swigregister = _IMP_npctransport.LinearInteractionPairScore_swigregister
884 LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
887 """Proxy of C++ IMP::npctransport::LinearWellPairScore class."""
889 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
893 __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k, std::string name) -> LinearWellPairScore
894 __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k) -> LinearWellPairScore
896 this = _IMP_npctransport.new_LinearWellPairScore(*args)
898 self.this.append(this)
899 except __builtin__.Exception:
902 def set_rest_length_factor(self, rest_length_factor):
903 """set_rest_length_factor(LinearWellPairScore self, double rest_length_factor)"""
904 return _IMP_npctransport.LinearWellPairScore_set_rest_length_factor(self, rest_length_factor)
907 def get_rest_length_factor(self):
908 """get_rest_length_factor(LinearWellPairScore self) -> double"""
909 return _IMP_npctransport.LinearWellPairScore_get_rest_length_factor(self)
913 """set_k(LinearWellPairScore self, double k)"""
914 return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
918 """get_k(LinearWellPairScore self) -> double"""
919 return _IMP_npctransport.LinearWellPairScore_get_k(self)
922 def do_get_inputs(self, m, pis):
923 """do_get_inputs(LinearWellPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
924 return _IMP_npctransport.LinearWellPairScore_do_get_inputs(self, m, pis)
927 def get_version_info(self):
928 """get_version_info(LinearWellPairScore self) -> VersionInfo"""
929 return _IMP_npctransport.LinearWellPairScore_get_version_info(self)
933 """__str__(LinearWellPairScore self) -> std::string"""
934 return _IMP_npctransport.LinearWellPairScore___str__(self)
938 """__repr__(LinearWellPairScore self) -> std::string"""
939 return _IMP_npctransport.LinearWellPairScore___repr__(self)
944 return _object_cast_to_LinearWellPairScore(o)
946 LinearWellPairScore_swigregister = _IMP_npctransport.LinearWellPairScore_swigregister
947 LinearWellPairScore_swigregister(LinearWellPairScore)
950 """Proxy of C++ IMP::npctransport::RelaxingSpring class."""
952 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
956 __init__(IMP::npctransport::RelaxingSpring self) -> RelaxingSpring
957 __init__(IMP::npctransport::RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
958 __init__(IMP::npctransport::RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
960 this = _IMP_npctransport.new_RelaxingSpring(*args)
962 self.this.append(this)
963 except __builtin__.Exception:
966 def show(self, *args):
968 show(RelaxingSpring self, _ostream out)
969 show(RelaxingSpring self)
971 return _IMP_npctransport.RelaxingSpring_show(self, *args)
974 def setup_particle(*args):
976 setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
977 setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
979 return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
981 setup_particle = staticmethod(setup_particle)
983 def get_is_setup(*args):
985 get_is_setup(_ParticleAdaptor p) -> bool
986 get_is_setup(Model m, ParticleIndex pi) -> bool
988 return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
990 get_is_setup = staticmethod(get_is_setup)
992 def get_bonded_particle_0_key():
993 """get_bonded_particle_0_key() -> ParticleIndexKey"""
994 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
996 get_bonded_particle_0_key = staticmethod(get_bonded_particle_0_key)
998 def get_bonded_particle_1_key():
999 """get_bonded_particle_1_key() -> ParticleIndexKey"""
1000 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1002 get_bonded_particle_1_key = staticmethod(get_bonded_particle_1_key)
1004 def get_equilibrium_rest_length_factor_key():
1005 """get_equilibrium_rest_length_factor_key() -> FloatKey"""
1006 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1008 get_equilibrium_rest_length_factor_key = staticmethod(get_equilibrium_rest_length_factor_key)
1010 def get_rest_length_key():
1011 """get_rest_length_key() -> FloatKey"""
1012 return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1014 get_rest_length_key = staticmethod(get_rest_length_key)
1016 def get_rest_length_diffusion_coefficient_key():
1017 """get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1018 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1020 get_rest_length_diffusion_coefficient_key = staticmethod(get_rest_length_diffusion_coefficient_key)
1022 def get_bonded_particle_0(self):
1023 """get_bonded_particle_0(RelaxingSpring self) -> Particle"""
1024 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0(self)
1027 def get_bonded_particle_1(self):
1028 """get_bonded_particle_1(RelaxingSpring self) -> Particle"""
1029 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1(self)
1032 def get_bonded_particle_index_0(self):
1033 """get_bonded_particle_index_0(RelaxingSpring self) -> ParticleIndex"""
1034 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_0(self)
1037 def get_bonded_particle_index_1(self):
1038 """get_bonded_particle_index_1(RelaxingSpring self) -> ParticleIndex"""
1039 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_1(self)
1042 def get_equilibrium_rest_length_factor(self):
1043 """get_equilibrium_rest_length_factor(RelaxingSpring self) -> IMP::Float"""
1044 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor(self)
1047 def set_equilibrium_rest_length_factor(self, t):
1048 """set_equilibrium_rest_length_factor(RelaxingSpring self, IMP::Float t)"""
1049 return _IMP_npctransport.RelaxingSpring_set_equilibrium_rest_length_factor(self, t)
1052 def get_rest_length(self):
1053 """get_rest_length(RelaxingSpring self) -> IMP::Float"""
1054 return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1057 def set_rest_length(self, t):
1058 """set_rest_length(RelaxingSpring self, IMP::Float t)"""
1059 return _IMP_npctransport.RelaxingSpring_set_rest_length(self, t)
1062 def get_rest_length_diffusion_coefficient(self):
1063 """get_rest_length_diffusion_coefficient(RelaxingSpring self) -> IMP::Float"""
1064 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient(self)
1067 def set_rest_length_diffusion_coefficient(self, t):
1068 """set_rest_length_diffusion_coefficient(RelaxingSpring self, IMP::Float t)"""
1069 return _IMP_npctransport.RelaxingSpring_set_rest_length_diffusion_coefficient(self, t)
1072 def add_to_rest_length_derivative(self, d, da):
1073 """add_to_rest_length_derivative(RelaxingSpring self, double d, DerivativeAccumulator da)"""
1074 return _IMP_npctransport.RelaxingSpring_add_to_rest_length_derivative(self, d, da)
1077 def get_rest_length_derivative(self):
1078 """get_rest_length_derivative(RelaxingSpring self) -> double"""
1079 return _IMP_npctransport.RelaxingSpring_get_rest_length_derivative(self)
1082 def add_attribute(self, *args):
1084 add_attribute(RelaxingSpring self, FloatKey k, IMP::Float v, bool opt)
1085 add_attribute(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1086 add_attribute(RelaxingSpring self, IntKey a0, IMP::Int a1)
1087 add_attribute(RelaxingSpring self, StringKey a0, IMP::String a1)
1088 add_attribute(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1089 add_attribute(RelaxingSpring self, ObjectKey a0, Object a1)
1091 return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1094 def get_value(self, *args):
1096 get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1097 get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1098 get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1099 get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1100 get_value(RelaxingSpring self, ObjectKey a0) -> Object
1102 return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1105 def set_value(self, *args):
1107 set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1108 set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1109 set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1110 set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1111 set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1113 return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1116 def remove_attribute(self, *args):
1118 remove_attribute(RelaxingSpring self, FloatKey a0)
1119 remove_attribute(RelaxingSpring self, IntKey a0)
1120 remove_attribute(RelaxingSpring self, StringKey a0)
1121 remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1122 remove_attribute(RelaxingSpring self, ObjectKey a0)
1124 return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1127 def has_attribute(self, *args):
1129 has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1130 has_attribute(RelaxingSpring self, IntKey a0) -> bool
1131 has_attribute(RelaxingSpring self, StringKey a0) -> bool
1132 has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1133 has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1135 return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1138 def get_derivative(self, a0):
1139 """get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1140 return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1144 """get_name(RelaxingSpring self) -> std::string"""
1145 return _IMP_npctransport.RelaxingSpring_get_name(self)
1148 def clear_caches(self):
1149 """clear_caches(RelaxingSpring self)"""
1150 return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1153 def set_name(self, a0):
1154 """set_name(RelaxingSpring self, std::string a0)"""
1155 return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1159 """set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1160 return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1163 def add_to_derivative(self, a0, a1, a2):
1164 """add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1165 return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1168 def set_is_optimized(self, a0, a1):
1169 """set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1170 return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1173 def get_is_optimized(self, a0):
1174 """get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1175 return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1179 """get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1180 return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1183 def __eq__(self, *args):
1185 __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1186 __eq__(RelaxingSpring self, Particle d) -> bool
1188 return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1191 def __ne__(self, *args):
1193 __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1194 __ne__(RelaxingSpring self, Particle d) -> bool
1196 return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1199 def __le__(self, *args):
1201 __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1202 __le__(RelaxingSpring self, Particle d) -> bool
1204 return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1207 def __lt__(self, *args):
1209 __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1210 __lt__(RelaxingSpring self, Particle d) -> bool
1212 return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1215 def __ge__(self, *args):
1217 __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1218 __ge__(RelaxingSpring self, Particle d) -> bool
1220 return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1223 def __gt__(self, *args):
1225 __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1226 __gt__(RelaxingSpring self, Particle d) -> bool
1228 return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1232 """__hash__(RelaxingSpring self) -> std::size_t"""
1233 return _IMP_npctransport.RelaxingSpring___hash__(self)
1237 """__str__(RelaxingSpring self) -> std::string"""
1238 return _IMP_npctransport.RelaxingSpring___str__(self)
1242 """__repr__(RelaxingSpring self) -> std::string"""
1243 return _IMP_npctransport.RelaxingSpring___repr__(self)
1245 __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1246 __del__ =
lambda self:
None
1247 RelaxingSpring_swigregister = _IMP_npctransport.RelaxingSpring_swigregister
1248 RelaxingSpring_swigregister(RelaxingSpring)
1250 def RelaxingSpring_setup_particle(*args):
1252 setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1253 RelaxingSpring_setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1255 return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1257 def RelaxingSpring_get_is_setup(*args):
1259 get_is_setup(_ParticleAdaptor p) -> bool
1260 RelaxingSpring_get_is_setup(Model m, ParticleIndex pi) -> bool
1262 return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1264 def RelaxingSpring_get_bonded_particle_0_key():
1265 """RelaxingSpring_get_bonded_particle_0_key() -> ParticleIndexKey"""
1266 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1268 def RelaxingSpring_get_bonded_particle_1_key():
1269 """RelaxingSpring_get_bonded_particle_1_key() -> ParticleIndexKey"""
1270 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1272 def RelaxingSpring_get_equilibrium_rest_length_factor_key():
1273 """RelaxingSpring_get_equilibrium_rest_length_factor_key() -> FloatKey"""
1274 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1276 def RelaxingSpring_get_rest_length_key():
1277 """RelaxingSpring_get_rest_length_key() -> FloatKey"""
1278 return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1280 def RelaxingSpring_get_rest_length_diffusion_coefficient_key():
1281 """RelaxingSpring_get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1282 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1285 """Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1287 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1291 __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2, std::string name) -> HarmonicSpringSingletonScore
1292 __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2) -> HarmonicSpringSingletonScore
1294 this = _IMP_npctransport.new_HarmonicSpringSingletonScore(*args)
1296 self.this.append(this)
1297 except __builtin__.Exception:
1300 def set_k1(self, k1):
1301 """set_k1(HarmonicSpringSingletonScore self, double k1)"""
1302 return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1306 """get_k1(HarmonicSpringSingletonScore self) -> double"""
1307 return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1310 def set_k2(self, k2):
1311 """set_k2(HarmonicSpringSingletonScore self, double k2)"""
1312 return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1316 """get_k2(HarmonicSpringSingletonScore self) -> double"""
1317 return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1320 def do_get_inputs(self, m, pis):
1321 """do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1322 return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1325 def get_version_info(self):
1326 """get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1327 return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1331 """__str__(HarmonicSpringSingletonScore self) -> std::string"""
1332 return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1336 """__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1337 return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1342 return _object_cast_to_HarmonicSpringSingletonScore(o)
1344 HarmonicSpringSingletonScore_swigregister = _IMP_npctransport.HarmonicSpringSingletonScore_swigregister
1345 HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1347 class LinearInteraction(object):
1348 """Proxy of C++ IMP::npctransport::LinearInteraction class."""
1350 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1351 __repr__ = _swig_repr
1353 def __init__(self, krep, attr_range, kattr):
1354 """__init__(IMP::npctransport::LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction"""
1355 this = _IMP_npctransport.new_LinearInteraction(krep, attr_range, kattr)
1357 self.this.append(this)
1358 except __builtin__.Exception:
1361 def show(self, *args):
1363 show(LinearInteraction self, _ostream out)
1364 show(LinearInteraction self)
1366 return _IMP_npctransport.LinearInteraction_show(self, *args)
1368 __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1369 __del__ =
lambda self:
None
1370 LinearInteraction_swigregister = _IMP_npctransport.LinearInteraction_swigregister
1371 LinearInteraction_swigregister(LinearInteraction)
1374 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> class."""
1376 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1377 __repr__ = _swig_repr
1381 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearSoftSphere
1382 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0) -> _DistancePairScoreForLinearSoftSphere
1384 this = _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args)
1386 self.this.append(this)
1387 except __builtin__.Exception:
1390 def do_get_inputs(self, m, pis):
1391 """do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1392 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1395 def get_score_functor(self):
1396 """get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1397 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1400 def get_version_info(self):
1401 """get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1402 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1404 _DistancePairScoreForLinearSoftSphere_swigregister = _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister
1405 _DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1407 class _DistancePairScoreForLinearInteraction(
IMP.PairScore):
1408 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> class."""
1410 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1411 __repr__ = _swig_repr
1415 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearInteraction
1416 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0) -> _DistancePairScoreForLinearInteraction
1418 this = _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args)
1420 self.this.append(this)
1421 except __builtin__.Exception:
1424 def do_get_inputs(self, m, pis):
1425 """do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1426 return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1429 def get_score_functor(self):
1430 """get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1431 return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1434 def get_version_info(self):
1435 """get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1436 return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1438 _DistancePairScoreForLinearInteraction_swigregister = _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister
1439 _DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1441 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1442 """Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1444 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1448 __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k, std::string name) -> FunctorLinearSoftSpherePairScore
1449 __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k) -> FunctorLinearSoftSpherePairScore
1451 this = _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args)
1453 self.this.append(this)
1454 except __builtin__.Exception:
1458 """__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1459 return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1463 """__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1464 return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1469 return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1471 FunctorLinearSoftSpherePairScore_swigregister = _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister
1472 FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1474 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1475 """Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1477 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1481 __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name) -> FunctorLinearInteractionPairScore
1482 __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr) -> FunctorLinearInteractionPairScore
1484 this = _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args)
1486 self.this.append(this)
1487 except __builtin__.Exception:
1491 """__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1492 return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1496 """__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1497 return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1502 return _object_cast_to_FunctorLinearInteractionPairScore(o)
1504 FunctorLinearInteractionPairScore_swigregister = _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister
1505 FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1508 """Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1510 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1514 __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport
1515 __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name) -> BrownianDynamicsTAMDWithSlabSupport
1516 __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m) -> BrownianDynamicsTAMDWithSlabSupport
1518 this = _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args)
1520 self.this.append(this)
1521 except __builtin__.Exception:
1525 """__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1526 return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1530 """__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1531 return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1536 return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1538 __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1539 __del__ =
lambda self:
None
1540 BrownianDynamicsTAMDWithSlabSupport_swigregister = _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister
1541 BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1543 class SitesPairScoreParameters(object):
1544 """Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1546 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1547 r = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set)
1548 k = _swig_property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set)
1549 r2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set)
1550 kr = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set)
1551 kr2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set)
1552 cosSigma1_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set)
1553 cosSigma2_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set)
1554 is_orientational = _swig_property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set)
1556 def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1558 __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters
1559 __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0) -> SitesPairScoreParameters
1560 __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient) -> SitesPairScoreParameters
1562 this = _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg)
1564 self.this.append(this)
1565 except __builtin__.Exception:
1568 def set_range(self, r):
1569 """set_range(SitesPairScoreParameters self, double r)"""
1570 return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1573 def set_force_coefficient(self, k):
1574 """set_force_coefficient(SitesPairScoreParameters self, double k)"""
1575 return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1578 def set_sigma1_max(self, sigma1_max_deg):
1579 """set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1580 return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1583 def set_sigma2_max(self, sigma2_max_deg):
1584 """set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1585 return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1588 def update_is_orientational(self):
1589 """update_is_orientational(SitesPairScoreParameters self)"""
1590 return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1593 def show(self, *args):
1595 show(SitesPairScoreParameters self, _ostream out)
1596 show(SitesPairScoreParameters self)
1598 return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1602 """__str__(SitesPairScoreParameters self) -> std::string"""
1603 return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1607 """__repr__(SitesPairScoreParameters self) -> std::string"""
1608 return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1610 __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1611 __del__ =
lambda self:
None
1612 SitesPairScoreParameters_swigregister = _IMP_npctransport.SitesPairScoreParameters_swigregister
1613 SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1616 """Proxy of C++ IMP::npctransport::SitesGeometry class."""
1618 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1621 """__init__(IMP::npctransport::SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1622 this = _IMP_npctransport.new_SitesGeometry(p, sites)
1624 self.this.append(this)
1625 except __builtin__.Exception:
1629 """__str__(SitesGeometry self) -> std::string"""
1630 return _IMP_npctransport.SitesGeometry___str__(self)
1634 """__repr__(SitesGeometry self) -> std::string"""
1635 return _IMP_npctransport.SitesGeometry___repr__(self)
1640 return _object_cast_to_SitesGeometry(o)
1642 SitesGeometry_swigregister = _IMP_npctransport.SitesGeometry_swigregister
1643 SitesGeometry_swigregister(SitesGeometry)
1646 """Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1648 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1651 """__init__(IMP::npctransport::TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1652 this = _IMP_npctransport.new_TypedSitesGeometry(sc)
1654 self.this.append(this)
1655 except __builtin__.Exception:
1658 def set_sites(self, t, s):
1659 """set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1660 return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1663 def get_version_info(self):
1664 """get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1665 return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1669 """__str__(TypedSitesGeometry self) -> std::string"""
1670 return _IMP_npctransport.TypedSitesGeometry___str__(self)
1674 """__repr__(TypedSitesGeometry self) -> std::string"""
1675 return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1680 return _object_cast_to_TypedSitesGeometry(o)
1682 TypedSitesGeometry_swigregister = _IMP_npctransport.TypedSitesGeometry_swigregister
1683 TypedSitesGeometry_swigregister(TypedSitesGeometry)
1685 class SitesPairScore(LinearInteractionPairScore):
1686 """Proxy of C++ IMP::npctransport::SitesPairScore class."""
1688 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1690 def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1691 """__init__(IMP::npctransport::SitesPairScore self, double range, double k, double sigma0_deg, double sigma1_deg, double range_nonspec_attraction, double k_nonspec_attraction, double k_nonspec_repulsion, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1) -> SitesPairScore"""
1692 this = _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1)
1694 self.this.append(this)
1695 except __builtin__.Exception:
1698 def get_sites_range(self):
1699 """get_sites_range(SitesPairScore self) -> double"""
1700 return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1703 def get_sites_k(self):
1704 """get_sites_k(SitesPairScore self) -> double"""
1705 return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1708 def get_parameters(self):
1709 """get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1710 return _IMP_npctransport.SitesPairScore_get_parameters(self)
1713 def set_sites(self, sites0, sites1):
1714 """set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1715 return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1718 def set_sites0(self, sites0):
1719 """set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1720 return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1723 def set_sites1(self, sites1):
1724 """set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1725 return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1729 """__str__(SitesPairScore self) -> std::string"""
1730 return _IMP_npctransport.SitesPairScore___str__(self)
1734 """__repr__(SitesPairScore self) -> std::string"""
1735 return _IMP_npctransport.SitesPairScore___repr__(self)
1740 return _object_cast_to_SitesPairScore(o)
1742 SitesPairScore_swigregister = _IMP_npctransport.SitesPairScore_swigregister
1743 SitesPairScore_swigregister(SitesPairScore)
1746 """Proxy of C++ IMP::npctransport::FGChain class."""
1748 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1752 __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name) -> FGChain
1753 __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0) -> FGChain
1754 __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0) -> FGChain
1755 __init__(IMP::npctransport::FGChain self, Particle root) -> FGChain
1757 this = _IMP_npctransport.new_FGChain(*args)
1759 self.this.append(this)
1760 except __builtin__.Exception:
1764 """get_root(FGChain self) -> Hierarchy"""
1765 return _IMP_npctransport.FGChain_get_root(self)
1768 def get_beads(self):
1769 """get_beads(FGChain self) -> IMP::ParticlesTemp"""
1770 return _IMP_npctransport.FGChain_get_beads(self)
1773 def get_bead(self, i):
1774 """get_bead(FGChain self, unsigned int i) -> Particle"""
1775 return _IMP_npctransport.FGChain_get_bead(self, i)
1778 def get_bead_index(self, i):
1779 """get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1780 return _IMP_npctransport.FGChain_get_bead_index(self, i)
1783 def get_number_of_beads(self):
1784 """get_number_of_beads(FGChain self) -> unsigned int"""
1785 return _IMP_npctransport.FGChain_get_number_of_beads(self)
1788 def get_chain_restraints(self, scoring_manager):
1789 """get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1790 return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1793 def set_rest_length_factor(self, rlf):
1794 """set_rest_length_factor(FGChain self, double rlf)"""
1795 return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1798 def set_backbone_k(self, k):
1799 """set_backbone_k(FGChain self, double k)"""
1800 return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1803 def get_rest_length_factor(self):
1804 """get_rest_length_factor(FGChain self) -> double"""
1805 return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1808 def get_backbone_k(self):
1809 """get_backbone_k(FGChain self) -> double"""
1810 return _IMP_npctransport.FGChain_get_backbone_k(self)
1813 def get_version_info(self):
1814 """get_version_info(FGChain self) -> VersionInfo"""
1815 return _IMP_npctransport.FGChain_get_version_info(self)
1819 """__str__(FGChain self) -> std::string"""
1820 return _IMP_npctransport.FGChain___str__(self)
1824 """__repr__(FGChain self) -> std::string"""
1825 return _IMP_npctransport.FGChain___repr__(self)
1830 return _object_cast_to_FGChain(o)
1832 FGChain_swigregister = _IMP_npctransport.FGChain_swigregister
1833 FGChain_swigregister(FGChain)
1837 """create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1838 return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1842 get_fg_chain(Hierarchy root) -> FGChain
1843 get_fg_chain(Particle p_root) -> FGChain
1845 return _IMP_npctransport.get_fg_chain(*args)
1847 """Proxy of C++ IMP::npctransport::Scoring class."""
1849 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1851 def __init__(self, owner_sd, data):
1852 """__init__(IMP::npctransport::Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1853 this = _IMP_npctransport.new_Scoring(owner_sd, data)
1855 self.this.append(this)
1856 except __builtin__.Exception:
1859 def get_scoring_function(self, force_update=False):
1861 get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction
1862 get_scoring_function(Scoring self) -> ScoringFunction
1864 return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1867 def get_scoring_function_restraints(self, force_update=False):
1869 get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints
1870 get_scoring_function_restraints(Scoring self) -> IMP::Restraints
1872 return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1875 def get_custom_scoring_function(self, *args):
1877 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1878 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1879 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1880 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1882 return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1885 def get_close_beads_container(self, update=False):
1887 get_close_beads_container(Scoring self, bool update=False) -> PairContainer
1888 get_close_beads_container(Scoring self) -> PairContainer
1890 return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1893 def get_predicates_pair_restraint(self, update=False):
1895 get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint
1896 get_predicates_pair_restraint(Scoring self) -> PredicatePairsRestraint
1898 return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1901 def get_bounding_box_restraint(self, update=False):
1903 get_bounding_box_restraint(Scoring self, bool update=False) -> Restraint
1904 get_bounding_box_restraint(Scoring self) -> Restraint
1906 return _IMP_npctransport.Scoring_get_bounding_box_restraint(self, update)
1909 def get_slab_restraint(self, update=False):
1911 get_slab_restraint(Scoring self, bool update=False) -> Restraint
1912 get_slab_restraint(Scoring self) -> Restraint
1914 return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1917 def add_interaction(self, idata):
1918 """add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1919 return _IMP_npctransport.Scoring_add_interaction(self, idata)
1922 def create_close_beads_container(self, *args):
1924 create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1925 create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1927 return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
1930 def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
1932 create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint
1933 create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs) -> PredicatePairsRestraint
1935 return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
1938 def create_bounding_box_restraint(self, beads):
1939 """create_bounding_box_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1940 return _IMP_npctransport.Scoring_create_bounding_box_restraint(self, beads)
1943 def create_slab_restraint(self, beads):
1944 """create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1945 return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
1948 def get_model(self):
1949 """get_model(Scoring self) -> Model"""
1950 return _IMP_npctransport.Scoring_get_model(self)
1954 """get_sd(Scoring self) -> SimulationData"""
1955 return _IMP_npctransport.Scoring_get_sd(self)
1958 def get_has_bounding_box(self):
1959 """get_has_bounding_box(Scoring self) -> bool"""
1960 return _IMP_npctransport.Scoring_get_has_bounding_box(self)
1963 def get_default_backbone_k(self):
1964 """get_default_backbone_k(Scoring self) -> double"""
1965 return _IMP_npctransport.Scoring_get_default_backbone_k(self)
1968 def get_is_backbone_harmonic(self):
1969 """get_is_backbone_harmonic(Scoring self) -> bool"""
1970 return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
1973 def get_excluded_volume_k(self):
1974 """get_excluded_volume_k(Scoring self) -> double"""
1975 return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
1978 def get_interaction_k(self):
1979 """get_interaction_k(Scoring self) -> double"""
1980 return _IMP_npctransport.Scoring_get_interaction_k(self)
1983 def get_predicate_pair_score(self, *args):
1985 get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1986 get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1988 return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
1991 def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
1993 get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double
1994 get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True) -> double
1995 get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2) -> double
1997 return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
2000 def get_ordered_type_pair_predicate(self):
2001 """get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
2002 return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
2005 def add_chain_restraints(self, chain):
2006 """add_chain_restraints(Scoring self, FGChain chain)"""
2007 return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
2010 def get_chain_restraints_on(self, beads):
2011 """get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
2012 return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
2015 def get_all_chain_restraints(self):
2016 """get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
2017 return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
2020 def remove_particle_type(self, pt):
2021 """remove_particle_type(Scoring self, ParticleType pt)"""
2022 return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
2025 def add_z_bias_restraint(self, *args):
2027 add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
2028 add_z_bias_restraint(Scoring self, Particle p, double k)
2030 return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
2033 def get_z_bias_restraints(self):
2034 """get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
2035 return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
2038 def create_z_bias_restraint(self, ps, k):
2039 """create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
2040 return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
2043 def add_custom_restraint(self, r):
2044 """add_custom_restraint(Scoring self, Restraint r)"""
2045 return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
2048 def add_custom_restraints(self, R):
2049 """add_custom_restraints(Scoring self, IMP::Restraints R)"""
2050 return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
2053 def clear_custom_restraints(self):
2054 """clear_custom_restraints(Scoring self)"""
2055 return _IMP_npctransport.Scoring_clear_custom_restraints(self)
2058 def get_custom_restraints(self):
2059 """get_custom_restraints(Scoring self) -> IMP::Restraints"""
2060 return _IMP_npctransport.Scoring_get_custom_restraints(self)
2063 def add_restrained_anchor_bead(self, p):
2064 """add_restrained_anchor_bead(Scoring self, Particle p)"""
2065 return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
2068 def get_pore_radius_restraint(self):
2069 """get_pore_radius_restraint(Scoring self) -> Restraint"""
2070 return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
2073 def get_range(self):
2074 """get_range(Scoring self) -> double"""
2075 return _IMP_npctransport.Scoring_get_range(self)
2078 def set_interaction_range_factor(self, type, value):
2079 """set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
2080 return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
2083 def set_interaction_k_factor(self, type, value):
2084 """set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
2085 return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
2088 def get_version_info(self):
2089 """get_version_info(Scoring self) -> VersionInfo"""
2090 return _IMP_npctransport.Scoring_get_version_info(self)
2094 """__str__(Scoring self) -> std::string"""
2095 return _IMP_npctransport.Scoring___str__(self)
2099 """__repr__(Scoring self) -> std::string"""
2100 return _IMP_npctransport.Scoring___repr__(self)
2105 return _object_cast_to_Scoring(o)
2107 Scoring_swigregister = _IMP_npctransport.Scoring_swigregister
2108 Scoring_swigregister(Scoring)
2110 class timer(object):
2111 """Proxy of C++ boost::timer class."""
2113 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2114 __repr__ = _swig_repr
2117 """__init__(boost::timer self) -> timer"""
2118 this = _IMP_npctransport.new_timer()
2120 self.this.append(this)
2121 except __builtin__.Exception:
2123 __swig_destroy__ = _IMP_npctransport.delete_timer
2124 __del__ =
lambda self:
None
2125 timer_swigregister = _IMP_npctransport.timer_swigregister
2126 timer_swigregister(timer)
2129 """Proxy of C++ IMP::npctransport::Statistics class."""
2131 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2133 def remove_particle_type(self, pt):
2134 """remove_particle_type(Statistics self, ParticleType pt)"""
2135 return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2138 def __init__(self, sd, statistics_interval_frames, output_file_name):
2139 """__init__(IMP::npctransport::Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2140 this = _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name)
2142 self.this.append(this)
2143 except __builtin__.Exception:
2146 def add_fg_chain_stats(self, fg_chain):
2147 """add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2148 return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2151 def add_floater_stats(self, p):
2152 """add_floater_stats(Statistics self, Particle p)"""
2153 return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2156 def add_interaction_stats(self, type0, type1):
2157 """add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2158 return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2161 def add_optimizer_states(self, o=None):
2163 add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates
2164 add_optimizer_states(Statistics self) -> IMP::OptimizerStates
2166 return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2169 def update_particle_type_zr_distribution_map(self, p):
2170 """update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2171 return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2174 def update_particle_type_xyz_distribution_map(self, p):
2175 """update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2176 return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2179 def update(self, timer, nf_new=1):
2181 update(Statistics self, timer timer, unsigned int nf_new=1)
2182 update(Statistics self, timer timer)
2184 return _IMP_npctransport.Statistics_update(self, timer, nf_new)
2187 def reset_statistics_optimizer_states(self):
2188 """reset_statistics_optimizer_states(Statistics self)"""
2189 return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2192 def set_interrupted(self, tf):
2193 """set_interrupted(Statistics self, bool tf)"""
2194 return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2197 def get_model(self):
2198 """get_model(Statistics self) -> Model"""
2199 return _IMP_npctransport.Statistics_get_model(self)
2203 """get_sd(Statistics self) -> SimulationData"""
2204 return _IMP_npctransport.Statistics_get_sd(self)
2207 def get_is_activated(self):
2208 """get_is_activated(Statistics self) -> bool"""
2209 return _IMP_npctransport.Statistics_get_is_activated(self)
2212 def get_output_file_name(self):
2213 """get_output_file_name(Statistics self) -> std::string"""
2214 return _IMP_npctransport.Statistics_get_output_file_name(self)
2217 def get_version_info(self):
2218 """get_version_info(Statistics self) -> VersionInfo"""
2219 return _IMP_npctransport.Statistics_get_version_info(self)
2223 """__str__(Statistics self) -> std::string"""
2224 return _IMP_npctransport.Statistics___str__(self)
2228 """__repr__(Statistics self) -> std::string"""
2229 return _IMP_npctransport.Statistics___repr__(self)
2234 return _object_cast_to_Statistics(o)
2236 Statistics_swigregister = _IMP_npctransport.Statistics_swigregister
2237 Statistics_swigregister(Statistics)
2240 def create_boost_timer():
2241 """create_boost_timer() -> timer"""
2242 return _IMP_npctransport.create_boost_timer()
2243 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2245 """Proxy of C++ IMP::npctransport::SimulationData class."""
2247 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2249 def get_output_npctransport_version(self):
2250 """get_output_npctransport_version(SimulationData self) -> double"""
2251 return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2254 def get_range(self):
2255 """get_range(SimulationData self) -> double"""
2256 return _IMP_npctransport.SimulationData_get_range(self)
2259 def get_output_statistics_interval_frames(self):
2260 """get_output_statistics_interval_frames(SimulationData self) -> int"""
2261 return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2264 def get_is_exclude_floaters_from_slab_initially(self):
2265 """get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2266 return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2269 def get_are_floaters_on_one_slab_side(self):
2270 """get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2271 return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2274 def get_is_xyz_hist_stats(self):
2275 """get_is_xyz_hist_stats(SimulationData self) -> bool"""
2276 return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2279 def get_angular_d_factor(self):
2280 """get_angular_d_factor(SimulationData self) -> double"""
2281 return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2286 __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name, std::string new_output_file) -> SimulationData
2287 __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name) -> SimulationData
2288 __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick) -> SimulationData
2290 this = _IMP_npctransport.new_SimulationData(*args)
2292 self.this.append(this)
2293 except __builtin__.Exception:
2296 def get_model(self):
2297 """get_model(SimulationData self) -> Model"""
2298 return _IMP_npctransport.SimulationData_get_model(self)
2301 def get_scoring(self):
2302 """get_scoring(SimulationData self) -> Scoring"""
2303 return _IMP_npctransport.SimulationData_get_scoring(self)
2306 def get_statistics(self):
2307 """get_statistics(SimulationData self) -> Statistics"""
2308 return _IMP_npctransport.SimulationData_get_statistics(self)
2311 def get_bd(self, recreate=False):
2313 get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics
2314 get_bd(SimulationData self) -> BrownianDynamics
2316 return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2319 def activate_statistics(self):
2320 """activate_statistics(SimulationData self)"""
2321 return _IMP_npctransport.SimulationData_activate_statistics(self)
2324 def get_statistics_fraction(self):
2325 """get_statistics_fraction(SimulationData self) -> double"""
2326 return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2329 def get_is_fg_bead(self, *args):
2331 get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2332 get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2334 return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2337 def get_is_fg_chain(self, *args):
2339 get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2340 get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2342 return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2345 def get_fg_bead_types(self):
2346 """get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2347 return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2350 def get_fg_chain_types(self):
2351 """get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2352 return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2355 def get_floater_types(self):
2356 """get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2357 return _IMP_npctransport.SimulationData_get_floater_types(self)
2360 def get_obstacle_types(self):
2361 """get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2362 return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2365 def get_fg_chain_roots(self):
2366 """get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2367 return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2370 def get_fg_chains(self):
2371 """get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2372 return _IMP_npctransport.SimulationData_get_fg_chains(self)
2375 def get_obstacle_particles(self):
2376 """get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2377 return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2380 def get_beads(self):
2381 """get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2382 return _IMP_npctransport.SimulationData_get_beads(self)
2385 def get_optimizable_beads(self):
2386 """get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2387 return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2390 def get_non_optimizable_beads(self):
2391 """get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2392 return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2395 def get_is_backbone_harmonic(self):
2396 """get_is_backbone_harmonic(SimulationData self) -> bool"""
2397 return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2400 def get_backbone_tau_ns(self):
2401 """get_backbone_tau_ns(SimulationData self) -> double"""
2402 return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2405 def get_temperature_k(self):
2406 """get_temperature_k(SimulationData self) -> double"""
2407 return _IMP_npctransport.SimulationData_get_temperature_k(self)
2410 def get_initial_simulation_time_ns(self):
2411 """get_initial_simulation_time_ns(SimulationData self) -> double"""
2412 return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2415 def get_site_centers(self, t0):
2416 """get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2417 return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2420 def get_sites(self, t0):
2421 """get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2422 return _IMP_npctransport.SimulationData_get_sites(self, t0)
2425 def set_sites(self, *args):
2427 set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2428 set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2430 return _IMP_npctransport.SimulationData_set_sites(self, *args)
2433 def get_site_display_radius(self, arg2):
2434 """get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2435 return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2438 def get_maximum_number_of_minutes(self):
2439 """get_maximum_number_of_minutes(SimulationData self) -> double"""
2440 return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2443 def remove_particle_type(self, pt):
2444 """remove_particle_type(SimulationData self, ParticleType pt)"""
2445 return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2448 def remove_fgs_with_prefix(self, s_fg_type):
2449 """remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2450 return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2454 """get_box(SimulationData self) -> BoundingBox3D"""
2455 return _IMP_npctransport.SimulationData_get_box(self)
2458 def get_box_size(self):
2459 """get_box_size(SimulationData self) -> double"""
2460 return _IMP_npctransport.SimulationData_get_box_size(self)
2463 def set_box_size(self, box_size):
2464 """set_box_size(SimulationData self, double box_size)"""
2465 return _IMP_npctransport.SimulationData_set_box_size(self, box_size)
2468 def get_has_slab(self):
2469 """get_has_slab(SimulationData self) -> bool"""
2470 return _IMP_npctransport.SimulationData_get_has_slab(self)
2473 def get_is_slab_with_cylindrical_pore(self):
2474 """get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2475 return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2478 def get_is_slab_with_toroidal_pore(self):
2479 """get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2480 return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2483 def get_slab_particle(self):
2484 """get_slab_particle(SimulationData self) -> Particle"""
2485 return _IMP_npctransport.SimulationData_get_slab_particle(self)
2488 def get_cylinder(self):
2489 """get_cylinder(SimulationData self) -> Cylinder3D"""
2490 return _IMP_npctransport.SimulationData_get_cylinder(self)
2493 def get_has_bounding_box(self):
2494 """get_has_bounding_box(SimulationData self) -> bool"""
2495 return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2498 def initialize_positions_from_rmf(self, fh, frame_number=-1):
2500 initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)
2501 initialize_positions_from_rmf(SimulationData self, FileConstHandle fh)
2503 return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2506 def link_rmf_file_handle(self, fh, is_restraints=True):
2508 link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)
2509 link_rmf_file_handle(SimulationData self, FileHandle fh)
2511 return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2514 def get_rmf_sos_writer(self):
2515 """get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2516 return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2519 def reset_rmf(self):
2520 """reset_rmf(SimulationData self)"""
2521 return _IMP_npctransport.SimulationData_reset_rmf(self)
2524 def switch_suspend_rmf(self, suspend):
2525 """switch_suspend_rmf(SimulationData self, bool suspend)"""
2526 return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2529 def write_geometry(self, out):
2530 """write_geometry(SimulationData self, std::string out)"""
2531 return _IMP_npctransport.SimulationData_write_geometry(self, out)
2534 def dump_geometry(self):
2535 """dump_geometry(SimulationData self)"""
2536 return _IMP_npctransport.SimulationData_dump_geometry(self)
2539 def get_root_of_type(self, type):
2540 """get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2541 return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2545 """get_number_of_frames(SimulationData self) -> unsigned int"""
2546 return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2549 def get_number_of_trials(self):
2550 """get_number_of_trials(SimulationData self) -> unsigned int"""
2551 return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2555 """get_root(SimulationData self) -> Hierarchy"""
2556 return _IMP_npctransport.SimulationData_get_root(self)
2559 def get_slab_thickness(self):
2560 """get_slab_thickness(SimulationData self) -> double"""
2561 return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2564 def get_tunnel_radius(self):
2565 """get_tunnel_radius(SimulationData self) -> double"""
2566 return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2569 def get_pore_radius(self):
2570 """get_pore_radius(SimulationData self) -> double"""
2571 return _IMP_npctransport.SimulationData_get_pore_radius(self)
2574 def get_tunnel_radius_k(self):
2575 """get_tunnel_radius_k(SimulationData self) -> double"""
2576 return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2579 def get_pore_radius_k(self):
2580 """get_pore_radius_k(SimulationData self) -> double"""
2581 return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2584 def get_is_pore_radius_dynamic(self):
2585 """get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2586 return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2589 def get_pore_anchored_beads_k(self):
2590 """get_pore_anchored_beads_k(SimulationData self) -> double"""
2591 return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2594 def get_static_geometry(self):
2595 """get_static_geometry(SimulationData self) -> Geometry"""
2596 return _IMP_npctransport.SimulationData_get_static_geometry(self)
2599 def get_rmf_dump_interval_frames(self):
2600 """get_rmf_dump_interval_frames(SimulationData self) -> int"""
2601 return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2604 def get_rmf_file_name(self):
2605 """get_rmf_file_name(SimulationData self) -> std::string"""
2606 return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2609 def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2611 set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)
2612 set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True)
2613 set_rmf_file(SimulationData self, std::string const & new_name)
2615 return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2618 def get_version_info(self):
2619 """get_version_info(SimulationData self) -> VersionInfo"""
2620 return _IMP_npctransport.SimulationData_get_version_info(self)
2624 """__str__(SimulationData self) -> std::string"""
2625 return _IMP_npctransport.SimulationData___str__(self)
2629 """__repr__(SimulationData self) -> std::string"""
2630 return _IMP_npctransport.SimulationData___repr__(self)
2635 return _object_cast_to_SimulationData(o)
2637 SimulationData_swigregister = _IMP_npctransport.SimulationData_swigregister
2638 SimulationData_swigregister(SimulationData)
2641 def get_simulation_data_key():
2642 """get_simulation_data_key() -> IMP::WeakObjectKey"""
2643 return _IMP_npctransport.get_simulation_data_key()
2645 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2646 """write_geometry(IMP::ParticlesTemp const & kaps, IMP::algebra::Sphere3Ds const & kap_sites, IMP::ParticlesTemp const & chains, IMP::algebra::Sphere3Ds const & chain_sites, IMP::RestraintsTemp const & rs, Writer out)"""
2647 return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2649 """Proxy of C++ IMP::npctransport::ParticleFactory class."""
2651 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2652 sd_ = _swig_property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set)
2653 radius_ = _swig_property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set)
2654 D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set)
2655 angular_D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set)
2656 color_ = _swig_property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set)
2657 type_ = _swig_property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set)
2661 __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name) -> ParticleFactory
2662 __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type) -> ParticleFactory
2664 this = _IMP_npctransport.new_ParticleFactory(*args)
2666 self.this.append(this)
2667 except __builtin__.Exception:
2670 def create(self, *args):
2672 create(ParticleFactory self, std::string name) -> Particle
2673 create(ParticleFactory self) -> Particle
2675 return _IMP_npctransport.ParticleFactory_create(self, *args)
2678 def get_model(self):
2679 """get_model(ParticleFactory self) -> Model"""
2680 return _IMP_npctransport.ParticleFactory_get_model(self)
2683 def get_simulation_data(self):
2684 """get_simulation_data(ParticleFactory self) -> SimulationData"""
2685 return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2688 def get_radius(self):
2689 """get_radius(ParticleFactory self) -> double"""
2690 return _IMP_npctransport.ParticleFactory_get_radius(self)
2693 def get_version_info(self):
2694 """get_version_info(ParticleFactory self) -> VersionInfo"""
2695 return _IMP_npctransport.ParticleFactory_get_version_info(self)
2699 """__str__(ParticleFactory self) -> std::string"""
2700 return _IMP_npctransport.ParticleFactory___str__(self)
2704 """__repr__(ParticleFactory self) -> std::string"""
2705 return _IMP_npctransport.ParticleFactory___repr__(self)
2710 return _object_cast_to_ParticleFactory(o)
2712 ParticleFactory_swigregister = _IMP_npctransport.ParticleFactory_swigregister
2713 ParticleFactory_swigregister(ParticleFactory)
2716 """Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2718 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2721 """__init__(IMP::npctransport::HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2722 this = _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh)
2724 self.this.append(this)
2725 except __builtin__.Exception:
2729 """get_name() -> char const *"""
2730 return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2732 get_name = staticmethod(get_name)
2735 """__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2736 return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2740 """__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2741 return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2746 return _object_cast_to_HierarchyWithSitesLoadLink(o)
2748 __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2749 __del__ =
lambda self:
None
2750 HierarchyWithSitesLoadLink_swigregister = _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister
2751 HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2753 def HierarchyWithSitesLoadLink_get_name():
2754 """HierarchyWithSitesLoadLink_get_name() -> char const *"""
2755 return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2758 """Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2760 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2763 """__init__(IMP::npctransport::HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2764 this = _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh)
2766 self.this.append(this)
2767 except __builtin__.Exception:
2771 """get_name() -> char const *"""
2772 return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2774 get_name = staticmethod(get_name)
2777 """__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2778 return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2782 """__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2783 return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2788 return _object_cast_to_HierarchyWithSitesSaveLink(o)
2790 __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2791 __del__ =
lambda self:
None
2792 HierarchyWithSitesSaveLink_swigregister = _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister
2793 HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2795 def HierarchyWithSitesSaveLink_get_name():
2796 """HierarchyWithSitesSaveLink_get_name() -> char const *"""
2797 return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2802 add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2803 add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2805 return _IMP_npctransport.add_test_sites(*args)
2809 add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2810 add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2812 return _IMP_npctransport.add_hierarchies_with_sites(*args)
2815 """add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2816 return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2819 """create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2820 return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2823 """link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2824 return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2826 """Proxy of C++ IMP::npctransport::Transporting class."""
2828 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2832 __init__(IMP::npctransport::Transporting self) -> Transporting
2833 __init__(IMP::npctransport::Transporting self, Model m, ParticleIndex id) -> Transporting
2834 __init__(IMP::npctransport::Transporting self, _ParticleAdaptor d) -> Transporting
2836 this = _IMP_npctransport.new_Transporting(*args)
2838 self.this.append(this)
2839 except __builtin__.Exception:
2842 def show(self, *args):
2844 show(Transporting self, _ostream out)
2845 show(Transporting self)
2847 return _IMP_npctransport.Transporting_show(self, *args)
2850 def setup_particle(*args):
2852 setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2853 setup_particle(Model m, ParticleIndex pi) -> Transporting
2854 setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
2855 setup_particle(_ParticleAdaptor decorator) -> Transporting
2857 return _IMP_npctransport.Transporting_setup_particle(*args)
2859 setup_particle = staticmethod(setup_particle)
2861 def get_is_setup(*args):
2863 get_is_setup(_ParticleAdaptor p) -> bool
2864 get_is_setup(Model m, ParticleIndex pi) -> bool
2866 return _IMP_npctransport.Transporting_get_is_setup(*args)
2868 get_is_setup = staticmethod(get_is_setup)
2870 def set_is_last_entry_from_top(self, is_last_entry_from_top):
2871 """set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2872 return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2875 def get_is_last_entry_from_top(self):
2876 """get_is_last_entry_from_top(Transporting self) -> bool"""
2877 return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2880 def get_is_last_entry_from_top_key():
2881 """get_is_last_entry_from_top_key() -> IntKey"""
2882 return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
2884 get_is_last_entry_from_top_key = staticmethod(get_is_last_entry_from_top_key)
2886 def set_last_tracked_z(self, last_tracked_z):
2887 """set_last_tracked_z(Transporting self, double last_tracked_z)"""
2888 return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
2891 def get_last_tracked_z(self):
2892 """get_last_tracked_z(Transporting self) -> double"""
2893 return _IMP_npctransport.Transporting_get_last_tracked_z(self)
2896 def get_last_tracked_z_key():
2897 """get_last_tracked_z_key() -> FloatKey"""
2898 return _IMP_npctransport.Transporting_get_last_tracked_z_key()
2900 get_last_tracked_z_key = staticmethod(get_last_tracked_z_key)
2902 def set_n_entries_bottom(self, n):
2903 """set_n_entries_bottom(Transporting self, int n)"""
2904 return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
2907 def get_n_entries_bottom(self):
2908 """get_n_entries_bottom(Transporting self) -> int"""
2909 return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
2912 def get_n_entries_bottom_key():
2913 """get_n_entries_bottom_key() -> IntKey"""
2914 return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
2916 get_n_entries_bottom_key = staticmethod(get_n_entries_bottom_key)
2918 def set_n_entries_top(self, n):
2919 """set_n_entries_top(Transporting self, int n)"""
2920 return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
2923 def get_n_entries_top(self):
2924 """get_n_entries_top(Transporting self) -> int"""
2925 return _IMP_npctransport.Transporting_get_n_entries_top(self)
2928 def get_n_entries_top_key():
2929 """get_n_entries_top_key() -> IntKey"""
2930 return _IMP_npctransport.Transporting_get_n_entries_top_key()
2932 get_n_entries_top_key = staticmethod(get_n_entries_top_key)
2934 def add_attribute(self, *args):
2936 add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
2937 add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
2938 add_attribute(Transporting self, IntKey a0, IMP::Int a1)
2939 add_attribute(Transporting self, StringKey a0, IMP::String a1)
2940 add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
2941 add_attribute(Transporting self, ObjectKey a0, Object a1)
2943 return _IMP_npctransport.Transporting_add_attribute(self, *args)
2946 def get_value(self, *args):
2948 get_value(Transporting self, FloatKey a0) -> IMP::Float
2949 get_value(Transporting self, IntKey a0) -> IMP::Int
2950 get_value(Transporting self, StringKey a0) -> IMP::String
2951 get_value(Transporting self, ParticleIndexKey a0) -> Particle
2952 get_value(Transporting self, ObjectKey a0) -> Object
2954 return _IMP_npctransport.Transporting_get_value(self, *args)
2957 def set_value(self, *args):
2959 set_value(Transporting self, FloatKey a0, IMP::Float a1)
2960 set_value(Transporting self, IntKey a0, IMP::Int a1)
2961 set_value(Transporting self, StringKey a0, IMP::String a1)
2962 set_value(Transporting self, ParticleIndexKey a0, Particle a1)
2963 set_value(Transporting self, ObjectKey a0, Object a1)
2965 return _IMP_npctransport.Transporting_set_value(self, *args)
2968 def remove_attribute(self, *args):
2970 remove_attribute(Transporting self, FloatKey a0)
2971 remove_attribute(Transporting self, IntKey a0)
2972 remove_attribute(Transporting self, StringKey a0)
2973 remove_attribute(Transporting self, ParticleIndexKey a0)
2974 remove_attribute(Transporting self, ObjectKey a0)
2976 return _IMP_npctransport.Transporting_remove_attribute(self, *args)
2979 def has_attribute(self, *args):
2981 has_attribute(Transporting self, FloatKey a0) -> bool
2982 has_attribute(Transporting self, IntKey a0) -> bool
2983 has_attribute(Transporting self, StringKey a0) -> bool
2984 has_attribute(Transporting self, ParticleIndexKey a0) -> bool
2985 has_attribute(Transporting self, ObjectKey a0) -> bool
2987 return _IMP_npctransport.Transporting_has_attribute(self, *args)
2990 def get_derivative(self, a0):
2991 """get_derivative(Transporting self, FloatKey a0) -> double"""
2992 return _IMP_npctransport.Transporting_get_derivative(self, a0)
2996 """get_name(Transporting self) -> std::string"""
2997 return _IMP_npctransport.Transporting_get_name(self)
3000 def clear_caches(self):
3001 """clear_caches(Transporting self)"""
3002 return _IMP_npctransport.Transporting_clear_caches(self)
3005 def set_name(self, a0):
3006 """set_name(Transporting self, std::string a0)"""
3007 return _IMP_npctransport.Transporting_set_name(self, a0)
3011 """set_check_level(Transporting self, IMP::CheckLevel a0)"""
3012 return _IMP_npctransport.Transporting_set_check_level(self, a0)
3015 def add_to_derivative(self, a0, a1, a2):
3016 """add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3017 return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
3020 def set_is_optimized(self, a0, a1):
3021 """set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
3022 return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
3025 def get_is_optimized(self, a0):
3026 """get_is_optimized(Transporting self, FloatKey a0) -> bool"""
3027 return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
3031 """get_check_level(Transporting self) -> IMP::CheckLevel"""
3032 return _IMP_npctransport.Transporting_get_check_level(self)
3035 def __eq__(self, *args):
3037 __eq__(Transporting self, Transporting o) -> bool
3038 __eq__(Transporting self, Particle d) -> bool
3040 return _IMP_npctransport.Transporting___eq__(self, *args)
3043 def __ne__(self, *args):
3045 __ne__(Transporting self, Transporting o) -> bool
3046 __ne__(Transporting self, Particle d) -> bool
3048 return _IMP_npctransport.Transporting___ne__(self, *args)
3051 def __le__(self, *args):
3053 __le__(Transporting self, Transporting o) -> bool
3054 __le__(Transporting self, Particle d) -> bool
3056 return _IMP_npctransport.Transporting___le__(self, *args)
3059 def __lt__(self, *args):
3061 __lt__(Transporting self, Transporting o) -> bool
3062 __lt__(Transporting self, Particle d) -> bool
3064 return _IMP_npctransport.Transporting___lt__(self, *args)
3067 def __ge__(self, *args):
3069 __ge__(Transporting self, Transporting o) -> bool
3070 __ge__(Transporting self, Particle d) -> bool
3072 return _IMP_npctransport.Transporting___ge__(self, *args)
3075 def __gt__(self, *args):
3077 __gt__(Transporting self, Transporting o) -> bool
3078 __gt__(Transporting self, Particle d) -> bool
3080 return _IMP_npctransport.Transporting___gt__(self, *args)
3084 """__hash__(Transporting self) -> std::size_t"""
3085 return _IMP_npctransport.Transporting___hash__(self)
3089 """__str__(Transporting self) -> std::string"""
3090 return _IMP_npctransport.Transporting___str__(self)
3094 """__repr__(Transporting self) -> std::string"""
3095 return _IMP_npctransport.Transporting___repr__(self)
3097 __swig_destroy__ = _IMP_npctransport.delete_Transporting
3098 __del__ =
lambda self:
None
3099 Transporting_swigregister = _IMP_npctransport.Transporting_swigregister
3100 Transporting_swigregister(Transporting)
3102 def Transporting_setup_particle(*args):
3104 setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
3105 setup_particle(Model m, ParticleIndex pi) -> Transporting
3106 setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
3107 Transporting_setup_particle(_ParticleAdaptor decorator) -> Transporting
3109 return _IMP_npctransport.Transporting_setup_particle(*args)
3111 def Transporting_get_is_setup(*args):
3113 get_is_setup(_ParticleAdaptor p) -> bool
3114 Transporting_get_is_setup(Model m, ParticleIndex pi) -> bool
3116 return _IMP_npctransport.Transporting_get_is_setup(*args)
3118 def Transporting_get_is_last_entry_from_top_key():
3119 """Transporting_get_is_last_entry_from_top_key() -> IntKey"""
3120 return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3122 def Transporting_get_last_tracked_z_key():
3123 """Transporting_get_last_tracked_z_key() -> FloatKey"""
3124 return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3126 def Transporting_get_n_entries_bottom_key():
3127 """Transporting_get_n_entries_bottom_key() -> IntKey"""
3128 return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3130 def Transporting_get_n_entries_top_key():
3131 """Transporting_get_n_entries_top_key() -> IntKey"""
3132 return _IMP_npctransport.Transporting_get_n_entries_top_key()
3135 def show_ranges(fname):
3136 """show_ranges(std::string fname)"""
3137 return _IMP_npctransport.show_ranges(fname)
3139 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
3140 """assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed) -> int"""
3141 return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
3143 def get_number_of_work_units(configuration_file):
3144 """get_number_of_work_units(std::string configuration_file) -> int"""
3145 return _IMP_npctransport.get_number_of_work_units(configuration_file)
3147 """Proxy of C++ IMP::npctransport::SlabWithPore class."""
3149 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3153 __init__(IMP::npctransport::SlabWithPore self) -> SlabWithPore
3154 __init__(IMP::npctransport::SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
3155 __init__(IMP::npctransport::SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
3157 this = _IMP_npctransport.new_SlabWithPore(*args)
3159 self.this.append(this)
3160 except __builtin__.Exception:
3163 def show(self, *args):
3165 show(SlabWithPore self, _ostream out)
3166 show(SlabWithPore self)
3168 return _IMP_npctransport.SlabWithPore_show(self, *args)
3171 def setup_particle(*args):
3173 setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3174 setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3176 return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3178 setup_particle = staticmethod(setup_particle)
3180 def get_is_setup(*args):
3182 get_is_setup(_ParticleAdaptor p) -> bool
3183 get_is_setup(Model m, ParticleIndex pi) -> bool
3185 return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3187 get_is_setup = staticmethod(get_is_setup)
3189 def set_thickness(self, thickness):
3190 """set_thickness(SlabWithPore self, double thickness)"""
3191 return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
3194 def get_thickness(self):
3195 """get_thickness(SlabWithPore self) -> IMP::Float"""
3196 return _IMP_npctransport.SlabWithPore_get_thickness(self)
3199 def get_pore_radius(self):
3200 """get_pore_radius(SlabWithPore self) -> IMP::Float"""
3201 return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
3204 def set_pore_radius(self, r):
3205 """set_pore_radius(SlabWithPore self, double r)"""
3206 return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
3209 def add_to_pore_radius_derivative(self, v, d):
3210 """add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
3211 return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
3214 def get_pore_radius_is_optimized(self):
3215 """get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
3216 return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
3219 def set_pore_radius_is_optimized(self, tf):
3220 """set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
3221 return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
3224 def get_thickness_key():
3225 """get_thickness_key() -> FloatKey"""
3226 return _IMP_npctransport.SlabWithPore_get_thickness_key()
3228 get_thickness_key = staticmethod(get_thickness_key)
3230 def get_pore_radius_key():
3231 """get_pore_radius_key() -> FloatKey"""
3232 return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3234 get_pore_radius_key = staticmethod(get_pore_radius_key)
3236 def add_attribute(self, *args):
3238 add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
3239 add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
3240 add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
3241 add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
3242 add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3243 add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
3245 return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
3248 def get_value(self, *args):
3250 get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
3251 get_value(SlabWithPore self, IntKey a0) -> IMP::Int
3252 get_value(SlabWithPore self, StringKey a0) -> IMP::String
3253 get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3254 get_value(SlabWithPore self, ObjectKey a0) -> Object
3256 return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3259 def set_value(self, *args):
3261 set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3262 set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3263 set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3264 set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3265 set_value(SlabWithPore self, ObjectKey a0, Object a1)
3267 return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3270 def remove_attribute(self, *args):
3272 remove_attribute(SlabWithPore self, FloatKey a0)
3273 remove_attribute(SlabWithPore self, IntKey a0)
3274 remove_attribute(SlabWithPore self, StringKey a0)
3275 remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3276 remove_attribute(SlabWithPore self, ObjectKey a0)
3278 return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3281 def has_attribute(self, *args):
3283 has_attribute(SlabWithPore self, FloatKey a0) -> bool
3284 has_attribute(SlabWithPore self, IntKey a0) -> bool
3285 has_attribute(SlabWithPore self, StringKey a0) -> bool
3286 has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3287 has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3289 return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3292 def get_derivative(self, a0):
3293 """get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3294 return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3298 """get_name(SlabWithPore self) -> std::string"""
3299 return _IMP_npctransport.SlabWithPore_get_name(self)
3302 def clear_caches(self):
3303 """clear_caches(SlabWithPore self)"""
3304 return _IMP_npctransport.SlabWithPore_clear_caches(self)
3307 def set_name(self, a0):
3308 """set_name(SlabWithPore self, std::string a0)"""
3309 return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3313 """set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3314 return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3317 def add_to_derivative(self, a0, a1, a2):
3318 """add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3319 return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3322 def set_is_optimized(self, a0, a1):
3323 """set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3324 return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3327 def get_is_optimized(self, a0):
3328 """get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3329 return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3333 """get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3334 return _IMP_npctransport.SlabWithPore_get_check_level(self)
3337 def __eq__(self, *args):
3339 __eq__(SlabWithPore self, SlabWithPore o) -> bool
3340 __eq__(SlabWithPore self, Particle d) -> bool
3342 return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3345 def __ne__(self, *args):
3347 __ne__(SlabWithPore self, SlabWithPore o) -> bool
3348 __ne__(SlabWithPore self, Particle d) -> bool
3350 return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3353 def __le__(self, *args):
3355 __le__(SlabWithPore self, SlabWithPore o) -> bool
3356 __le__(SlabWithPore self, Particle d) -> bool
3358 return _IMP_npctransport.SlabWithPore___le__(self, *args)
3361 def __lt__(self, *args):
3363 __lt__(SlabWithPore self, SlabWithPore o) -> bool
3364 __lt__(SlabWithPore self, Particle d) -> bool
3366 return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3369 def __ge__(self, *args):
3371 __ge__(SlabWithPore self, SlabWithPore o) -> bool
3372 __ge__(SlabWithPore self, Particle d) -> bool
3374 return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3377 def __gt__(self, *args):
3379 __gt__(SlabWithPore self, SlabWithPore o) -> bool
3380 __gt__(SlabWithPore self, Particle d) -> bool
3382 return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3386 """__hash__(SlabWithPore self) -> std::size_t"""
3387 return _IMP_npctransport.SlabWithPore___hash__(self)
3391 """__str__(SlabWithPore self) -> std::string"""
3392 return _IMP_npctransport.SlabWithPore___str__(self)
3396 """__repr__(SlabWithPore self) -> std::string"""
3397 return _IMP_npctransport.SlabWithPore___repr__(self)
3399 __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3400 __del__ =
lambda self:
None
3401 SlabWithPore_swigregister = _IMP_npctransport.SlabWithPore_swigregister
3402 SlabWithPore_swigregister(SlabWithPore)
3404 def SlabWithPore_setup_particle(*args):
3406 setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3407 SlabWithPore_setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3409 return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3411 def SlabWithPore_get_is_setup(*args):
3413 get_is_setup(_ParticleAdaptor p) -> bool
3414 SlabWithPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3416 return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3418 def SlabWithPore_get_thickness_key():
3419 """SlabWithPore_get_thickness_key() -> FloatKey"""
3420 return _IMP_npctransport.SlabWithPore_get_thickness_key()
3422 def SlabWithPore_get_pore_radius_key():
3423 """SlabWithPore_get_pore_radius_key() -> FloatKey"""
3424 return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3426 class SlabWithCylindricalPore(SlabWithPore):
3427 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3429 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3433 __init__(IMP::npctransport::SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3434 __init__(IMP::npctransport::SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3435 __init__(IMP::npctransport::SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3437 this = _IMP_npctransport.new_SlabWithCylindricalPore(*args)
3439 self.this.append(this)
3440 except __builtin__.Exception:
3443 def show(self, *args):
3445 show(SlabWithCylindricalPore self, _ostream out)
3446 show(SlabWithCylindricalPore self)
3448 return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3451 def setup_particle(*args):
3453 setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3454 setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3456 return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3458 setup_particle = staticmethod(setup_particle)
3460 def get_is_setup(*args):
3462 get_is_setup(_ParticleAdaptor p) -> bool
3463 get_is_setup(Model m, ParticleIndex pi) -> bool
3465 return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3467 get_is_setup = staticmethod(get_is_setup)
3469 def get_cylindrical_pore_key():
3470 """get_cylindrical_pore_key() -> IntKey"""
3471 return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3473 get_cylindrical_pore_key = staticmethod(get_cylindrical_pore_key)
3475 def add_attribute(self, *args):
3477 add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3478 add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3479 add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3480 add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3481 add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3482 add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3484 return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3487 def get_value(self, *args):
3489 get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3490 get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3491 get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3492 get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3493 get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3495 return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3498 def set_value(self, *args):
3500 set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3501 set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3502 set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3503 set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3504 set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3506 return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3509 def remove_attribute(self, *args):
3511 remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3512 remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3513 remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3514 remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3515 remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3517 return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3520 def has_attribute(self, *args):
3522 has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3523 has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3524 has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3525 has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3526 has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3528 return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3531 def get_derivative(self, a0):
3532 """get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3533 return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3537 """get_name(SlabWithCylindricalPore self) -> std::string"""
3538 return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3541 def clear_caches(self):
3542 """clear_caches(SlabWithCylindricalPore self)"""
3543 return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3546 def set_name(self, a0):
3547 """set_name(SlabWithCylindricalPore self, std::string a0)"""
3548 return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3552 """set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3553 return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3556 def add_to_derivative(self, a0, a1, a2):
3557 """add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3558 return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3561 def set_is_optimized(self, a0, a1):
3562 """set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3563 return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3566 def get_is_optimized(self, a0):
3567 """get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3568 return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3572 """get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3573 return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3576 def __eq__(self, *args):
3578 __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3579 __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3581 return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3584 def __ne__(self, *args):
3586 __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3587 __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3589 return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3592 def __le__(self, *args):
3594 __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3595 __le__(SlabWithCylindricalPore self, Particle d) -> bool
3597 return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3600 def __lt__(self, *args):
3602 __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3603 __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3605 return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3608 def __ge__(self, *args):
3610 __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3611 __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3613 return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3616 def __gt__(self, *args):
3618 __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3619 __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3621 return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3625 """__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3626 return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3630 """__str__(SlabWithCylindricalPore self) -> std::string"""
3631 return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3635 """__repr__(SlabWithCylindricalPore self) -> std::string"""
3636 return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3638 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3639 __del__ =
lambda self:
None
3640 SlabWithCylindricalPore_swigregister = _IMP_npctransport.SlabWithCylindricalPore_swigregister
3641 SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3643 def SlabWithCylindricalPore_setup_particle(*args):
3645 setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3646 SlabWithCylindricalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3648 return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3650 def SlabWithCylindricalPore_get_is_setup(*args):
3652 get_is_setup(_ParticleAdaptor p) -> bool
3653 SlabWithCylindricalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3655 return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3657 def SlabWithCylindricalPore_get_cylindrical_pore_key():
3658 """SlabWithCylindricalPore_get_cylindrical_pore_key() -> IntKey"""
3659 return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3661 class SlabWithToroidalPore(SlabWithPore):
3662 """Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3664 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3668 __init__(IMP::npctransport::SlabWithToroidalPore self) -> SlabWithToroidalPore
3669 __init__(IMP::npctransport::SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3670 __init__(IMP::npctransport::SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3672 this = _IMP_npctransport.new_SlabWithToroidalPore(*args)
3674 self.this.append(this)
3675 except __builtin__.Exception:
3678 def show(self, *args):
3680 show(SlabWithToroidalPore self, _ostream out)
3681 show(SlabWithToroidalPore self)
3683 return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3686 def setup_particle(*args):
3688 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3689 setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
3690 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3691 setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3693 return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3695 setup_particle = staticmethod(setup_particle)
3697 def get_is_setup(*args):
3699 get_is_setup(_ParticleAdaptor p) -> bool
3700 get_is_setup(Model m, ParticleIndex pi) -> bool
3702 return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3704 get_is_setup = staticmethod(get_is_setup)
3706 def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3707 """set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3708 return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3711 def get_minor_radius_h2v_aspect_ratio(self):
3712 """get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3713 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3716 def get_vertical_minor_radius(self):
3717 """get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3718 return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3721 def set_vertical_minor_radius(self, rv):
3722 """set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3723 return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3726 def get_horizontal_minor_radius(self):
3727 """get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3728 return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3731 def set_horizontal_minor_radius(self, rh):
3732 """set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3733 return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3736 def get_minor_radius_h2v_aspect_ratio_key():
3737 """get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3738 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3740 get_minor_radius_h2v_aspect_ratio_key = staticmethod(get_minor_radius_h2v_aspect_ratio_key)
3742 def get_toroidal_pore_key():
3743 """get_toroidal_pore_key() -> IntKey"""
3744 return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3746 get_toroidal_pore_key = staticmethod(get_toroidal_pore_key)
3748 def add_attribute(self, *args):
3750 add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3751 add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3752 add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3753 add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3754 add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3755 add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3757 return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3760 def get_value(self, *args):
3762 get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3763 get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3764 get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3765 get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3766 get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3768 return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3771 def set_value(self, *args):
3773 set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3774 set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3775 set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3776 set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3777 set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3779 return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3782 def remove_attribute(self, *args):
3784 remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3785 remove_attribute(SlabWithToroidalPore self, IntKey a0)
3786 remove_attribute(SlabWithToroidalPore self, StringKey a0)
3787 remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3788 remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3790 return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3793 def has_attribute(self, *args):
3795 has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3796 has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3797 has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3798 has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3799 has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3801 return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3804 def get_derivative(self, a0):
3805 """get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3806 return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3810 """get_name(SlabWithToroidalPore self) -> std::string"""
3811 return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3814 def clear_caches(self):
3815 """clear_caches(SlabWithToroidalPore self)"""
3816 return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3819 def set_name(self, a0):
3820 """set_name(SlabWithToroidalPore self, std::string a0)"""
3821 return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3825 """set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3826 return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3829 def add_to_derivative(self, a0, a1, a2):
3830 """add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3831 return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3834 def set_is_optimized(self, a0, a1):
3835 """set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3836 return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3839 def get_is_optimized(self, a0):
3840 """get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3841 return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
3845 """get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
3846 return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
3849 def __eq__(self, *args):
3851 __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3852 __eq__(SlabWithToroidalPore self, Particle d) -> bool
3854 return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
3857 def __ne__(self, *args):
3859 __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3860 __ne__(SlabWithToroidalPore self, Particle d) -> bool
3862 return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
3865 def __le__(self, *args):
3867 __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3868 __le__(SlabWithToroidalPore self, Particle d) -> bool
3870 return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
3873 def __lt__(self, *args):
3875 __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3876 __lt__(SlabWithToroidalPore self, Particle d) -> bool
3878 return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
3881 def __ge__(self, *args):
3883 __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3884 __ge__(SlabWithToroidalPore self, Particle d) -> bool
3886 return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
3889 def __gt__(self, *args):
3891 __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3892 __gt__(SlabWithToroidalPore self, Particle d) -> bool
3894 return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
3898 """__hash__(SlabWithToroidalPore self) -> std::size_t"""
3899 return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
3903 """__str__(SlabWithToroidalPore self) -> std::string"""
3904 return _IMP_npctransport.SlabWithToroidalPore___str__(self)
3908 """__repr__(SlabWithToroidalPore self) -> std::string"""
3909 return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
3911 __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
3912 __del__ =
lambda self:
None
3913 SlabWithToroidalPore_swigregister = _IMP_npctransport.SlabWithToroidalPore_swigregister
3914 SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
3916 def SlabWithToroidalPore_setup_particle(*args):
3918 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3919 setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
3920 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3921 SlabWithToroidalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3923 return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3925 def SlabWithToroidalPore_get_is_setup(*args):
3927 get_is_setup(_ParticleAdaptor p) -> bool
3928 SlabWithToroidalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3930 return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3932 def SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key():
3933 """SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3934 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3936 def SlabWithToroidalPore_get_toroidal_pore_key():
3937 """SlabWithToroidalPore_get_toroidal_pore_key() -> IntKey"""
3938 return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3941 def __lshift__(*args):
3943 __lshift__(_ostream out, RelaxingSpring n) -> _ostream
3944 __lshift__(_ostream out, Transporting n) -> _ostream
3945 __lshift__(_ostream out, SlabWithPore n) -> _ostream
3946 __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
3947 __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
3949 return _IMP_npctransport.__lshift__(*args)
3951 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
3953 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3956 """__init__(IMP::npctransport::SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
3957 this = _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k)
3959 self.this.append(this)
3960 except __builtin__.Exception:
3963 def get_displacement_direction(self, slab, v):
3964 """get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
3965 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
3968 def get_displacement_magnitude(self, slab, v):
3969 """get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
3970 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
3973 def do_get_inputs(self, m, pis):
3974 """do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3975 return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
3978 def get_version_info(self):
3979 """get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
3980 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
3984 """__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
3985 return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
3989 """__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
3990 return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
3995 return _object_cast_to_SlabWithCylindricalPorePairScore(o)
3997 SlabWithCylindricalPorePairScore_swigregister = _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister
3998 SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
4001 """Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
4003 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4006 """__init__(IMP::npctransport::SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
4007 this = _IMP_npctransport.new_SlabWithToroidalPorePairScore(k)
4009 self.this.append(this)
4010 except __builtin__.Exception:
4013 def do_get_inputs(self, m, pis):
4014 """do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4015 return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
4018 def get_version_info(self):
4019 """get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
4020 return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
4024 """__str__(SlabWithToroidalPorePairScore self) -> std::string"""
4025 return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
4029 """__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
4030 return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
4035 return _object_cast_to_SlabWithToroidalPorePairScore(o)
4037 SlabWithToroidalPorePairScore_swigregister = _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister
4038 SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
4041 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
4043 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4045 def __init__(self, height, radius, length):
4046 """__init__(IMP::npctransport::SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
4047 this = _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length)
4049 self.this.append(this)
4050 except __builtin__.Exception:
4053 def get_version_info(self):
4054 """get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
4055 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
4059 """__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4060 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
4064 """__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4065 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
4070 return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
4072 SlabWithCylindricalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister
4073 SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
4076 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
4078 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4080 def __init__(self, height, radius, length):
4081 """__init__(IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
4082 this = _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length)
4084 self.this.append(this)
4085 except __builtin__.Exception:
4089 """__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4090 return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
4094 """__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4095 return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
4100 return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
4102 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
4103 __del__ =
lambda self:
None
4104 SlabWithCylindricalPoreSurfaceGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister
4105 SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
4108 """Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
4110 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4114 __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
4115 __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
4117 this = _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args)
4119 self.this.append(this)
4120 except __builtin__.Exception:
4123 def get_version_info(self):
4124 """get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
4125 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
4129 """__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4130 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
4134 """__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4135 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
4140 return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
4142 SlabWithToroidalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister
4143 SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
4146 """Proxy of C++ IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> class."""
4148 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4149 __repr__ = _swig_repr
4152 """__init__(IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
4153 this = _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k)
4155 self.this.append(this)
4156 except __builtin__.Exception:
4159 def do_get_inputs(self, m, pis):
4160 """do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4161 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
4164 def get_unary_function(self):
4165 """get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
4166 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
4169 def get_version_info(self):
4170 """get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
4171 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
4173 _GenericAttributeSingletonScoreForPoreRadus_swigregister = _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister
4174 _GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
4176 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
4177 """Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
4179 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4182 """__init__(IMP::npctransport::PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
4183 this = _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k)
4185 self.this.append(this)
4186 except __builtin__.Exception:
4190 """set_k(PoreRadiusSingletonScore self, double k)"""
4191 return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
4195 """__str__(PoreRadiusSingletonScore self) -> std::string"""
4196 return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
4200 """__repr__(PoreRadiusSingletonScore self) -> std::string"""
4201 return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
4206 return _object_cast_to_PoreRadiusSingletonScore(o)
4208 PoreRadiusSingletonScore_swigregister = _IMP_npctransport.PoreRadiusSingletonScore_swigregister
4209 PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
4212 """Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
4214 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4216 def __init__(self, bottom, top, k):
4217 """__init__(IMP::npctransport::ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
4218 this = _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k)
4220 self.this.append(this)
4221 except __builtin__.Exception:
4224 def get_bottom_z(self):
4225 """get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
4226 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
4229 def get_top_z(self):
4230 """get_top_z(ExcludeZRangeSingletonScore self) -> double"""
4231 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
4235 """get_k(ExcludeZRangeSingletonScore self) -> double"""
4236 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
4239 def do_get_inputs(self, m, pis):
4240 """do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4241 return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
4244 def get_version_info(self):
4245 """get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
4246 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
4250 """__str__(ExcludeZRangeSingletonScore self) -> std::string"""
4251 return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
4255 """__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
4256 return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
4261 return _object_cast_to_ExcludeZRangeSingletonScore(o)
4263 ExcludeZRangeSingletonScore_swigregister = _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister
4264 ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
4267 """Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
4269 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4273 __init__(IMP::npctransport::ZBiasSingletonScore self, double k, double max_r) -> ZBiasSingletonScore
4274 __init__(IMP::npctransport::ZBiasSingletonScore self, double k) -> ZBiasSingletonScore
4276 this = _IMP_npctransport.new_ZBiasSingletonScore(*args)
4278 self.this.append(this)
4279 except __builtin__.Exception:
4283 """get_k(ZBiasSingletonScore self) -> double"""
4284 return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
4288 """set_k(ZBiasSingletonScore self, double k)"""
4289 return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
4292 def do_get_inputs(self, m, pis):
4293 """do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4294 return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
4297 def get_version_info(self):
4298 """get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
4299 return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
4303 """__str__(ZBiasSingletonScore self) -> std::string"""
4304 return _IMP_npctransport.ZBiasSingletonScore___str__(self)
4308 """__repr__(ZBiasSingletonScore self) -> std::string"""
4309 return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
4314 return _object_cast_to_ZBiasSingletonScore(o)
4316 ZBiasSingletonScore_swigregister = _IMP_npctransport.ZBiasSingletonScore_swigregister
4317 ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
4320 """Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
4322 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4324 def __init__(self, p, statistics_manager=None, periodicity=1):
4326 __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState
4327 __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None) -> BodyStatisticsOptimizerState
4328 __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p) -> BodyStatisticsOptimizerState
4330 this = _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity)
4332 self.this.append(this)
4333 except __builtin__.Exception:
4336 def get_correlation_time(self):
4337 """get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4338 return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4342 """get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4343 return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4346 def update_particle_type_zr_distribution_map(self):
4347 """update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4348 return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4351 def do_update(self, call_num):
4352 """do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4353 return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4356 def get_version_info(self):
4357 """get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4358 return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4362 """__str__(BodyStatisticsOptimizerState self) -> std::string"""
4363 return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4367 """__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4368 return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4373 return _object_cast_to_BodyStatisticsOptimizerState(o)
4375 BodyStatisticsOptimizerState_swigregister = _IMP_npctransport.BodyStatisticsOptimizerState_swigregister
4376 BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4379 """Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
4381 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4383 def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4385 __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0, WeakPointer< IMP::atom::Simulator > owner=0) -> ParticleTransportStatisticsOptimizerState
4386 __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0) -> ParticleTransportStatisticsOptimizerState
4387 __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z) -> ParticleTransportStatisticsOptimizerState
4389 this = _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner)
4391 self.this.append(this)
4392 except __builtin__.Exception:
4395 def set_owner(self, owner):
4396 """set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4397 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4400 def get_owner(self):
4401 """get_owner(ParticleTransportStatisticsOptimizerState self) -> WeakPointer< IMP::atom::Simulator >"""
4402 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4405 def get_n_transports_up(self):
4406 """get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4407 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4410 def get_n_transports_down(self):
4411 """get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4412 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4415 def get_total_n_transports(self):
4416 """get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4417 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4420 def get_transport_time_points_in_ns(self):
4421 """get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4422 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4425 def do_update(self, call_num):
4426 """do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4427 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4430 def get_version_info(self):
4431 """get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4432 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4436 """__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4437 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4441 """__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4442 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4447 return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4449 ParticleTransportStatisticsOptimizerState_swigregister = _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister
4450 ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4453 """Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
4455 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4457 def __init__(self, ps, periodicity=1):
4459 __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState
4460 __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps) -> ChainStatisticsOptimizerState
4462 this = _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity)
4464 self.this.append(this)
4465 except __builtin__.Exception:
4468 def get_correlation_time(self):
4469 """get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4470 return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4473 def get_local_diffusion_coefficients(self):
4474 """get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4475 return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4479 """get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
4480 return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
4483 def get_mean_radius_of_gyration(self):
4484 """get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4485 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
4488 def get_mean_square_radius_of_gyration(self):
4489 """get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4490 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4493 def get_mean_end_to_end_distance(self):
4494 """get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4495 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4498 def get_mean_square_end_to_end_distance(self):
4499 """get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4500 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4503 def get_mean_bond_distance(self):
4504 """get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4505 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4508 def get_mean_square_bond_distance(self):
4509 """get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4510 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4513 def do_update(self, call_num):
4514 """do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4515 return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4518 def get_version_info(self):
4519 """get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4520 return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4524 """__str__(ChainStatisticsOptimizerState self) -> std::string"""
4525 return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4529 """__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4530 return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4535 return _object_cast_to_ChainStatisticsOptimizerState(o)
4537 ChainStatisticsOptimizerState_swigregister = _IMP_npctransport.ChainStatisticsOptimizerState_swigregister
4538 ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4541 """Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4543 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4545 def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4547 __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0, double slack=1.0) -> BipartitePairsStatisticsOptimizerState
4548 __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0) -> BipartitePairsStatisticsOptimizerState
4549 __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII) -> BipartitePairsStatisticsOptimizerState
4551 this = _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack)
4553 self.this.append(this)
4554 except __builtin__.Exception:
4557 def get_interaction_type(self):
4558 """get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4559 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4562 def get_average_number_of_contacts(self):
4563 """get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4564 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4567 def get_average_off_per_contact_per_ns(self):
4568 """get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4569 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4572 def get_average_off_per_bound_I_per_ns(self):
4573 """get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4574 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4577 def get_average_off_per_bound_II_per_ns(self):
4578 """get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4579 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4582 def get_average_on_per_missing_contact_per_ns(self):
4583 """get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4584 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4587 def get_average_on_per_unbound_I_per_ns(self):
4588 """get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4589 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4592 def get_average_on_per_unbound_II_per_ns(self):
4593 """get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4594 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4597 def get_average_fraction_bound_particles_I(self):
4598 """get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4599 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4602 def get_average_fraction_bound_particles_II(self):
4603 """get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4604 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4607 def get_average_fraction_bound_particle_sites_I(self):
4608 """get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4609 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4612 def get_average_fraction_bound_particle_sites_II(self):
4613 """get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4614 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4617 def get_number_of_particles_1(self):
4618 """get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4619 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4622 def get_number_of_particles_2(self):
4623 """get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4624 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4627 def get_misc_stats_period_ns(self):
4628 """get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4629 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4632 def get_off_stats_period_ns(self):
4633 """get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4634 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4637 def get_off_I_stats_period_ns(self):
4638 """get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4639 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4642 def get_off_II_stats_period_ns(self):
4643 """get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4644 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4647 def get_on_stats_period_ns(self):
4648 """get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4649 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4652 def get_on_I_stats_period_ns(self):
4653 """get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4654 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4657 def get_on_II_stats_period_ns(self):
4658 """get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4659 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4662 def get_version_info(self):
4663 """get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4664 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4668 """__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4669 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4673 """__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4674 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4679 return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4681 BipartitePairsStatisticsOptimizerState_swigregister = _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister
4682 BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4685 def get_close_pairs_range(*args):
4687 get_close_pairs_range(double max_range, double max_range_factor) -> double
4688 get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4690 return _IMP_npctransport.get_close_pairs_range(*args)
4694 get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0) -> double
4695 get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1) -> double
4696 get_time_step(double max_d_factor, double max_k, double min_radius, double min_range) -> double
4697 get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4698 get_time_step(::npctransport_proto::Assignment const & config) -> double
4700 return _IMP_npctransport.get_time_step(*args)
4703 """get_frames_from_ns(double ns, double time_step) -> int"""
4704 return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4707 """get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4708 return _IMP_npctransport.get_number_of_frames(config, time_step)
4711 """get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4712 return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4716 get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int
4717 get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4719 return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4723 get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int
4724 get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4726 return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4730 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False, bool are_fgs_pre_initialized=False)
4731 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False)
4732 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0)
4733 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False)
4734 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints)
4735 initialize_positions(SimulationData sd)
4737 return _IMP_npctransport.initialize_positions(*args)
4738 class Avro2PBReader(object):
4739 """Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4741 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4745 __init__(IMP::npctransport::Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4746 __init__(IMP::npctransport::Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4748 this = _IMP_npctransport.new_Avro2PBReader(*args)
4750 self.this.append(this)
4751 except __builtin__.Exception:
4753 __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4754 __del__ =
lambda self:
None
4756 def read_next(self):
4757 """read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4758 return _IMP_npctransport.Avro2PBReader_read_next(self)
4761 def get_is_valid(self):
4762 """get_is_valid(Avro2PBReader self) -> bool"""
4763 return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4766 def get_cur_file_name(self):
4767 """get_cur_file_name(Avro2PBReader self) -> std::string"""
4768 return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4771 def show(self, *args):
4773 show(Avro2PBReader self, _ostream out)
4774 show(Avro2PBReader self)
4776 return _IMP_npctransport.Avro2PBReader_show(self, *args)
4780 """__str__(Avro2PBReader self) -> std::string"""
4781 return _IMP_npctransport.Avro2PBReader___str__(self)
4785 """__repr__(Avro2PBReader self) -> std::string"""
4786 return _IMP_npctransport.Avro2PBReader___repr__(self)
4788 Avro2PBReader_swigregister = _IMP_npctransport.Avro2PBReader_swigregister
4789 Avro2PBReader_swigregister(Avro2PBReader)
4793 """get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4794 return _IMP_npctransport.get_optimizable_particles(particles)
4797 """get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4798 return _IMP_npctransport.get_non_optimizable_particles(particles)
4801 """get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4802 return _IMP_npctransport.get_particle_indexes(particles)
4805 """get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4806 return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4809 """get_maximal_number_of_unordered_pairs(IMP::ParticlesTemp const & ps0, IMP::ParticlesTemp const & ps1) -> unsigned int"""
4810 return _IMP_npctransport.get_maximal_number_of_unordered_pairs(ps0, ps1)
4813 """get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4814 return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4816 def get_spheres_centers(spheres):
4817 """get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4818 return _IMP_npctransport.get_spheres_centers(spheres)
4821 """copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4822 return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4825 """copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4826 return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4829 """copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4830 return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4833 from .npctransport_pb2
import *
4834 import google.protobuf
4836 print(
"no protobuf support in python")
4837 from ._configuration
import *
4840 def get_module_version():
4841 """get_module_version() -> std::string const"""
4842 return _IMP_npctransport.get_module_version()
4845 """get_example_path(std::string fname) -> std::string"""
4846 return _IMP_npctransport.get_example_path(fname)
4849 """get_data_path(std::string fname) -> std::string"""
4850 return _IMP_npctransport.get_data_path(fname)
4852 from .
import _version_check
4853 _version_check.check_version(get_module_version())
4854 __version__ = get_module_version()
Abstract class for scoring object(s) of type ParticleIndexPair.
CheckLevel get_check_level()
Get the current audit mode.
FGChain * create_fg_chain(IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
Various classes to hold sets of particles.
int assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed)
The base class for geometry.
int get_output_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
A base class for geometry from a set of particles.
double get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0)
Make CGAL functionality available to IMP.
void copy_FGs_coordinates(SimulationData const *src_sd, SimulationData *trg_sd)
copy coordinates of src_sd to trg_sd for FG repeats only
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
int get_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)
void get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
Simple Brownian dynamics simulator.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
Common base class for heavy weight IMP objects.
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
int get_number_of_frames(const ::npctransport_proto::Assignment &config, double time_step)
Abstract class for scoring object(s) of type ParticleIndex.
int get_frames_from_ns(double ns, double time_step)
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
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.
ParticlesTemp get_optimizable_particles(ParticlesTemp const &particles)
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...
int get_dump_interval_in_frames(const ::npctransport_proto::Assignment &config, double time_step)
atom::Hierarchies create_hierarchies_with_sites(RMF::FileConstHandle fh, Model *m)
unsigned int get_maximal_number_of_unordered_pairs(ParticlesTemp const &ps0, ParticlesTemp const &ps1)
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
void add_hierarchies_with_sites(RMF::FileHandle fh, const atom::Hierarchies &hs)
InteractionType make_unordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
FGChain * get_fg_chain(atom::Hierarchy root)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for developing and analyzing benchmarks of IMP code.
InteractionType make_ordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
convenience method for creating and interaction type in swig
Support for the RMF file format for storing hierarchical molecular data and markup.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Display an IMP::core::XYZR particle as a ball.
void add_test_sites(RMF::FileHandle fh, core::ParticleType t, double display_radius, algebra::Vector3Ds sites)
algebra::Sphere3Ds get_spheres_from_vectors(V3iter first, V3iter last, double radius)
convert vectors to spheres of passed radius