11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 import _IMP_npctransport
19 import builtins
as __builtin__
25 strthis =
"proxy of " + self.this.__repr__()
26 except __builtin__.Exception:
28 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
31 def _swig_setattr_nondynamic_instance_variable(set):
32 def set_instance_attr(self, name, value):
34 set(self, name, value)
35 elif name ==
"thisown":
37 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
38 set(self, name, value)
40 raise AttributeError(
"You cannot add instance attributes to %s" % self)
41 return set_instance_attr
44 def _swig_setattr_nondynamic_class_variable(set):
45 def set_class_attr(cls, name, value):
46 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
49 raise AttributeError(
"You cannot add class attributes to %s" % cls)
53 def _swig_add_metaclass(metaclass):
54 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
56 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
60 class _SwigNonDynamicMeta(type):
61 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
67 class IMP_NPCTRANSPORT_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_NPCTRANSPORT_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_npctransport.delete_IMP_NPCTRANSPORT_SwigPyIterator
78 r"""value(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
79 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_value(self)
82 r"""incr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator"""
83 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator"""
87 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
95 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator"""
99 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_copy(self)
102 r"""next(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
103 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_next(self)
106 r"""__next__(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
107 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___next__(self)
110 r"""previous(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
111 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
115 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
119 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
123 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
127 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
131 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
135 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator
140 __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___sub__(self, *args)
147 _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_swigregister(IMP_NPCTRANSPORT_SwigPyIterator)
154 IMP_DEBUG = _IMP_npctransport.IMP_DEBUG
156 IMP_RELEASE = _IMP_npctransport.IMP_RELEASE
158 IMP_SILENT = _IMP_npctransport.IMP_SILENT
160 IMP_PROGRESS = _IMP_npctransport.IMP_PROGRESS
162 IMP_TERSE = _IMP_npctransport.IMP_TERSE
164 IMP_VERBOSE = _IMP_npctransport.IMP_VERBOSE
166 IMP_MEMORY = _IMP_npctransport.IMP_MEMORY
168 IMP_NONE = _IMP_npctransport.IMP_NONE
170 IMP_USAGE = _IMP_npctransport.IMP_USAGE
172 IMP_INTERNAL = _IMP_npctransport.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_npctransport.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_npctransport.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_npctransport.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_npctransport.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
198 class _DirectorObjects(object):
199 """@internal Simple class to keep references to director objects
200 to prevent premature deletion."""
203 def register(self, obj):
204 """Take a reference to a director object; will only work for
205 refcounted C++ classes"""
206 if hasattr(obj,
'get_ref_count'):
207 self._objects.append(obj)
209 """Only drop our reference and allow cleanup by Python if no other
210 Python references exist (we hold 3 references: one in self._objects,
211 one in x, and one in the argument list for getrefcount) *and* no
212 other C++ references exist (the Python object always holds one)"""
213 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
214 or x.get_ref_count() > 1]
218 def get_object_count(self):
219 """Get number of director objects (useful for testing only)"""
220 return len(self._objects)
221 _director_objects = _DirectorObjects()
223 class _ostream(object):
224 r"""Proxy of C++ std::ostream class."""
226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
228 def __init__(self, *args, **kwargs):
229 raise AttributeError(
"No constructor defined")
230 __repr__ = _swig_repr
232 def write(self, osa_buf):
233 r"""write(_ostream self, char const * osa_buf)"""
234 return _IMP_npctransport._ostream_write(self, osa_buf)
237 _IMP_npctransport._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
241 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
243 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
245 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
247 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
249 IMP_BENCHMARK_HAS_NUMPY = _IMP_npctransport.IMP_BENCHMARK_HAS_NUMPY
251 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
254 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
256 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
258 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
260 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
262 IMP_CGAL_HAS_NUMPY = _IMP_npctransport.IMP_CGAL_HAS_NUMPY
264 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
267 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
269 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
271 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
273 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
275 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
277 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
279 IMP_ALGEBRA_HAS_NUMPY = _IMP_npctransport.IMP_ALGEBRA_HAS_NUMPY
281 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
283 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
286 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
288 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
290 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
292 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
294 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
296 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
298 IMP_DISPLAY_HAS_NUMPY = _IMP_npctransport.IMP_DISPLAY_HAS_NUMPY
300 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
303 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
305 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
307 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
309 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
311 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
313 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
315 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
317 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_NUMPY
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
322 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
324 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
326 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
328 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
330 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
334 IMP_STATISTICS_HAS_NUMPY = _IMP_npctransport.IMP_STATISTICS_HAS_NUMPY
336 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
339 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
341 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
343 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
345 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
349 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
351 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
353 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
355 IMP_CORE_HAS_NUMPY = _IMP_npctransport.IMP_CORE_HAS_NUMPY
357 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
360 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
362 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
364 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
366 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
368 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
370 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
372 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
374 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
376 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
378 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
380 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
382 IMP_CONTAINER_HAS_NUMPY = _IMP_npctransport.IMP_CONTAINER_HAS_NUMPY
384 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
386 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
388 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
390 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
393 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
395 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
397 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
399 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
401 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
403 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
405 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
407 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
409 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
411 IMP_ATOM_HAS_NUMPY = _IMP_npctransport.IMP_ATOM_HAS_NUMPY
413 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
415 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
417 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
419 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
421 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
423 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
426 IMP_EM_HAS_IMP_CGAL = _IMP_npctransport.IMP_EM_HAS_IMP_CGAL
428 IMP_EM_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_EM_HAS_IMP_CONTAINER
430 IMP_EM_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_EM_HAS_IMP_DISPLAY
432 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_EM_HAS_IMP_SCORE_FUNCTOR
434 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_FILESYSTEM
436 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
438 IMP_EM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_EM_HAS_BOOST_RANDOM
440 IMP_EM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_EM_HAS_BOOST_REGEX
442 IMP_EM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_SYSTEM
444 IMP_EM_HAS_CGAL = _IMP_npctransport.IMP_EM_HAS_CGAL
446 IMP_EM_HAS_HDF5 = _IMP_npctransport.IMP_EM_HAS_HDF5
448 IMP_EM_HAS_NUMPY = _IMP_npctransport.IMP_EM_HAS_NUMPY
450 IMP_EM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_EM_HAS_PYTHON_IHM
452 IMPEM_SHOW_WARNINGS = _IMP_npctransport.IMPEM_SHOW_WARNINGS
455 IMP_SAXS_HAS_IMP_CGAL = _IMP_npctransport.IMP_SAXS_HAS_IMP_CGAL
457 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_SAXS_HAS_IMP_CONTAINER
459 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_SAXS_HAS_IMP_DISPLAY
461 IMP_SAXS_HAS_IMP_KERNEL = _IMP_npctransport.IMP_SAXS_HAS_IMP_KERNEL
463 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
465 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_FILESYSTEM
467 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
469 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_RANDOM
471 IMP_SAXS_HAS_BOOST_REGEX = _IMP_npctransport.IMP_SAXS_HAS_BOOST_REGEX
473 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_SYSTEM
475 IMP_SAXS_HAS_CGAL = _IMP_npctransport.IMP_SAXS_HAS_CGAL
477 IMP_SAXS_HAS_HDF5 = _IMP_npctransport.IMP_SAXS_HAS_HDF5
479 IMP_SAXS_HAS_NUMPY = _IMP_npctransport.IMP_SAXS_HAS_NUMPY
481 IMP_SAXS_HAS_PYTHON_IHM = _IMP_npctransport.IMP_SAXS_HAS_PYTHON_IHM
483 IMPSAXS_SHOW_WARNINGS = _IMP_npctransport.IMPSAXS_SHOW_WARNINGS
486 IMP_ISD_HAS_IMP_CGAL = _IMP_npctransport.IMP_ISD_HAS_IMP_CGAL
488 IMP_ISD_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_ISD_HAS_IMP_DISPLAY
490 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
492 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_FILESYSTEM
494 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
496 IMP_ISD_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ISD_HAS_BOOST_RANDOM
498 IMP_ISD_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ISD_HAS_BOOST_REGEX
500 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_SYSTEM
502 IMP_ISD_HAS_CGAL = _IMP_npctransport.IMP_ISD_HAS_CGAL
504 IMP_ISD_HAS_HDF5 = _IMP_npctransport.IMP_ISD_HAS_HDF5
506 IMP_ISD_HAS_NUMPY = _IMP_npctransport.IMP_ISD_HAS_NUMPY
508 IMP_ISD_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ISD_HAS_PYTHON_IHM
510 IMPISD_SHOW_WARNINGS = _IMP_npctransport.IMPISD_SHOW_WARNINGS
513 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
515 IMP_RMF_HAS_IMP_EM = _IMP_npctransport.IMP_RMF_HAS_IMP_EM
517 IMP_RMF_HAS_IMP_SAXS = _IMP_npctransport.IMP_RMF_HAS_IMP_SAXS
519 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
521 IMP_RMF_HAS_IMP_STATISTICS = _IMP_npctransport.IMP_RMF_HAS_IMP_STATISTICS
523 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
525 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
527 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
529 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
531 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
533 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
535 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
537 IMP_RMF_HAS_NUMPY = _IMP_npctransport.IMP_RMF_HAS_NUMPY
539 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
541 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
545 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
547 IMP_NPCTRANSPORT_HAS_IMP_EM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_EM
549 IMP_NPCTRANSPORT_HAS_IMP_ISD = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_ISD
551 IMP_NPCTRANSPORT_HAS_IMP_SAXS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_SAXS
553 IMP_NPCTRANSPORT_HAS_ABSEIL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_ABSEIL
555 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
557 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
559 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
561 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
563 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
565 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
567 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
569 IMP_NPCTRANSPORT_HAS_NUMPY = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_NUMPY
571 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
573 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
576 _object_types.append(
"SitesPairScore")
579 def _object_cast_to_SitesPairScore(o):
580 r"""_object_cast_to_SitesPairScore(Object o) -> SitesPairScore"""
581 return _IMP_npctransport._object_cast_to_SitesPairScore(o)
583 _object_types.append(
"Scoring")
586 def _object_cast_to_Scoring(o):
587 r"""_object_cast_to_Scoring(Object o) -> Scoring"""
588 return _IMP_npctransport._object_cast_to_Scoring(o)
590 _object_types.append(
"BrownianDynamicsTAMDWithSlabSupport")
593 def _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o):
594 r"""_object_cast_to_BrownianDynamicsTAMDWithSlabSupport(Object o) -> BrownianDynamicsTAMDWithSlabSupport"""
595 return _IMP_npctransport._object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
597 _object_types.append(
"Statistics")
600 def _object_cast_to_Statistics(o):
601 r"""_object_cast_to_Statistics(Object o) -> Statistics"""
602 return _IMP_npctransport._object_cast_to_Statistics(o)
604 _object_types.append(
"SimulationData")
607 def _object_cast_to_SimulationData(o):
608 r"""_object_cast_to_SimulationData(Object o) -> SimulationData"""
609 return _IMP_npctransport._object_cast_to_SimulationData(o)
611 _object_types.append(
"SitesGeometry")
614 def _object_cast_to_SitesGeometry(o):
615 r"""_object_cast_to_SitesGeometry(Object o) -> SitesGeometry"""
616 return _IMP_npctransport._object_cast_to_SitesGeometry(o)
618 _object_types.append(
"TypedSitesGeometry")
621 def _object_cast_to_TypedSitesGeometry(o):
622 r"""_object_cast_to_TypedSitesGeometry(Object o) -> TypedSitesGeometry"""
623 return _IMP_npctransport._object_cast_to_TypedSitesGeometry(o)
625 _object_types.append(
"SlabWithCylindricalPorePairScore")
628 def _object_cast_to_SlabWithCylindricalPorePairScore(o):
629 r"""_object_cast_to_SlabWithCylindricalPorePairScore(Object o) -> SlabWithCylindricalPorePairScore"""
630 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPorePairScore(o)
632 _object_types.append(
"SlabWithToroidalPorePairScore")
635 def _object_cast_to_SlabWithToroidalPorePairScore(o):
636 r"""_object_cast_to_SlabWithToroidalPorePairScore(Object o) -> SlabWithToroidalPorePairScore"""
637 return _IMP_npctransport._object_cast_to_SlabWithToroidalPorePairScore(o)
639 _object_types.append(
"PoreRadiusSingletonScore")
642 def _object_cast_to_PoreRadiusSingletonScore(o):
643 r"""_object_cast_to_PoreRadiusSingletonScore(Object o) -> PoreRadiusSingletonScore"""
644 return _IMP_npctransport._object_cast_to_PoreRadiusSingletonScore(o)
646 _object_types.append(
"ExcludeZRangeSingletonScore")
649 def _object_cast_to_ExcludeZRangeSingletonScore(o):
650 r"""_object_cast_to_ExcludeZRangeSingletonScore(Object o) -> ExcludeZRangeSingletonScore"""
651 return _IMP_npctransport._object_cast_to_ExcludeZRangeSingletonScore(o)
653 _object_types.append(
"ZBiasSingletonScore")
656 def _object_cast_to_ZBiasSingletonScore(o):
657 r"""_object_cast_to_ZBiasSingletonScore(Object o) -> ZBiasSingletonScore"""
658 return _IMP_npctransport._object_cast_to_ZBiasSingletonScore(o)
660 _object_types.append(
"SlabWithCylindricalPoreWireGeometry")
663 def _object_cast_to_SlabWithCylindricalPoreWireGeometry(o):
664 r"""_object_cast_to_SlabWithCylindricalPoreWireGeometry(Object o) -> SlabWithCylindricalPoreWireGeometry"""
665 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
667 _object_types.append(
"SlabWithCylindricalPoreSurfaceGeometry")
670 def _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o):
671 r"""_object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(Object o) -> SlabWithCylindricalPoreSurfaceGeometry"""
672 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
674 _object_types.append(
"SlabWithToroidalPoreWireGeometry")
677 def _object_cast_to_SlabWithToroidalPoreWireGeometry(o):
678 r"""_object_cast_to_SlabWithToroidalPoreWireGeometry(Object o) -> SlabWithToroidalPoreWireGeometry"""
679 return _IMP_npctransport._object_cast_to_SlabWithToroidalPoreWireGeometry(o)
681 _object_types.append(
"LinearSoftSpherePairScore")
684 def _object_cast_to_LinearSoftSpherePairScore(o):
685 r"""_object_cast_to_LinearSoftSpherePairScore(Object o) -> LinearSoftSpherePairScore"""
686 return _IMP_npctransport._object_cast_to_LinearSoftSpherePairScore(o)
688 _object_types.append(
"FunctorLinearSoftSpherePairScore")
691 def _object_cast_to_FunctorLinearSoftSpherePairScore(o):
692 r"""_object_cast_to_FunctorLinearSoftSpherePairScore(Object o) -> FunctorLinearSoftSpherePairScore"""
693 return _IMP_npctransport._object_cast_to_FunctorLinearSoftSpherePairScore(o)
695 _object_types.append(
"LinearInteractionPairScore")
698 def _object_cast_to_LinearInteractionPairScore(o):
699 r"""_object_cast_to_LinearInteractionPairScore(Object o) -> LinearInteractionPairScore"""
700 return _IMP_npctransport._object_cast_to_LinearInteractionPairScore(o)
702 _object_types.append(
"FunctorLinearInteractionPairScore")
705 def _object_cast_to_FunctorLinearInteractionPairScore(o):
706 r"""_object_cast_to_FunctorLinearInteractionPairScore(Object o) -> FunctorLinearInteractionPairScore"""
707 return _IMP_npctransport._object_cast_to_FunctorLinearInteractionPairScore(o)
709 _object_types.append(
"LinearWellPairScore")
712 def _object_cast_to_LinearWellPairScore(o):
713 r"""_object_cast_to_LinearWellPairScore(Object o) -> LinearWellPairScore"""
714 return _IMP_npctransport._object_cast_to_LinearWellPairScore(o)
716 _object_types.append(
"HarmonicSpringSingletonScore")
719 def _object_cast_to_HarmonicSpringSingletonScore(o):
720 r"""_object_cast_to_HarmonicSpringSingletonScore(Object o) -> HarmonicSpringSingletonScore"""
721 return _IMP_npctransport._object_cast_to_HarmonicSpringSingletonScore(o)
723 _object_types.append(
"HierarchyWithSitesSaveLink")
726 def _object_cast_to_HierarchyWithSitesSaveLink(o):
727 r"""_object_cast_to_HierarchyWithSitesSaveLink(Object o) -> HierarchyWithSitesSaveLink"""
728 return _IMP_npctransport._object_cast_to_HierarchyWithSitesSaveLink(o)
730 _object_types.append(
"HierarchyWithSitesLoadLink")
733 def _object_cast_to_HierarchyWithSitesLoadLink(o):
734 r"""_object_cast_to_HierarchyWithSitesLoadLink(Object o) -> HierarchyWithSitesLoadLink"""
735 return _IMP_npctransport._object_cast_to_HierarchyWithSitesLoadLink(o)
737 _object_types.append(
"ChainStatisticsOptimizerState")
740 def _object_cast_to_ChainStatisticsOptimizerState(o):
741 r"""_object_cast_to_ChainStatisticsOptimizerState(Object o) -> ChainStatisticsOptimizerState"""
742 return _IMP_npctransport._object_cast_to_ChainStatisticsOptimizerState(o)
744 _object_types.append(
"BodyStatisticsOptimizerState")
747 def _object_cast_to_BodyStatisticsOptimizerState(o):
748 r"""_object_cast_to_BodyStatisticsOptimizerState(Object o) -> BodyStatisticsOptimizerState"""
749 return _IMP_npctransport._object_cast_to_BodyStatisticsOptimizerState(o)
751 _object_types.append(
"BipartitePairsStatisticsOptimizerState")
754 def _object_cast_to_BipartitePairsStatisticsOptimizerState(o):
755 r"""_object_cast_to_BipartitePairsStatisticsOptimizerState(Object o) -> BipartitePairsStatisticsOptimizerState"""
756 return _IMP_npctransport._object_cast_to_BipartitePairsStatisticsOptimizerState(o)
758 _object_types.append(
"ParticleTransportStatisticsOptimizerState")
761 def _object_cast_to_ParticleTransportStatisticsOptimizerState(o):
762 r"""_object_cast_to_ParticleTransportStatisticsOptimizerState(Object o) -> ParticleTransportStatisticsOptimizerState"""
763 return _IMP_npctransport._object_cast_to_ParticleTransportStatisticsOptimizerState(o)
765 _object_types.append(
"FGChain")
768 def _object_cast_to_FGChain(o):
769 r"""_object_cast_to_FGChain(Object o) -> FGChain"""
770 return _IMP_npctransport._object_cast_to_FGChain(o)
772 _object_types.append(
"ParticleFactory")
775 def _object_cast_to_ParticleFactory(o):
776 r"""_object_cast_to_ParticleFactory(Object o) -> ParticleFactory"""
777 return _IMP_npctransport._object_cast_to_ParticleFactory(o)
780 _plural_types.append(
"Avro2PBReaders")
781 _value_types.append(
"Avro2PBReader")
784 SitesPairScoreParametersList=list
785 _plural_types.append(
"SitesPairScoreParametersList")
786 _value_types.append(
"SitesPairScoreParameters")
789 def Transportings(l=[]):
790 return [Transporting(x)
for x
in l]
791 _plural_types.append(
"Transportings")
794 _value_types.append(
"Transporting")
797 def SlabWithPores(l=[]):
798 return [SlabWithPore(x)
for x
in l]
799 _plural_types.append(
"SlabWithPores")
802 _value_types.append(
"SlabWithPore")
805 def SlabWithCylindricalPores(l=[]):
806 return [SlabWithCylindricalPore(x)
for x
in l]
807 _plural_types.append(
"SlabWithCylindricalPores")
810 _value_types.append(
"SlabWithCylindricalPore")
813 def RelaxingSprings(l=[]):
814 return [RelaxingSpring(x)
for x
in l]
815 _plural_types.append(
"RelaxingSprings")
818 _value_types.append(
"RelaxingSpring")
821 def SlabWithToroidalPores(l=[]):
822 return [SlabWithToroidalPore(x)
for x
in l]
823 _plural_types.append(
"SlabWithToroidalPores")
826 _value_types.append(
"SlabWithToroidalPore")
828 class _DoubleParameter(object):
829 r"""Proxy of C++ IMP::npctransport::Parameter< double > class."""
831 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
832 __repr__ = _swig_repr
836 __init__(_DoubleParameter self) -> _DoubleParameter
837 __init__(_DoubleParameter self, double t) -> _DoubleParameter
839 _IMP_npctransport._DoubleParameter_swiginit(self, _IMP_npctransport.new__DoubleParameter(*args))
842 r"""get_value(_DoubleParameter self) -> double"""
843 return _IMP_npctransport._DoubleParameter_get_value(self)
846 r"""is_init(_DoubleParameter self) -> bool"""
847 return _IMP_npctransport._DoubleParameter_is_init(self)
848 __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
851 _IMP_npctransport._DoubleParameter_swigregister(_DoubleParameter)
852 class _IntParameter(object):
853 r"""Proxy of C++ IMP::npctransport::Parameter< int > class."""
855 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
856 __repr__ = _swig_repr
860 __init__(_IntParameter self) -> _IntParameter
861 __init__(_IntParameter self, int t) -> _IntParameter
863 _IMP_npctransport._IntParameter_swiginit(self, _IMP_npctransport.new__IntParameter(*args))
866 r"""get_value(_IntParameter self) -> int"""
867 return _IMP_npctransport._IntParameter_get_value(self)
870 r"""is_init(_IntParameter self) -> bool"""
871 return _IMP_npctransport._IntParameter_is_init(self)
872 __swig_destroy__ = _IMP_npctransport.delete__IntParameter
875 _IMP_npctransport._IntParameter_swigregister(_IntParameter)
876 class _BoolParameter(object):
877 r"""Proxy of C++ IMP::npctransport::Parameter< bool > class."""
879 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
880 __repr__ = _swig_repr
884 __init__(_BoolParameter self) -> _BoolParameter
885 __init__(_BoolParameter self, bool t) -> _BoolParameter
887 _IMP_npctransport._BoolParameter_swiginit(self, _IMP_npctransport.new__BoolParameter(*args))
890 r"""get_value(_BoolParameter self) -> bool"""
891 return _IMP_npctransport._BoolParameter_get_value(self)
894 r"""is_init(_BoolParameter self) -> bool"""
895 return _IMP_npctransport._BoolParameter_is_init(self)
896 __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
899 _IMP_npctransport._BoolParameter_swigregister(_BoolParameter)
902 r"""make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
903 return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
906 r"""make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
907 return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
911 make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
912 make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
914 return _IMP_npctransport.make_unordered_particle_index_pair(*args)
916 r"""Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class."""
918 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
921 r"""__init__(LinearSoftSpherePairScore self, double k, std::string name="LinearSSPairScore%1%") -> LinearSoftSpherePairScore"""
922 _IMP_npctransport.LinearSoftSpherePairScore_swiginit(self, _IMP_npctransport.new_LinearSoftSpherePairScore(*args))
924 def do_get_inputs(self, m, pis):
925 r"""do_get_inputs(LinearSoftSpherePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
926 return _IMP_npctransport.LinearSoftSpherePairScore_do_get_inputs(self, m, pis)
929 r"""get_k(LinearSoftSpherePairScore self) -> double"""
930 return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
932 def get_version_info(self):
933 r"""get_version_info(LinearSoftSpherePairScore self) -> VersionInfo"""
934 return _IMP_npctransport.LinearSoftSpherePairScore_get_version_info(self)
935 __swig_destroy__ = _IMP_npctransport.delete_LinearSoftSpherePairScore
938 r"""__str__(LinearSoftSpherePairScore self) -> std::string"""
939 return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
942 r"""__repr__(LinearSoftSpherePairScore self) -> std::string"""
943 return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
947 return _object_cast_to_LinearSoftSpherePairScore(o)
951 _IMP_npctransport.LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
953 r"""Proxy of C++ IMP::npctransport::LinearInteractionPairScore class."""
955 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
958 r"""__init__(LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr, std::string name="LinearIDPairScore%1%") -> LinearInteractionPairScore"""
959 _IMP_npctransport.LinearInteractionPairScore_swiginit(self, _IMP_npctransport.new_LinearInteractionPairScore(*args))
961 def evaluate_if_good_index(self, *args):
963 evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPair const & p, DerivativeAccumulator da, double max) -> double
964 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
966 return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
968 def do_get_inputs(self, m, pis):
969 r"""do_get_inputs(LinearInteractionPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
970 return _IMP_npctransport.LinearInteractionPairScore_do_get_inputs(self, m, pis)
972 def get_range_attraction(self):
973 r"""get_range_attraction(LinearInteractionPairScore self) -> double"""
974 return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
976 def get_k_attraction(self):
977 r"""get_k_attraction(LinearInteractionPairScore self) -> double"""
978 return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
980 def set_k_attraction(self, k_attr):
981 r"""set_k_attraction(LinearInteractionPairScore self, double k_attr)"""
982 return _IMP_npctransport.LinearInteractionPairScore_set_k_attraction(self, k_attr)
984 def get_k_repulsion(self):
985 r"""get_k_repulsion(LinearInteractionPairScore self) -> double"""
986 return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
988 def set_k_repulsion(self, k_rep):
989 r"""set_k_repulsion(LinearInteractionPairScore self, double k_rep)"""
990 return _IMP_npctransport.LinearInteractionPairScore_set_k_repulsion(self, k_rep)
992 def get_version_info(self):
993 r"""get_version_info(LinearInteractionPairScore self) -> VersionInfo"""
994 return _IMP_npctransport.LinearInteractionPairScore_get_version_info(self)
995 __swig_destroy__ = _IMP_npctransport.delete_LinearInteractionPairScore
998 r"""__str__(LinearInteractionPairScore self) -> std::string"""
999 return _IMP_npctransport.LinearInteractionPairScore___str__(self)
1002 r"""__repr__(LinearInteractionPairScore self) -> std::string"""
1003 return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
1007 return _object_cast_to_LinearInteractionPairScore(o)
1011 _IMP_npctransport.LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
1013 r"""Proxy of C++ IMP::npctransport::LinearWellPairScore class."""
1015 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1018 r"""__init__(LinearWellPairScore self, double rest_length_factor, double k, std::string name="LinearIDPairScore%1%") -> LinearWellPairScore"""
1019 _IMP_npctransport.LinearWellPairScore_swiginit(self, _IMP_npctransport.new_LinearWellPairScore(*args))
1021 def set_rest_length_factor(self, rest_length_factor):
1022 r"""set_rest_length_factor(LinearWellPairScore self, double rest_length_factor)"""
1023 return _IMP_npctransport.LinearWellPairScore_set_rest_length_factor(self, rest_length_factor)
1025 def get_rest_length_factor(self):
1026 r"""get_rest_length_factor(LinearWellPairScore self) -> double"""
1027 return _IMP_npctransport.LinearWellPairScore_get_rest_length_factor(self)
1030 r"""set_k(LinearWellPairScore self, double k)"""
1031 return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
1034 r"""get_k(LinearWellPairScore self) -> double"""
1035 return _IMP_npctransport.LinearWellPairScore_get_k(self)
1037 def do_get_inputs(self, m, pis):
1038 r"""do_get_inputs(LinearWellPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1039 return _IMP_npctransport.LinearWellPairScore_do_get_inputs(self, m, pis)
1041 def get_version_info(self):
1042 r"""get_version_info(LinearWellPairScore self) -> VersionInfo"""
1043 return _IMP_npctransport.LinearWellPairScore_get_version_info(self)
1044 __swig_destroy__ = _IMP_npctransport.delete_LinearWellPairScore
1047 r"""__str__(LinearWellPairScore self) -> std::string"""
1048 return _IMP_npctransport.LinearWellPairScore___str__(self)
1051 r"""__repr__(LinearWellPairScore self) -> std::string"""
1052 return _IMP_npctransport.LinearWellPairScore___repr__(self)
1056 return _object_cast_to_LinearWellPairScore(o)
1060 _IMP_npctransport.LinearWellPairScore_swigregister(LinearWellPairScore)
1062 r"""Proxy of C++ IMP::npctransport::RelaxingSpring class."""
1064 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1068 __init__(RelaxingSpring self) -> RelaxingSpring
1069 __init__(RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
1070 __init__(RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
1072 _IMP_npctransport.RelaxingSpring_swiginit(self, _IMP_npctransport.new_RelaxingSpring(*args))
1074 def show(self, *args):
1075 r"""show(RelaxingSpring self, _ostream out=std::cout)"""
1076 return _IMP_npctransport.RelaxingSpring_show(self, *args)
1079 def setup_particle(*args):
1081 setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1082 setup_particle(_ParticleAdaptor pa, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1084 return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1087 def get_is_setup(*args):
1089 get_is_setup(_ParticleAdaptor p) -> bool
1090 get_is_setup(Model m, ParticleIndex pi) -> bool
1092 return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1095 def get_bonded_particle_0_key():
1096 r"""get_bonded_particle_0_key() -> ParticleIndexKey"""
1097 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1100 def get_bonded_particle_1_key():
1101 r"""get_bonded_particle_1_key() -> ParticleIndexKey"""
1102 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1105 def get_equilibrium_rest_length_factor_key():
1106 r"""get_equilibrium_rest_length_factor_key() -> FloatKey"""
1107 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1110 def get_rest_length_key():
1111 r"""get_rest_length_key() -> FloatKey"""
1112 return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1115 def get_rest_length_diffusion_coefficient_key():
1116 r"""get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1117 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1119 def get_bonded_particle_0(self):
1120 r"""get_bonded_particle_0(RelaxingSpring self) -> Particle"""
1121 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0(self)
1123 def get_bonded_particle_1(self):
1124 r"""get_bonded_particle_1(RelaxingSpring self) -> Particle"""
1125 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1(self)
1127 def get_bonded_particle_index_0(self):
1128 r"""get_bonded_particle_index_0(RelaxingSpring self) -> ParticleIndex"""
1129 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_0(self)
1131 def get_bonded_particle_index_1(self):
1132 r"""get_bonded_particle_index_1(RelaxingSpring self) -> ParticleIndex"""
1133 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_1(self)
1135 def get_equilibrium_rest_length_factor(self):
1136 r"""get_equilibrium_rest_length_factor(RelaxingSpring self) -> IMP::Float"""
1137 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor(self)
1139 def set_equilibrium_rest_length_factor(self, t):
1140 r"""set_equilibrium_rest_length_factor(RelaxingSpring self, IMP::Float t)"""
1141 return _IMP_npctransport.RelaxingSpring_set_equilibrium_rest_length_factor(self, t)
1143 def get_rest_length(self):
1144 r"""get_rest_length(RelaxingSpring self) -> IMP::Float"""
1145 return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1147 def set_rest_length(self, t):
1148 r"""set_rest_length(RelaxingSpring self, IMP::Float t)"""
1149 return _IMP_npctransport.RelaxingSpring_set_rest_length(self, t)
1151 def get_rest_length_diffusion_coefficient(self):
1152 r"""get_rest_length_diffusion_coefficient(RelaxingSpring self) -> IMP::Float"""
1153 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient(self)
1155 def set_rest_length_diffusion_coefficient(self, t):
1156 r"""set_rest_length_diffusion_coefficient(RelaxingSpring self, IMP::Float t)"""
1157 return _IMP_npctransport.RelaxingSpring_set_rest_length_diffusion_coefficient(self, t)
1159 def add_to_rest_length_derivative(self, d, da):
1160 r"""add_to_rest_length_derivative(RelaxingSpring self, double d, DerivativeAccumulator da)"""
1161 return _IMP_npctransport.RelaxingSpring_add_to_rest_length_derivative(self, d, da)
1163 def get_rest_length_derivative(self):
1164 r"""get_rest_length_derivative(RelaxingSpring self) -> double"""
1165 return _IMP_npctransport.RelaxingSpring_get_rest_length_derivative(self)
1167 def add_attribute(self, *args):
1169 add_attribute(RelaxingSpring self, FloatKey k, IMP::Float v, bool opt)
1170 add_attribute(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1171 add_attribute(RelaxingSpring self, IntKey a0, IMP::Int a1)
1172 add_attribute(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1173 add_attribute(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1174 add_attribute(RelaxingSpring self, StringKey a0, IMP::String a1)
1175 add_attribute(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1176 add_attribute(RelaxingSpring self, ObjectKey a0, Object a1)
1177 add_attribute(RelaxingSpring self, SparseFloatKey a0, IMP::Float a1)
1178 add_attribute(RelaxingSpring self, SparseIntKey a0, IMP::Int a1)
1179 add_attribute(RelaxingSpring self, SparseStringKey a0, IMP::String a1)
1180 add_attribute(RelaxingSpring self, SparseParticleIndexKey a0, ParticleIndex a1)
1182 return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1184 def get_value(self, *args):
1186 get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1187 get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1188 get_value(RelaxingSpring self, FloatsKey a0) -> IMP::Floats
1189 get_value(RelaxingSpring self, IntsKey a0) -> IMP::Ints
1190 get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1191 get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1192 get_value(RelaxingSpring self, ObjectKey a0) -> Object
1193 get_value(RelaxingSpring self, SparseFloatKey a0) -> IMP::Float
1194 get_value(RelaxingSpring self, SparseIntKey a0) -> IMP::Int
1195 get_value(RelaxingSpring self, SparseStringKey a0) -> IMP::String
1196 get_value(RelaxingSpring self, SparseParticleIndexKey a0) -> ParticleIndex
1198 return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1200 def set_value(self, *args):
1202 set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1203 set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1204 set_value(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1205 set_value(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1206 set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1207 set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1208 set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1209 set_value(RelaxingSpring self, SparseFloatKey a0, IMP::Float a1)
1210 set_value(RelaxingSpring self, SparseIntKey a0, IMP::Int a1)
1211 set_value(RelaxingSpring self, SparseStringKey a0, IMP::String a1)
1212 set_value(RelaxingSpring self, SparseParticleIndexKey a0, ParticleIndex a1)
1214 return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1216 def remove_attribute(self, *args):
1218 remove_attribute(RelaxingSpring self, FloatKey a0)
1219 remove_attribute(RelaxingSpring self, IntKey a0)
1220 remove_attribute(RelaxingSpring self, FloatsKey a0)
1221 remove_attribute(RelaxingSpring self, IntsKey a0)
1222 remove_attribute(RelaxingSpring self, StringKey a0)
1223 remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1224 remove_attribute(RelaxingSpring self, ObjectKey a0)
1225 remove_attribute(RelaxingSpring self, SparseFloatKey a0)
1226 remove_attribute(RelaxingSpring self, SparseIntKey a0)
1227 remove_attribute(RelaxingSpring self, SparseStringKey a0)
1228 remove_attribute(RelaxingSpring self, SparseParticleIndexKey a0)
1230 return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1232 def has_attribute(self, *args):
1234 has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1235 has_attribute(RelaxingSpring self, IntKey a0) -> bool
1236 has_attribute(RelaxingSpring self, FloatsKey a0) -> bool
1237 has_attribute(RelaxingSpring self, IntsKey a0) -> bool
1238 has_attribute(RelaxingSpring self, StringKey a0) -> bool
1239 has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1240 has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1241 has_attribute(RelaxingSpring self, SparseFloatKey a0) -> bool
1242 has_attribute(RelaxingSpring self, SparseIntKey a0) -> bool
1243 has_attribute(RelaxingSpring self, SparseStringKey a0) -> bool
1244 has_attribute(RelaxingSpring self, SparseParticleIndexKey a0) -> bool
1246 return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1248 def get_derivative(self, a0):
1249 r"""get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1250 return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1253 r"""get_name(RelaxingSpring self) -> std::string"""
1254 return _IMP_npctransport.RelaxingSpring_get_name(self)
1256 def clear_caches(self):
1257 r"""clear_caches(RelaxingSpring self)"""
1258 return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1260 def set_name(self, a0):
1261 r"""set_name(RelaxingSpring self, std::string a0)"""
1262 return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1265 r"""set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1266 return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1268 def add_to_derivative(self, a0, a1, a2):
1269 r"""add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1270 return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1272 def set_is_optimized(self, a0, a1):
1273 r"""set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1274 return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1276 def get_is_optimized(self, a0):
1277 r"""get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1278 return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1281 r"""get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1282 return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1284 def __eq__(self, *args):
1286 __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1287 __eq__(RelaxingSpring self, Particle d) -> bool
1289 return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1291 def __ne__(self, *args):
1293 __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1294 __ne__(RelaxingSpring self, Particle d) -> bool
1296 return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1298 def __le__(self, *args):
1300 __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1301 __le__(RelaxingSpring self, Particle d) -> bool
1303 return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1305 def __lt__(self, *args):
1307 __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1308 __lt__(RelaxingSpring self, Particle d) -> bool
1310 return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1312 def __ge__(self, *args):
1314 __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1315 __ge__(RelaxingSpring self, Particle d) -> bool
1317 return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1319 def __gt__(self, *args):
1321 __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1322 __gt__(RelaxingSpring self, Particle d) -> bool
1324 return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1327 r"""__hash__(RelaxingSpring self) -> std::size_t"""
1328 return _IMP_npctransport.RelaxingSpring___hash__(self)
1331 r"""__str__(RelaxingSpring self) -> std::string"""
1332 return _IMP_npctransport.RelaxingSpring___str__(self)
1335 r"""__repr__(RelaxingSpring self) -> std::string"""
1336 return _IMP_npctransport.RelaxingSpring___repr__(self)
1338 def _get_as_binary(self):
1339 r"""_get_as_binary(RelaxingSpring self) -> PyObject *"""
1340 return _IMP_npctransport.RelaxingSpring__get_as_binary(self)
1342 def _set_from_binary(self, p):
1343 r"""_set_from_binary(RelaxingSpring self, PyObject * p)"""
1344 return _IMP_npctransport.RelaxingSpring__set_from_binary(self, p)
1346 def __getstate__(self):
1347 p = self._get_as_binary()
1348 if len(self.__dict__) > 1:
1349 d = self.__dict__.copy()
1354 def __setstate__(self, p):
1355 if not hasattr(self,
'this'):
1357 if isinstance(p, tuple):
1359 self.__dict__.update(d)
1360 return self._set_from_binary(p)
1362 __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1365 _IMP_npctransport.RelaxingSpring_swigregister(RelaxingSpring)
1367 r"""Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1369 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1372 r"""__init__(HarmonicSpringSingletonScore self, double k1, double k2, std::string name="HarmonicSpringSingletonScore%1%") -> HarmonicSpringSingletonScore"""
1373 _IMP_npctransport.HarmonicSpringSingletonScore_swiginit(self, _IMP_npctransport.new_HarmonicSpringSingletonScore(*args))
1375 def set_k1(self, k1):
1376 r"""set_k1(HarmonicSpringSingletonScore self, double k1)"""
1377 return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1380 r"""get_k1(HarmonicSpringSingletonScore self) -> double"""
1381 return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1383 def set_k2(self, k2):
1384 r"""set_k2(HarmonicSpringSingletonScore self, double k2)"""
1385 return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1388 r"""get_k2(HarmonicSpringSingletonScore self) -> double"""
1389 return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1391 def do_get_inputs(self, m, pis):
1392 r"""do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1393 return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1395 def get_version_info(self):
1396 r"""get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1397 return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1398 __swig_destroy__ = _IMP_npctransport.delete_HarmonicSpringSingletonScore
1401 r"""__str__(HarmonicSpringSingletonScore self) -> std::string"""
1402 return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1405 r"""__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1406 return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1410 return _object_cast_to_HarmonicSpringSingletonScore(o)
1414 _IMP_npctransport.HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1415 class LinearInteraction(object):
1416 r"""Proxy of C++ IMP::npctransport::LinearInteraction class."""
1418 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1419 __repr__ = _swig_repr
1423 __init__(LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction
1424 __init__(LinearInteraction self) -> LinearInteraction
1426 _IMP_npctransport.LinearInteraction_swiginit(self, _IMP_npctransport.new_LinearInteraction(*args))
1428 def show(self, *args):
1429 r"""show(LinearInteraction self, _ostream out=std::cout)"""
1430 return _IMP_npctransport.LinearInteraction_show(self, *args)
1431 __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1434 _IMP_npctransport.LinearInteraction_swigregister(LinearInteraction)
1436 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::npctransport::LinearSoftSphereScore > class."""
1438 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1439 __repr__ = _swig_repr
1443 __init__(_DistancePairScoreForLinearSoftSphere self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _DistancePairScoreForLinearSoftSphere
1444 __init__(_DistancePairScoreForLinearSoftSphere self) -> _DistancePairScoreForLinearSoftSphere
1446 _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swiginit(self, _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args))
1448 def do_get_inputs(self, m, pis):
1449 r"""do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1450 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1452 def get_score_functor(self):
1453 r"""get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1454 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1456 def get_version_info(self):
1457 r"""get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1458 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1459 __swig_destroy__ = _IMP_npctransport.delete__DistancePairScoreForLinearSoftSphere
1462 _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1463 class _DistancePairScoreForLinearInteraction(
IMP.PairScore):
1464 r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::npctransport::LinearInteractionScore > class."""
1466 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1467 __repr__ = _swig_repr
1471 __init__(_DistancePairScoreForLinearInteraction self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _DistancePairScoreForLinearInteraction
1472 __init__(_DistancePairScoreForLinearInteraction self) -> _DistancePairScoreForLinearInteraction
1474 _IMP_npctransport._DistancePairScoreForLinearInteraction_swiginit(self, _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args))
1476 def do_get_inputs(self, m, pis):
1477 r"""do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1478 return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1480 def get_score_functor(self):
1481 r"""get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1482 return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1484 def get_version_info(self):
1485 r"""get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1486 return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1487 __swig_destroy__ = _IMP_npctransport.delete__DistancePairScoreForLinearInteraction
1490 _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1491 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1492 r"""Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1494 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1497 r"""__init__(FunctorLinearSoftSpherePairScore self, double k, std::string name="LinearSSPairScore%1%") -> FunctorLinearSoftSpherePairScore"""
1498 _IMP_npctransport.FunctorLinearSoftSpherePairScore_swiginit(self, _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args))
1499 __swig_destroy__ = _IMP_npctransport.delete_FunctorLinearSoftSpherePairScore
1502 r"""__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1503 return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1506 r"""__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1507 return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1511 return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1515 _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1516 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1517 r"""Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1519 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1522 r"""__init__(FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name="LinearSSPairScore%1%") -> FunctorLinearInteractionPairScore"""
1523 _IMP_npctransport.FunctorLinearInteractionPairScore_swiginit(self, _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args))
1524 __swig_destroy__ = _IMP_npctransport.delete_FunctorLinearInteractionPairScore
1527 r"""__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1528 return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1531 r"""__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1532 return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1536 return _object_cast_to_FunctorLinearInteractionPairScore(o)
1540 _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1542 r"""Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1544 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1547 r"""__init__(BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name="BrownianDynamicsTAMDWithSlabSupport%1%", double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport"""
1548 _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swiginit(self, _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args))
1551 r"""__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1552 return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1555 r"""__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1556 return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1560 return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1562 __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1565 _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1566 class SitesPairScoreParameters(object):
1567 r"""Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1569 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1570 r = property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set, doc=
r"""r : double""")
1571 k = property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set, doc=
r"""k : double""")
1572 r2 = property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set, doc=
r"""r2 : double""")
1573 kr = property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set, doc=
r"""kr : double""")
1574 kr2 = property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set, doc=
r"""kr2 : double""")
1575 cosSigma1_max = property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set, doc=
r"""cosSigma1_max : double""")
1576 cosSigma2_max = property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set, doc=
r"""cosSigma2_max : double""")
1577 is_orientational = property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set, doc=
r"""is_orientational : bool""")
1579 def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1580 r"""__init__(SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters"""
1581 _IMP_npctransport.SitesPairScoreParameters_swiginit(self, _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg))
1583 def set_range(self, r):
1584 r"""set_range(SitesPairScoreParameters self, double r)"""
1585 return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1587 def set_force_coefficient(self, k):
1588 r"""set_force_coefficient(SitesPairScoreParameters self, double k)"""
1589 return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1591 def set_sigma1_max(self, sigma1_max_deg):
1592 r"""set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1593 return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1595 def set_sigma2_max(self, sigma2_max_deg):
1596 r"""set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1597 return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1599 def update_is_orientational(self):
1600 r"""update_is_orientational(SitesPairScoreParameters self)"""
1601 return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1603 def show(self, *args):
1604 r"""show(SitesPairScoreParameters self, _ostream out=std::cout)"""
1605 return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1608 r"""__str__(SitesPairScoreParameters self) -> std::string"""
1609 return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1612 r"""__repr__(SitesPairScoreParameters self) -> std::string"""
1613 return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1614 __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1617 _IMP_npctransport.SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1619 r"""Proxy of C++ IMP::npctransport::SitesGeometry class."""
1621 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1624 r"""__init__(SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1625 _IMP_npctransport.SitesGeometry_swiginit(self, _IMP_npctransport.new_SitesGeometry(p, sites))
1626 __swig_destroy__ = _IMP_npctransport.delete_SitesGeometry
1629 r"""__str__(SitesGeometry self) -> std::string"""
1630 return _IMP_npctransport.SitesGeometry___str__(self)
1633 r"""__repr__(SitesGeometry self) -> std::string"""
1634 return _IMP_npctransport.SitesGeometry___repr__(self)
1638 return _object_cast_to_SitesGeometry(o)
1642 _IMP_npctransport.SitesGeometry_swigregister(SitesGeometry)
1644 r"""Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1646 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1649 r"""__init__(TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1650 _IMP_npctransport.TypedSitesGeometry_swiginit(self, _IMP_npctransport.new_TypedSitesGeometry(sc))
1652 def set_sites(self, t, s):
1653 r"""set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1654 return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1656 def get_version_info(self):
1657 r"""get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1658 return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1659 __swig_destroy__ = _IMP_npctransport.delete_TypedSitesGeometry
1662 r"""__str__(TypedSitesGeometry self) -> std::string"""
1663 return _IMP_npctransport.TypedSitesGeometry___str__(self)
1666 r"""__repr__(TypedSitesGeometry self) -> std::string"""
1667 return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1671 return _object_cast_to_TypedSitesGeometry(o)
1675 _IMP_npctransport.TypedSitesGeometry_swigregister(TypedSitesGeometry)
1676 class SitesPairScore(LinearInteractionPairScore):
1677 r"""Proxy of C++ IMP::npctransport::SitesPairScore class."""
1679 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1681 def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1682 r"""__init__(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"""
1683 _IMP_npctransport.SitesPairScore_swiginit(self, _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1))
1685 def get_sites_range(self):
1686 r"""get_sites_range(SitesPairScore self) -> double"""
1687 return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1689 def get_sites_k(self):
1690 r"""get_sites_k(SitesPairScore self) -> double"""
1691 return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1693 def get_parameters(self):
1694 r"""get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1695 return _IMP_npctransport.SitesPairScore_get_parameters(self)
1696 __swig_destroy__ = _IMP_npctransport.delete_SitesPairScore
1698 def set_sites(self, sites0, sites1):
1699 r"""set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1700 return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1702 def set_sites0(self, sites0):
1703 r"""set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1704 return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1706 def set_sites1(self, sites1):
1707 r"""set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1708 return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1711 r"""__str__(SitesPairScore self) -> std::string"""
1712 return _IMP_npctransport.SitesPairScore___str__(self)
1715 r"""__repr__(SitesPairScore self) -> std::string"""
1716 return _IMP_npctransport.SitesPairScore___repr__(self)
1720 return _object_cast_to_SitesPairScore(o)
1724 _IMP_npctransport.SitesPairScore_swigregister(SitesPairScore)
1726 r"""Proxy of C++ IMP::npctransport::FGChain class."""
1728 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1731 r"""__init__(FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name="chain %1%") -> FGChain"""
1732 _IMP_npctransport.FGChain_swiginit(self, _IMP_npctransport.new_FGChain(*args))
1735 r"""get_root(FGChain self) -> Hierarchy"""
1736 return _IMP_npctransport.FGChain_get_root(self)
1738 def get_beads(self):
1739 r"""get_beads(FGChain self) -> IMP::ParticlesTemp"""
1740 return _IMP_npctransport.FGChain_get_beads(self)
1742 def get_bead(self, i):
1743 r"""get_bead(FGChain self, unsigned int i) -> Particle"""
1744 return _IMP_npctransport.FGChain_get_bead(self, i)
1746 def get_bead_index(self, i):
1747 r"""get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1748 return _IMP_npctransport.FGChain_get_bead_index(self, i)
1750 def get_number_of_beads(self):
1751 r"""get_number_of_beads(FGChain self) -> unsigned int"""
1752 return _IMP_npctransport.FGChain_get_number_of_beads(self)
1754 def get_chain_restraints(self, scoring_manager):
1755 r"""get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1756 return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1758 def set_rest_length_factor(self, rlf):
1759 r"""set_rest_length_factor(FGChain self, double rlf)"""
1760 return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1762 def set_backbone_k(self, k):
1763 r"""set_backbone_k(FGChain self, double k)"""
1764 return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1766 def get_rest_length_factor(self):
1767 r"""get_rest_length_factor(FGChain self) -> double"""
1768 return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1770 def get_backbone_k(self):
1771 r"""get_backbone_k(FGChain self) -> double"""
1772 return _IMP_npctransport.FGChain_get_backbone_k(self)
1774 def get_version_info(self):
1775 r"""get_version_info(FGChain self) -> VersionInfo"""
1776 return _IMP_npctransport.FGChain_get_version_info(self)
1777 __swig_destroy__ = _IMP_npctransport.delete_FGChain
1780 r"""__str__(FGChain self) -> std::string"""
1781 return _IMP_npctransport.FGChain___str__(self)
1784 r"""__repr__(FGChain self) -> std::string"""
1785 return _IMP_npctransport.FGChain___repr__(self)
1789 return _object_cast_to_FGChain(o)
1793 _IMP_npctransport.FGChain_swigregister(FGChain)
1796 r"""create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1797 return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1801 get_fg_chain(Hierarchy root) -> FGChain
1802 get_fg_chain(Particle p_root) -> FGChain
1804 return _IMP_npctransport.get_fg_chain(*args)
1806 r"""Proxy of C++ IMP::npctransport::Scoring class."""
1808 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1810 def __init__(self, owner_sd, data):
1811 r"""__init__(Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1812 _IMP_npctransport.Scoring_swiginit(self, _IMP_npctransport.new_Scoring(owner_sd, data))
1814 def get_scoring_function(self, force_update=False):
1815 r"""get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction"""
1816 return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1818 def get_scoring_function_restraints(self, force_update=False):
1819 r"""get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints"""
1820 return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1822 def get_custom_scoring_function(self, *args):
1824 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
1825 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
1827 return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1829 def get_close_beads_container(self, update=False):
1830 r"""get_close_beads_container(Scoring self, bool update=False) -> PairContainer"""
1831 return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1833 def get_predicates_pair_restraint(self, update=False):
1834 r"""get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint"""
1835 return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1837 def get_bounding_volume_restraint(self, update=False):
1838 r"""get_bounding_volume_restraint(Scoring self, bool update=False) -> Restraint"""
1839 return _IMP_npctransport.Scoring_get_bounding_volume_restraint(self, update)
1841 def get_slab_restraint(self, update=False):
1842 r"""get_slab_restraint(Scoring self, bool update=False) -> Restraint"""
1843 return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1845 def add_interaction(self, idata):
1846 r"""add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1847 return _IMP_npctransport.Scoring_add_interaction(self, idata)
1849 def create_close_beads_container(self, *args):
1851 create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1852 create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1854 return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
1856 def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
1857 r"""create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint"""
1858 return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
1860 def create_bounding_volume_restraint(self, beads):
1861 r"""create_bounding_volume_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1862 return _IMP_npctransport.Scoring_create_bounding_volume_restraint(self, beads)
1864 def create_slab_restraint(self, beads):
1865 r"""create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1866 return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
1868 def get_model(self):
1869 r"""get_model(Scoring self) -> Model"""
1870 return _IMP_npctransport.Scoring_get_model(self)
1873 r"""get_sd(Scoring self) -> SimulationData"""
1874 return _IMP_npctransport.Scoring_get_sd(self)
1876 def get_has_bounding_box(self):
1877 r"""get_has_bounding_box(Scoring self) -> bool"""
1878 return _IMP_npctransport.Scoring_get_has_bounding_box(self)
1880 def get_has_bounding_sphere(self):
1881 r"""get_has_bounding_sphere(Scoring self) -> bool"""
1882 return _IMP_npctransport.Scoring_get_has_bounding_sphere(self)
1884 def get_has_bounding_volume(self):
1885 r"""get_has_bounding_volume(Scoring self) -> bool"""
1886 return _IMP_npctransport.Scoring_get_has_bounding_volume(self)
1888 def get_default_backbone_k(self):
1889 r"""get_default_backbone_k(Scoring self) -> double"""
1890 return _IMP_npctransport.Scoring_get_default_backbone_k(self)
1892 def get_is_backbone_harmonic(self):
1893 r"""get_is_backbone_harmonic(Scoring self) -> bool"""
1894 return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
1896 def get_excluded_volume_k(self):
1897 r"""get_excluded_volume_k(Scoring self) -> double"""
1898 return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
1900 def get_interaction_k(self):
1901 r"""get_interaction_k(Scoring self) -> double"""
1902 return _IMP_npctransport.Scoring_get_interaction_k(self)
1904 def get_predicate_pair_score(self, *args):
1906 get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1907 get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1909 return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
1911 def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
1912 r"""get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double"""
1913 return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
1915 def get_ordered_type_pair_predicate(self):
1916 r"""get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
1917 return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
1919 def add_chain_restraints(self, chain):
1920 r"""add_chain_restraints(Scoring self, FGChain chain)"""
1921 return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
1923 def get_chain_restraints_on(self, beads):
1924 r"""get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
1925 return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
1927 def get_all_chain_restraints(self):
1928 r"""get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
1929 return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
1931 def remove_particle_type(self, pt):
1932 r"""remove_particle_type(Scoring self, ParticleType pt)"""
1933 return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
1935 def add_z_bias_restraint(self, *args):
1937 add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
1938 add_z_bias_restraint(Scoring self, Particle p, double k)
1940 return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
1942 def get_z_bias_restraints(self):
1943 r"""get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
1944 return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
1946 def create_z_bias_restraint(self, ps, k):
1947 r"""create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
1948 return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
1950 def add_custom_restraint(self, r):
1951 r"""add_custom_restraint(Scoring self, Restraint r)"""
1952 return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
1954 def add_custom_restraints(self, R):
1955 r"""add_custom_restraints(Scoring self, IMP::Restraints R)"""
1956 return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
1958 def clear_custom_restraints(self):
1959 r"""clear_custom_restraints(Scoring self)"""
1960 return _IMP_npctransport.Scoring_clear_custom_restraints(self)
1962 def get_custom_restraints(self):
1963 r"""get_custom_restraints(Scoring self) -> IMP::Restraints"""
1964 return _IMP_npctransport.Scoring_get_custom_restraints(self)
1966 def add_restrained_anchor_bead(self, p):
1967 r"""add_restrained_anchor_bead(Scoring self, Particle p)"""
1968 return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
1970 def get_pore_radius_restraint(self):
1971 r"""get_pore_radius_restraint(Scoring self) -> Restraint"""
1972 return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
1974 def get_range(self):
1975 r"""get_range(Scoring self) -> double"""
1976 return _IMP_npctransport.Scoring_get_range(self)
1978 def set_interaction_range_factor(self, type, value):
1979 r"""set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
1980 return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
1982 def set_interaction_k_factor(self, type, value):
1983 r"""set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
1984 return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
1986 def get_version_info(self):
1987 r"""get_version_info(Scoring self) -> VersionInfo"""
1988 return _IMP_npctransport.Scoring_get_version_info(self)
1989 __swig_destroy__ = _IMP_npctransport.delete_Scoring
1992 r"""__str__(Scoring self) -> std::string"""
1993 return _IMP_npctransport.Scoring___str__(self)
1996 r"""__repr__(Scoring self) -> std::string"""
1997 return _IMP_npctransport.Scoring___repr__(self)
2001 return _object_cast_to_Scoring(o)
2005 _IMP_npctransport.Scoring_swigregister(Scoring)
2006 class SimpleTimer(object):
2007 r"""Proxy of C++ IMP::internal::SimpleTimer class."""
2009 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2010 __repr__ = _swig_repr
2013 r"""__init__(SimpleTimer self) -> SimpleTimer"""
2014 _IMP_npctransport.SimpleTimer_swiginit(self, _IMP_npctransport.new_SimpleTimer())
2015 __swig_destroy__ = _IMP_npctransport.delete_SimpleTimer
2018 _IMP_npctransport.SimpleTimer_swigregister(SimpleTimer)
2020 r"""Proxy of C++ IMP::npctransport::Statistics class."""
2022 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2024 def remove_particle_type(self, pt):
2025 r"""remove_particle_type(Statistics self, ParticleType pt)"""
2026 return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2028 def __init__(self, sd, statistics_interval_frames, output_file_name):
2029 r"""__init__(Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2030 _IMP_npctransport.Statistics_swiginit(self, _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name))
2032 def add_fg_chain_stats(self, fg_chain):
2033 r"""add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2034 return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2036 def add_floater_stats(self, p):
2037 r"""add_floater_stats(Statistics self, Particle p)"""
2038 return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2040 def add_interaction_stats(self, type0, type1):
2041 r"""add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2042 return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2044 def add_optimizer_states(self, o=None):
2045 r"""add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates"""
2046 return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2048 def update_particle_type_zr_distribution_map(self, p):
2049 r"""update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2050 return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2052 def update_particle_type_xyz_distribution_map(self, p):
2053 r"""update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2054 return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2056 def update(self, timer, nf_new=1, force_full_output=False):
2057 r"""update(Statistics self, SimpleTimer timer, unsigned int nf_new=1, bool force_full_output=False)"""
2058 return _IMP_npctransport.Statistics_update(self, timer, nf_new, force_full_output)
2060 def reset_statistics_optimizer_states(self):
2061 r"""reset_statistics_optimizer_states(Statistics self)"""
2062 return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2064 def set_interrupted(self, tf):
2065 r"""set_interrupted(Statistics self, bool tf)"""
2066 return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2068 def get_model(self):
2069 r"""get_model(Statistics self) -> Model"""
2070 return _IMP_npctransport.Statistics_get_model(self)
2073 r"""get_sd(Statistics self) -> SimulationData"""
2074 return _IMP_npctransport.Statistics_get_sd(self)
2076 def get_is_activated(self):
2077 r"""get_is_activated(Statistics self) -> bool"""
2078 return _IMP_npctransport.Statistics_get_is_activated(self)
2080 def get_output_file_name(self):
2081 r"""get_output_file_name(Statistics self) -> std::string"""
2082 return _IMP_npctransport.Statistics_get_output_file_name(self)
2084 def get_version_info(self):
2085 r"""get_version_info(Statistics self) -> VersionInfo"""
2086 return _IMP_npctransport.Statistics_get_version_info(self)
2087 __swig_destroy__ = _IMP_npctransport.delete_Statistics
2090 r"""__str__(Statistics self) -> std::string"""
2091 return _IMP_npctransport.Statistics___str__(self)
2094 r"""__repr__(Statistics self) -> std::string"""
2095 return _IMP_npctransport.Statistics___repr__(self)
2099 return _object_cast_to_Statistics(o)
2103 _IMP_npctransport.Statistics_swigregister(Statistics)
2105 def create_boost_timer():
2106 r"""create_boost_timer() -> SimpleTimer"""
2107 return _IMP_npctransport.create_boost_timer()
2108 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2111 r"""Proxy of C++ IMP::npctransport::SimulationData class."""
2113 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2115 def get_output_npctransport_version(self):
2116 r"""get_output_npctransport_version(SimulationData self) -> double"""
2117 return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2119 def get_range(self):
2120 r"""get_range(SimulationData self) -> double"""
2121 return _IMP_npctransport.SimulationData_get_range(self)
2123 def get_output_statistics_interval_frames(self):
2124 r"""get_output_statistics_interval_frames(SimulationData self) -> int"""
2125 return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2127 def get_full_output_statistics_interval_factor(self):
2128 r"""get_full_output_statistics_interval_factor(SimulationData self) -> int"""
2129 return _IMP_npctransport.SimulationData_get_full_output_statistics_interval_factor(self)
2131 def get_is_multiple_hdf5s(self):
2132 r"""get_is_multiple_hdf5s(SimulationData self) -> bool"""
2133 return _IMP_npctransport.SimulationData_get_is_multiple_hdf5s(self)
2135 def get_is_exclude_floaters_from_slab_initially(self):
2136 r"""get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2137 return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2139 def get_are_floaters_on_one_slab_side(self):
2140 r"""get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2141 return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2143 def get_is_xyz_hist_stats(self):
2144 r"""get_is_xyz_hist_stats(SimulationData self) -> bool"""
2145 return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2147 def get_xyz_stats_crop_factor(self):
2148 r"""get_xyz_stats_crop_factor(SimulationData self) -> double"""
2149 return _IMP_npctransport.SimulationData_get_xyz_stats_crop_factor(self)
2151 def get_xyz_stats_voxel_size_A(self):
2152 r"""get_xyz_stats_voxel_size_A(SimulationData self) -> double"""
2153 return _IMP_npctransport.SimulationData_get_xyz_stats_voxel_size_A(self)
2155 def get_xyz_stats_max_box_size_A(self):
2156 r"""get_xyz_stats_max_box_size_A(SimulationData self) -> double"""
2157 return _IMP_npctransport.SimulationData_get_xyz_stats_max_box_size_A(self)
2159 def get_angular_d_factor(self):
2160 r"""get_angular_d_factor(SimulationData self) -> double"""
2161 return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2164 r"""__init__(SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name=std::string(), std::string new_output_file="") -> SimulationData"""
2165 _IMP_npctransport.SimulationData_swiginit(self, _IMP_npctransport.new_SimulationData(*args))
2167 def get_model(self):
2168 r"""get_model(SimulationData self) -> Model"""
2169 return _IMP_npctransport.SimulationData_get_model(self)
2171 def get_scoring(self):
2172 r"""get_scoring(SimulationData self) -> Scoring"""
2173 return _IMP_npctransport.SimulationData_get_scoring(self)
2175 def get_statistics(self):
2176 r"""get_statistics(SimulationData self) -> Statistics"""
2177 return _IMP_npctransport.SimulationData_get_statistics(self)
2179 def get_bd(self, recreate=False):
2180 r"""get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics"""
2181 return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2183 def activate_statistics(self):
2184 r"""activate_statistics(SimulationData self)"""
2185 return _IMP_npctransport.SimulationData_activate_statistics(self)
2187 def get_statistics_fraction(self):
2188 r"""get_statistics_fraction(SimulationData self) -> double"""
2189 return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2191 def get_is_fg_bead(self, *args):
2193 get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2194 get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2196 return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2198 def get_is_fg_chain(self, *args):
2200 get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2201 get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2203 return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2205 def get_fg_bead_types(self):
2206 r"""get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2207 return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2209 def get_fg_chain_types(self):
2210 r"""get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2211 return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2213 def get_floater_types(self):
2214 r"""get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2215 return _IMP_npctransport.SimulationData_get_floater_types(self)
2217 def get_obstacle_types(self):
2218 r"""get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2219 return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2221 def get_fg_chain_roots(self):
2222 r"""get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2223 return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2225 def get_fg_chains(self):
2226 r"""get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2227 return _IMP_npctransport.SimulationData_get_fg_chains(self)
2229 def get_obstacle_particles(self):
2230 r"""get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2231 return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2233 def get_beads(self):
2234 r"""get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2235 return _IMP_npctransport.SimulationData_get_beads(self)
2237 def get_optimizable_beads(self):
2238 r"""get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2239 return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2241 def get_non_optimizable_beads(self):
2242 r"""get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2243 return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2245 def get_is_backbone_harmonic(self):
2246 r"""get_is_backbone_harmonic(SimulationData self) -> bool"""
2247 return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2249 def get_backbone_tau_ns(self):
2250 r"""get_backbone_tau_ns(SimulationData self) -> double"""
2251 return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2253 def get_temperature_k(self):
2254 r"""get_temperature_k(SimulationData self) -> double"""
2255 return _IMP_npctransport.SimulationData_get_temperature_k(self)
2257 def get_initial_simulation_time_ns(self):
2258 r"""get_initial_simulation_time_ns(SimulationData self) -> double"""
2259 return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2261 def get_site_centers(self, t0):
2262 r"""get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2263 return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2265 def get_sites(self, t0):
2266 r"""get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2267 return _IMP_npctransport.SimulationData_get_sites(self, t0)
2269 def set_sites(self, *args):
2271 set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2272 set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2274 return _IMP_npctransport.SimulationData_set_sites(self, *args)
2276 def get_site_display_radius(self, arg2):
2277 r"""get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2278 return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2280 def get_maximum_number_of_minutes(self):
2281 r"""get_maximum_number_of_minutes(SimulationData self) -> double"""
2282 return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2284 def remove_particle_type(self, pt):
2285 r"""remove_particle_type(SimulationData self, ParticleType pt)"""
2286 return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2288 def remove_fgs_with_prefix(self, s_fg_type):
2289 r"""remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2290 return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2292 def get_bounding_box(self):
2293 r"""get_bounding_box(SimulationData self) -> BoundingBox3D"""
2294 return _IMP_npctransport.SimulationData_get_bounding_box(self)
2296 def get_bounding_sphere(self):
2297 r"""get_bounding_sphere(SimulationData self) -> Sphere3D"""
2298 return _IMP_npctransport.SimulationData_get_bounding_sphere(self)
2300 def get_bounding_box_size(self):
2301 r"""get_bounding_box_size(SimulationData self) -> double"""
2302 return _IMP_npctransport.SimulationData_get_bounding_box_size(self)
2304 def set_bounding_box_size(self, box_size):
2305 r"""set_bounding_box_size(SimulationData self, double box_size)"""
2306 return _IMP_npctransport.SimulationData_set_bounding_box_size(self, box_size)
2308 def get_bounding_sphere_radius(self):
2309 r"""get_bounding_sphere_radius(SimulationData self) -> double"""
2310 return _IMP_npctransport.SimulationData_get_bounding_sphere_radius(self)
2312 def set_bounding_sphere_radius(self, sphere_radius):
2313 r"""set_bounding_sphere_radius(SimulationData self, double sphere_radius)"""
2314 return _IMP_npctransport.SimulationData_set_bounding_sphere_radius(self, sphere_radius)
2316 def get_bounding_volume(self):
2317 r"""get_bounding_volume(SimulationData self) -> double"""
2318 return _IMP_npctransport.SimulationData_get_bounding_volume(self)
2320 def set_bounding_volume(self, volume_A3):
2321 r"""set_bounding_volume(SimulationData self, double volume_A3)"""
2322 return _IMP_npctransport.SimulationData_set_bounding_volume(self, volume_A3)
2324 def get_has_slab(self):
2325 r"""get_has_slab(SimulationData self) -> bool"""
2326 return _IMP_npctransport.SimulationData_get_has_slab(self)
2328 def get_is_slab_with_cylindrical_pore(self):
2329 r"""get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2330 return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2332 def get_is_slab_with_toroidal_pore(self):
2333 r"""get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2334 return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2336 def get_slab_particle(self):
2337 r"""get_slab_particle(SimulationData self) -> Particle"""
2338 return _IMP_npctransport.SimulationData_get_slab_particle(self)
2340 def get_cylinder(self):
2341 r"""get_cylinder(SimulationData self) -> Cylinder3D"""
2342 return _IMP_npctransport.SimulationData_get_cylinder(self)
2344 def get_has_bounding_box(self):
2345 r"""get_has_bounding_box(SimulationData self) -> bool"""
2346 return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2348 def get_has_bounding_sphere(self):
2349 r"""get_has_bounding_sphere(SimulationData self) -> bool"""
2350 return _IMP_npctransport.SimulationData_get_has_bounding_sphere(self)
2352 def get_has_bounding_volume(self):
2353 r"""get_has_bounding_volume(SimulationData self) -> bool"""
2354 return _IMP_npctransport.SimulationData_get_has_bounding_volume(self)
2356 def initialize_positions_from_rmf(self, fh, frame_number=-1):
2357 r"""initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)"""
2358 return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2360 def link_rmf_file_handle(self, fh, is_restraints=True):
2361 r"""link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)"""
2362 return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2364 def get_rmf_sos_writer(self):
2365 r"""get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2366 return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2368 def reset_rmf(self):
2369 r"""reset_rmf(SimulationData self)"""
2370 return _IMP_npctransport.SimulationData_reset_rmf(self)
2372 def switch_suspend_rmf(self, suspend):
2373 r"""switch_suspend_rmf(SimulationData self, bool suspend)"""
2374 return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2376 def write_geometry(self, out):
2377 r"""write_geometry(SimulationData self, std::string out)"""
2378 return _IMP_npctransport.SimulationData_write_geometry(self, out)
2380 def dump_geometry(self):
2381 r"""dump_geometry(SimulationData self)"""
2382 return _IMP_npctransport.SimulationData_dump_geometry(self)
2384 def get_root_of_type(self, type):
2385 r"""get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2386 return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2389 r"""get_number_of_frames(SimulationData self) -> unsigned int"""
2390 return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2392 def get_number_of_trials(self):
2393 r"""get_number_of_trials(SimulationData self) -> unsigned int"""
2394 return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2397 r"""get_root(SimulationData self) -> Hierarchy"""
2398 return _IMP_npctransport.SimulationData_get_root(self)
2400 def get_slab_thickness(self):
2401 r"""get_slab_thickness(SimulationData self) -> double"""
2402 return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2404 def get_tunnel_radius(self):
2405 r"""get_tunnel_radius(SimulationData self) -> double"""
2406 return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2408 def get_pore_radius(self):
2409 r"""get_pore_radius(SimulationData self) -> double"""
2410 return _IMP_npctransport.SimulationData_get_pore_radius(self)
2412 def get_tunnel_radius_k(self):
2413 r"""get_tunnel_radius_k(SimulationData self) -> double"""
2414 return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2416 def get_pore_radius_k(self):
2417 r"""get_pore_radius_k(SimulationData self) -> double"""
2418 return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2420 def get_is_pore_radius_dynamic(self):
2421 r"""get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2422 return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2424 def get_pore_anchored_beads_k(self):
2425 r"""get_pore_anchored_beads_k(SimulationData self) -> double"""
2426 return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2428 def get_static_geometry(self):
2429 r"""get_static_geometry(SimulationData self) -> Geometry"""
2430 return _IMP_npctransport.SimulationData_get_static_geometry(self)
2432 def get_rmf_dump_interval_frames(self):
2433 r"""get_rmf_dump_interval_frames(SimulationData self) -> int"""
2434 return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2436 def get_rmf_file_name(self):
2437 r"""get_rmf_file_name(SimulationData self) -> std::string"""
2438 return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2440 def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2441 r"""set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)"""
2442 return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2444 def get_version_info(self):
2445 r"""get_version_info(SimulationData self) -> VersionInfo"""
2446 return _IMP_npctransport.SimulationData_get_version_info(self)
2447 __swig_destroy__ = _IMP_npctransport.delete_SimulationData
2450 r"""__str__(SimulationData self) -> std::string"""
2451 return _IMP_npctransport.SimulationData___str__(self)
2454 r"""__repr__(SimulationData self) -> std::string"""
2455 return _IMP_npctransport.SimulationData___repr__(self)
2459 return _object_cast_to_SimulationData(o)
2463 _IMP_npctransport.SimulationData_swigregister(SimulationData)
2465 def get_simulation_data_key():
2466 r"""get_simulation_data_key() -> IMP::WeakObjectKey"""
2467 return _IMP_npctransport.get_simulation_data_key()
2469 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2470 r"""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)"""
2471 return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2473 r"""Proxy of C++ IMP::npctransport::ParticleFactory class."""
2475 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2476 sd_ = property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set, doc=
r"""sd_ : IMP::WeakPointer<(IMP::npctransport::SimulationData)>""")
2477 radius_ = property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set, doc=
r"""radius_ : double""")
2478 D_factor_ = property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set, doc=
r"""D_factor_ : double""")
2479 angular_D_factor_ = property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set, doc=
r"""angular_D_factor_ : double""")
2480 color_ = property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set, doc=
r"""color_ : IMP::display::Color""")
2481 type_ = property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set, doc=
r"""type_ : IMP::core::ParticleType""")
2484 r"""__init__(ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name="Particle factory %1%") -> ParticleFactory"""
2485 _IMP_npctransport.ParticleFactory_swiginit(self, _IMP_npctransport.new_ParticleFactory(*args))
2487 def create(self, *args):
2488 r"""create(ParticleFactory self, std::string name="") -> Particle"""
2489 return _IMP_npctransport.ParticleFactory_create(self, *args)
2491 def get_model(self):
2492 r"""get_model(ParticleFactory self) -> Model"""
2493 return _IMP_npctransport.ParticleFactory_get_model(self)
2495 def get_simulation_data(self):
2496 r"""get_simulation_data(ParticleFactory self) -> SimulationData"""
2497 return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2499 def get_radius(self):
2500 r"""get_radius(ParticleFactory self) -> double"""
2501 return _IMP_npctransport.ParticleFactory_get_radius(self)
2503 def get_version_info(self):
2504 r"""get_version_info(ParticleFactory self) -> VersionInfo"""
2505 return _IMP_npctransport.ParticleFactory_get_version_info(self)
2506 __swig_destroy__ = _IMP_npctransport.delete_ParticleFactory
2509 r"""__str__(ParticleFactory self) -> std::string"""
2510 return _IMP_npctransport.ParticleFactory___str__(self)
2513 r"""__repr__(ParticleFactory self) -> std::string"""
2514 return _IMP_npctransport.ParticleFactory___repr__(self)
2518 return _object_cast_to_ParticleFactory(o)
2522 _IMP_npctransport.ParticleFactory_swigregister(ParticleFactory)
2524 r"""Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2526 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2529 r"""__init__(HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2530 _IMP_npctransport.HierarchyWithSitesLoadLink_swiginit(self, _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh))
2534 r"""get_name() -> char const *"""
2535 return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2538 r"""__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2539 return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2542 r"""__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2543 return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2547 return _object_cast_to_HierarchyWithSitesLoadLink(o)
2549 __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2552 _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2554 r"""Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2556 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2559 r"""__init__(HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2560 _IMP_npctransport.HierarchyWithSitesSaveLink_swiginit(self, _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh))
2564 r"""get_name() -> char const *"""
2565 return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2568 r"""__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2569 return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2572 r"""__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2573 return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2577 return _object_cast_to_HierarchyWithSitesSaveLink(o)
2579 __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2582 _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2586 add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2587 add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2589 return _IMP_npctransport.add_test_sites(*args)
2593 add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2594 add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2596 return _IMP_npctransport.add_hierarchies_with_sites(*args)
2599 r"""add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2600 return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2603 r"""create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2604 return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2607 r"""link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2608 return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2610 r"""Proxy of C++ IMP::npctransport::Transporting class."""
2612 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2616 __init__(Transporting self) -> Transporting
2617 __init__(Transporting self, Model m, ParticleIndex id) -> Transporting
2618 __init__(Transporting self, _ParticleAdaptor d) -> Transporting
2620 _IMP_npctransport.Transporting_swiginit(self, _IMP_npctransport.new_Transporting(*args))
2622 def show(self, *args):
2623 r"""show(Transporting self, _ostream out=std::cout)"""
2624 return _IMP_npctransport.Transporting_show(self, *args)
2627 def setup_particle(*args):
2629 setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2630 setup_particle(_ParticleAdaptor pa, bool is_last_entry_from_top=False) -> Transporting
2632 return _IMP_npctransport.Transporting_setup_particle(*args)
2635 def get_is_setup(*args):
2637 get_is_setup(_ParticleAdaptor p) -> bool
2638 get_is_setup(Model m, ParticleIndex pi) -> bool
2640 return _IMP_npctransport.Transporting_get_is_setup(*args)
2642 def set_is_last_entry_from_top(self, is_last_entry_from_top):
2643 r"""set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2644 return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2646 def get_is_last_entry_from_top(self):
2647 r"""get_is_last_entry_from_top(Transporting self) -> bool"""
2648 return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2651 def get_is_last_entry_from_top_key():
2652 r"""get_is_last_entry_from_top_key() -> IntKey"""
2653 return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
2655 def set_last_tracked_z(self, last_tracked_z):
2656 r"""set_last_tracked_z(Transporting self, double last_tracked_z)"""
2657 return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
2659 def get_last_tracked_z(self):
2660 r"""get_last_tracked_z(Transporting self) -> double"""
2661 return _IMP_npctransport.Transporting_get_last_tracked_z(self)
2664 def get_last_tracked_z_key():
2665 r"""get_last_tracked_z_key() -> FloatKey"""
2666 return _IMP_npctransport.Transporting_get_last_tracked_z_key()
2668 def set_n_entries_bottom(self, n):
2669 r"""set_n_entries_bottom(Transporting self, int n)"""
2670 return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
2672 def get_n_entries_bottom(self):
2673 r"""get_n_entries_bottom(Transporting self) -> int"""
2674 return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
2677 def get_n_entries_bottom_key():
2678 r"""get_n_entries_bottom_key() -> IntKey"""
2679 return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
2681 def set_n_entries_top(self, n):
2682 r"""set_n_entries_top(Transporting self, int n)"""
2683 return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
2685 def get_n_entries_top(self):
2686 r"""get_n_entries_top(Transporting self) -> int"""
2687 return _IMP_npctransport.Transporting_get_n_entries_top(self)
2690 def get_n_entries_top_key():
2691 r"""get_n_entries_top_key() -> IntKey"""
2692 return _IMP_npctransport.Transporting_get_n_entries_top_key()
2694 def add_attribute(self, *args):
2696 add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
2697 add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
2698 add_attribute(Transporting self, IntKey a0, IMP::Int a1)
2699 add_attribute(Transporting self, FloatsKey a0, IMP::Floats a1)
2700 add_attribute(Transporting self, IntsKey a0, IMP::Ints a1)
2701 add_attribute(Transporting self, StringKey a0, IMP::String a1)
2702 add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
2703 add_attribute(Transporting self, ObjectKey a0, Object a1)
2704 add_attribute(Transporting self, SparseFloatKey a0, IMP::Float a1)
2705 add_attribute(Transporting self, SparseIntKey a0, IMP::Int a1)
2706 add_attribute(Transporting self, SparseStringKey a0, IMP::String a1)
2707 add_attribute(Transporting self, SparseParticleIndexKey a0, ParticleIndex a1)
2709 return _IMP_npctransport.Transporting_add_attribute(self, *args)
2711 def get_value(self, *args):
2713 get_value(Transporting self, FloatKey a0) -> IMP::Float
2714 get_value(Transporting self, IntKey a0) -> IMP::Int
2715 get_value(Transporting self, FloatsKey a0) -> IMP::Floats
2716 get_value(Transporting self, IntsKey a0) -> IMP::Ints
2717 get_value(Transporting self, StringKey a0) -> IMP::String
2718 get_value(Transporting self, ParticleIndexKey a0) -> Particle
2719 get_value(Transporting self, ObjectKey a0) -> Object
2720 get_value(Transporting self, SparseFloatKey a0) -> IMP::Float
2721 get_value(Transporting self, SparseIntKey a0) -> IMP::Int
2722 get_value(Transporting self, SparseStringKey a0) -> IMP::String
2723 get_value(Transporting self, SparseParticleIndexKey a0) -> ParticleIndex
2725 return _IMP_npctransport.Transporting_get_value(self, *args)
2727 def set_value(self, *args):
2729 set_value(Transporting self, FloatKey a0, IMP::Float a1)
2730 set_value(Transporting self, IntKey a0, IMP::Int a1)
2731 set_value(Transporting self, FloatsKey a0, IMP::Floats a1)
2732 set_value(Transporting self, IntsKey a0, IMP::Ints a1)
2733 set_value(Transporting self, StringKey a0, IMP::String a1)
2734 set_value(Transporting self, ParticleIndexKey a0, Particle a1)
2735 set_value(Transporting self, ObjectKey a0, Object a1)
2736 set_value(Transporting self, SparseFloatKey a0, IMP::Float a1)
2737 set_value(Transporting self, SparseIntKey a0, IMP::Int a1)
2738 set_value(Transporting self, SparseStringKey a0, IMP::String a1)
2739 set_value(Transporting self, SparseParticleIndexKey a0, ParticleIndex a1)
2741 return _IMP_npctransport.Transporting_set_value(self, *args)
2743 def remove_attribute(self, *args):
2745 remove_attribute(Transporting self, FloatKey a0)
2746 remove_attribute(Transporting self, IntKey a0)
2747 remove_attribute(Transporting self, FloatsKey a0)
2748 remove_attribute(Transporting self, IntsKey a0)
2749 remove_attribute(Transporting self, StringKey a0)
2750 remove_attribute(Transporting self, ParticleIndexKey a0)
2751 remove_attribute(Transporting self, ObjectKey a0)
2752 remove_attribute(Transporting self, SparseFloatKey a0)
2753 remove_attribute(Transporting self, SparseIntKey a0)
2754 remove_attribute(Transporting self, SparseStringKey a0)
2755 remove_attribute(Transporting self, SparseParticleIndexKey a0)
2757 return _IMP_npctransport.Transporting_remove_attribute(self, *args)
2759 def has_attribute(self, *args):
2761 has_attribute(Transporting self, FloatKey a0) -> bool
2762 has_attribute(Transporting self, IntKey a0) -> bool
2763 has_attribute(Transporting self, FloatsKey a0) -> bool
2764 has_attribute(Transporting self, IntsKey a0) -> bool
2765 has_attribute(Transporting self, StringKey a0) -> bool
2766 has_attribute(Transporting self, ParticleIndexKey a0) -> bool
2767 has_attribute(Transporting self, ObjectKey a0) -> bool
2768 has_attribute(Transporting self, SparseFloatKey a0) -> bool
2769 has_attribute(Transporting self, SparseIntKey a0) -> bool
2770 has_attribute(Transporting self, SparseStringKey a0) -> bool
2771 has_attribute(Transporting self, SparseParticleIndexKey a0) -> bool
2773 return _IMP_npctransport.Transporting_has_attribute(self, *args)
2775 def get_derivative(self, a0):
2776 r"""get_derivative(Transporting self, FloatKey a0) -> double"""
2777 return _IMP_npctransport.Transporting_get_derivative(self, a0)
2780 r"""get_name(Transporting self) -> std::string"""
2781 return _IMP_npctransport.Transporting_get_name(self)
2783 def clear_caches(self):
2784 r"""clear_caches(Transporting self)"""
2785 return _IMP_npctransport.Transporting_clear_caches(self)
2787 def set_name(self, a0):
2788 r"""set_name(Transporting self, std::string a0)"""
2789 return _IMP_npctransport.Transporting_set_name(self, a0)
2792 r"""set_check_level(Transporting self, IMP::CheckLevel a0)"""
2793 return _IMP_npctransport.Transporting_set_check_level(self, a0)
2795 def add_to_derivative(self, a0, a1, a2):
2796 r"""add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2797 return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
2799 def set_is_optimized(self, a0, a1):
2800 r"""set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
2801 return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
2803 def get_is_optimized(self, a0):
2804 r"""get_is_optimized(Transporting self, FloatKey a0) -> bool"""
2805 return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
2808 r"""get_check_level(Transporting self) -> IMP::CheckLevel"""
2809 return _IMP_npctransport.Transporting_get_check_level(self)
2811 def __eq__(self, *args):
2813 __eq__(Transporting self, Transporting o) -> bool
2814 __eq__(Transporting self, Particle d) -> bool
2816 return _IMP_npctransport.Transporting___eq__(self, *args)
2818 def __ne__(self, *args):
2820 __ne__(Transporting self, Transporting o) -> bool
2821 __ne__(Transporting self, Particle d) -> bool
2823 return _IMP_npctransport.Transporting___ne__(self, *args)
2825 def __le__(self, *args):
2827 __le__(Transporting self, Transporting o) -> bool
2828 __le__(Transporting self, Particle d) -> bool
2830 return _IMP_npctransport.Transporting___le__(self, *args)
2832 def __lt__(self, *args):
2834 __lt__(Transporting self, Transporting o) -> bool
2835 __lt__(Transporting self, Particle d) -> bool
2837 return _IMP_npctransport.Transporting___lt__(self, *args)
2839 def __ge__(self, *args):
2841 __ge__(Transporting self, Transporting o) -> bool
2842 __ge__(Transporting self, Particle d) -> bool
2844 return _IMP_npctransport.Transporting___ge__(self, *args)
2846 def __gt__(self, *args):
2848 __gt__(Transporting self, Transporting o) -> bool
2849 __gt__(Transporting self, Particle d) -> bool
2851 return _IMP_npctransport.Transporting___gt__(self, *args)
2854 r"""__hash__(Transporting self) -> std::size_t"""
2855 return _IMP_npctransport.Transporting___hash__(self)
2858 r"""__str__(Transporting self) -> std::string"""
2859 return _IMP_npctransport.Transporting___str__(self)
2862 r"""__repr__(Transporting self) -> std::string"""
2863 return _IMP_npctransport.Transporting___repr__(self)
2865 def _get_as_binary(self):
2866 r"""_get_as_binary(Transporting self) -> PyObject *"""
2867 return _IMP_npctransport.Transporting__get_as_binary(self)
2869 def _set_from_binary(self, p):
2870 r"""_set_from_binary(Transporting self, PyObject * p)"""
2871 return _IMP_npctransport.Transporting__set_from_binary(self, p)
2873 def __getstate__(self):
2874 p = self._get_as_binary()
2875 if len(self.__dict__) > 1:
2876 d = self.__dict__.copy()
2881 def __setstate__(self, p):
2882 if not hasattr(self,
'this'):
2884 if isinstance(p, tuple):
2886 self.__dict__.update(d)
2887 return self._set_from_binary(p)
2889 __swig_destroy__ = _IMP_npctransport.delete_Transporting
2892 _IMP_npctransport.Transporting_swigregister(Transporting)
2894 def show_ranges(fname):
2895 r"""show_ranges(std::string fname)"""
2896 return _IMP_npctransport.show_ranges(fname)
2898 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
2899 r"""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"""
2900 return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
2902 def get_number_of_work_units(configuration_file):
2903 r"""get_number_of_work_units(std::string configuration_file) -> int"""
2904 return _IMP_npctransport.get_number_of_work_units(configuration_file)
2906 r"""Proxy of C++ IMP::npctransport::SlabWithPore class."""
2908 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2912 __init__(SlabWithPore self) -> SlabWithPore
2913 __init__(SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
2914 __init__(SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
2916 _IMP_npctransport.SlabWithPore_swiginit(self, _IMP_npctransport.new_SlabWithPore(*args))
2918 def show(self, *args):
2919 r"""show(SlabWithPore self, _ostream out=std::cout)"""
2920 return _IMP_npctransport.SlabWithPore_show(self, *args)
2923 def setup_particle(*args):
2925 setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
2926 setup_particle(_ParticleAdaptor pa, double thickness, double pore_radius) -> SlabWithPore
2928 return _IMP_npctransport.SlabWithPore_setup_particle(*args)
2931 def get_is_setup(*args):
2933 get_is_setup(_ParticleAdaptor p) -> bool
2934 get_is_setup(Model m, ParticleIndex pi) -> bool
2936 return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
2938 def set_thickness(self, thickness):
2939 r"""set_thickness(SlabWithPore self, double thickness)"""
2940 return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
2942 def get_thickness(self):
2943 r"""get_thickness(SlabWithPore self) -> IMP::Float"""
2944 return _IMP_npctransport.SlabWithPore_get_thickness(self)
2946 def get_pore_radius(self):
2947 r"""get_pore_radius(SlabWithPore self) -> IMP::Float"""
2948 return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
2950 def set_pore_radius(self, r):
2951 r"""set_pore_radius(SlabWithPore self, double r)"""
2952 return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
2954 def add_to_pore_radius_derivative(self, v, d):
2955 r"""add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
2956 return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
2958 def get_pore_radius_is_optimized(self):
2959 r"""get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
2960 return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
2962 def set_pore_radius_is_optimized(self, tf):
2963 r"""set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
2964 return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
2967 def get_thickness_key():
2968 r"""get_thickness_key() -> FloatKey"""
2969 return _IMP_npctransport.SlabWithPore_get_thickness_key()
2972 def get_pore_radius_key():
2973 r"""get_pore_radius_key() -> FloatKey"""
2974 return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
2976 def add_attribute(self, *args):
2978 add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
2979 add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
2980 add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
2981 add_attribute(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
2982 add_attribute(SlabWithPore self, IntsKey a0, IMP::Ints a1)
2983 add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
2984 add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
2985 add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
2986 add_attribute(SlabWithPore self, SparseFloatKey a0, IMP::Float a1)
2987 add_attribute(SlabWithPore self, SparseIntKey a0, IMP::Int a1)
2988 add_attribute(SlabWithPore self, SparseStringKey a0, IMP::String a1)
2989 add_attribute(SlabWithPore self, SparseParticleIndexKey a0, ParticleIndex a1)
2991 return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
2993 def get_value(self, *args):
2995 get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
2996 get_value(SlabWithPore self, IntKey a0) -> IMP::Int
2997 get_value(SlabWithPore self, FloatsKey a0) -> IMP::Floats
2998 get_value(SlabWithPore self, IntsKey a0) -> IMP::Ints
2999 get_value(SlabWithPore self, StringKey a0) -> IMP::String
3000 get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3001 get_value(SlabWithPore self, ObjectKey a0) -> Object
3002 get_value(SlabWithPore self, SparseFloatKey a0) -> IMP::Float
3003 get_value(SlabWithPore self, SparseIntKey a0) -> IMP::Int
3004 get_value(SlabWithPore self, SparseStringKey a0) -> IMP::String
3005 get_value(SlabWithPore self, SparseParticleIndexKey a0) -> ParticleIndex
3007 return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3009 def set_value(self, *args):
3011 set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3012 set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3013 set_value(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3014 set_value(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3015 set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3016 set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3017 set_value(SlabWithPore self, ObjectKey a0, Object a1)
3018 set_value(SlabWithPore self, SparseFloatKey a0, IMP::Float a1)
3019 set_value(SlabWithPore self, SparseIntKey a0, IMP::Int a1)
3020 set_value(SlabWithPore self, SparseStringKey a0, IMP::String a1)
3021 set_value(SlabWithPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3023 return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3025 def remove_attribute(self, *args):
3027 remove_attribute(SlabWithPore self, FloatKey a0)
3028 remove_attribute(SlabWithPore self, IntKey a0)
3029 remove_attribute(SlabWithPore self, FloatsKey a0)
3030 remove_attribute(SlabWithPore self, IntsKey a0)
3031 remove_attribute(SlabWithPore self, StringKey a0)
3032 remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3033 remove_attribute(SlabWithPore self, ObjectKey a0)
3034 remove_attribute(SlabWithPore self, SparseFloatKey a0)
3035 remove_attribute(SlabWithPore self, SparseIntKey a0)
3036 remove_attribute(SlabWithPore self, SparseStringKey a0)
3037 remove_attribute(SlabWithPore self, SparseParticleIndexKey a0)
3039 return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3041 def has_attribute(self, *args):
3043 has_attribute(SlabWithPore self, FloatKey a0) -> bool
3044 has_attribute(SlabWithPore self, IntKey a0) -> bool
3045 has_attribute(SlabWithPore self, FloatsKey a0) -> bool
3046 has_attribute(SlabWithPore self, IntsKey a0) -> bool
3047 has_attribute(SlabWithPore self, StringKey a0) -> bool
3048 has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3049 has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3050 has_attribute(SlabWithPore self, SparseFloatKey a0) -> bool
3051 has_attribute(SlabWithPore self, SparseIntKey a0) -> bool
3052 has_attribute(SlabWithPore self, SparseStringKey a0) -> bool
3053 has_attribute(SlabWithPore self, SparseParticleIndexKey a0) -> bool
3055 return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3057 def get_derivative(self, a0):
3058 r"""get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3059 return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3062 r"""get_name(SlabWithPore self) -> std::string"""
3063 return _IMP_npctransport.SlabWithPore_get_name(self)
3065 def clear_caches(self):
3066 r"""clear_caches(SlabWithPore self)"""
3067 return _IMP_npctransport.SlabWithPore_clear_caches(self)
3069 def set_name(self, a0):
3070 r"""set_name(SlabWithPore self, std::string a0)"""
3071 return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3074 r"""set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3075 return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3077 def add_to_derivative(self, a0, a1, a2):
3078 r"""add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3079 return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3081 def set_is_optimized(self, a0, a1):
3082 r"""set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3083 return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3085 def get_is_optimized(self, a0):
3086 r"""get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3087 return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3090 r"""get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3091 return _IMP_npctransport.SlabWithPore_get_check_level(self)
3093 def __eq__(self, *args):
3095 __eq__(SlabWithPore self, SlabWithPore o) -> bool
3096 __eq__(SlabWithPore self, Particle d) -> bool
3098 return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3100 def __ne__(self, *args):
3102 __ne__(SlabWithPore self, SlabWithPore o) -> bool
3103 __ne__(SlabWithPore self, Particle d) -> bool
3105 return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3107 def __le__(self, *args):
3109 __le__(SlabWithPore self, SlabWithPore o) -> bool
3110 __le__(SlabWithPore self, Particle d) -> bool
3112 return _IMP_npctransport.SlabWithPore___le__(self, *args)
3114 def __lt__(self, *args):
3116 __lt__(SlabWithPore self, SlabWithPore o) -> bool
3117 __lt__(SlabWithPore self, Particle d) -> bool
3119 return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3121 def __ge__(self, *args):
3123 __ge__(SlabWithPore self, SlabWithPore o) -> bool
3124 __ge__(SlabWithPore self, Particle d) -> bool
3126 return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3128 def __gt__(self, *args):
3130 __gt__(SlabWithPore self, SlabWithPore o) -> bool
3131 __gt__(SlabWithPore self, Particle d) -> bool
3133 return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3136 r"""__hash__(SlabWithPore self) -> std::size_t"""
3137 return _IMP_npctransport.SlabWithPore___hash__(self)
3140 r"""__str__(SlabWithPore self) -> std::string"""
3141 return _IMP_npctransport.SlabWithPore___str__(self)
3144 r"""__repr__(SlabWithPore self) -> std::string"""
3145 return _IMP_npctransport.SlabWithPore___repr__(self)
3147 def _get_as_binary(self):
3148 r"""_get_as_binary(SlabWithPore self) -> PyObject *"""
3149 return _IMP_npctransport.SlabWithPore__get_as_binary(self)
3151 def _set_from_binary(self, p):
3152 r"""_set_from_binary(SlabWithPore self, PyObject * p)"""
3153 return _IMP_npctransport.SlabWithPore__set_from_binary(self, p)
3155 def __getstate__(self):
3156 p = self._get_as_binary()
3157 if len(self.__dict__) > 1:
3158 d = self.__dict__.copy()
3163 def __setstate__(self, p):
3164 if not hasattr(self,
'this'):
3166 if isinstance(p, tuple):
3168 self.__dict__.update(d)
3169 return self._set_from_binary(p)
3171 __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3174 _IMP_npctransport.SlabWithPore_swigregister(SlabWithPore)
3175 class SlabWithCylindricalPore(SlabWithPore):
3176 r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3178 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3182 __init__(SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3183 __init__(SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3184 __init__(SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3186 _IMP_npctransport.SlabWithCylindricalPore_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPore(*args))
3188 def show(self, *args):
3189 r"""show(SlabWithCylindricalPore self, _ostream out=std::cout)"""
3190 return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3193 def setup_particle(*args):
3195 setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3196 setup_particle(_ParticleAdaptor pa, double thickness, double radius) -> SlabWithCylindricalPore
3198 return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3201 def get_is_setup(*args):
3203 get_is_setup(_ParticleAdaptor p) -> bool
3204 get_is_setup(Model m, ParticleIndex pi) -> bool
3206 return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3209 def get_cylindrical_pore_key():
3210 r"""get_cylindrical_pore_key() -> IntKey"""
3211 return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3213 def add_attribute(self, *args):
3215 add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3216 add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3217 add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3218 add_attribute(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3219 add_attribute(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3220 add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3221 add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3222 add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3223 add_attribute(SlabWithCylindricalPore self, SparseFloatKey a0, IMP::Float a1)
3224 add_attribute(SlabWithCylindricalPore self, SparseIntKey a0, IMP::Int a1)
3225 add_attribute(SlabWithCylindricalPore self, SparseStringKey a0, IMP::String a1)
3226 add_attribute(SlabWithCylindricalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3228 return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3230 def get_value(self, *args):
3232 get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3233 get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3234 get_value(SlabWithCylindricalPore self, FloatsKey a0) -> IMP::Floats
3235 get_value(SlabWithCylindricalPore self, IntsKey a0) -> IMP::Ints
3236 get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3237 get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3238 get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3239 get_value(SlabWithCylindricalPore self, SparseFloatKey a0) -> IMP::Float
3240 get_value(SlabWithCylindricalPore self, SparseIntKey a0) -> IMP::Int
3241 get_value(SlabWithCylindricalPore self, SparseStringKey a0) -> IMP::String
3242 get_value(SlabWithCylindricalPore self, SparseParticleIndexKey a0) -> ParticleIndex
3244 return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3246 def set_value(self, *args):
3248 set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3249 set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3250 set_value(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3251 set_value(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3252 set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3253 set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3254 set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3255 set_value(SlabWithCylindricalPore self, SparseFloatKey a0, IMP::Float a1)
3256 set_value(SlabWithCylindricalPore self, SparseIntKey a0, IMP::Int a1)
3257 set_value(SlabWithCylindricalPore self, SparseStringKey a0, IMP::String a1)
3258 set_value(SlabWithCylindricalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3260 return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3262 def remove_attribute(self, *args):
3264 remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3265 remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3266 remove_attribute(SlabWithCylindricalPore self, FloatsKey a0)
3267 remove_attribute(SlabWithCylindricalPore self, IntsKey a0)
3268 remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3269 remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3270 remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3271 remove_attribute(SlabWithCylindricalPore self, SparseFloatKey a0)
3272 remove_attribute(SlabWithCylindricalPore self, SparseIntKey a0)
3273 remove_attribute(SlabWithCylindricalPore self, SparseStringKey a0)
3274 remove_attribute(SlabWithCylindricalPore self, SparseParticleIndexKey a0)
3276 return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3278 def has_attribute(self, *args):
3280 has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3281 has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3282 has_attribute(SlabWithCylindricalPore self, FloatsKey a0) -> bool
3283 has_attribute(SlabWithCylindricalPore self, IntsKey a0) -> bool
3284 has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3285 has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3286 has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3287 has_attribute(SlabWithCylindricalPore self, SparseFloatKey a0) -> bool
3288 has_attribute(SlabWithCylindricalPore self, SparseIntKey a0) -> bool
3289 has_attribute(SlabWithCylindricalPore self, SparseStringKey a0) -> bool
3290 has_attribute(SlabWithCylindricalPore self, SparseParticleIndexKey a0) -> bool
3292 return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3294 def get_derivative(self, a0):
3295 r"""get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3296 return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3299 r"""get_name(SlabWithCylindricalPore self) -> std::string"""
3300 return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3302 def clear_caches(self):
3303 r"""clear_caches(SlabWithCylindricalPore self)"""
3304 return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3306 def set_name(self, a0):
3307 r"""set_name(SlabWithCylindricalPore self, std::string a0)"""
3308 return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3311 r"""set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3312 return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3314 def add_to_derivative(self, a0, a1, a2):
3315 r"""add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3316 return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3318 def set_is_optimized(self, a0, a1):
3319 r"""set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3320 return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3322 def get_is_optimized(self, a0):
3323 r"""get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3324 return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3327 r"""get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3328 return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3330 def __eq__(self, *args):
3332 __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3333 __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3335 return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3337 def __ne__(self, *args):
3339 __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3340 __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3342 return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3344 def __le__(self, *args):
3346 __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3347 __le__(SlabWithCylindricalPore self, Particle d) -> bool
3349 return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3351 def __lt__(self, *args):
3353 __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3354 __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3356 return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3358 def __ge__(self, *args):
3360 __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3361 __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3363 return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3365 def __gt__(self, *args):
3367 __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3368 __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3370 return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3373 r"""__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3374 return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3377 r"""__str__(SlabWithCylindricalPore self) -> std::string"""
3378 return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3381 r"""__repr__(SlabWithCylindricalPore self) -> std::string"""
3382 return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3384 def _get_as_binary(self):
3385 r"""_get_as_binary(SlabWithCylindricalPore self) -> PyObject *"""
3386 return _IMP_npctransport.SlabWithCylindricalPore__get_as_binary(self)
3388 def _set_from_binary(self, p):
3389 r"""_set_from_binary(SlabWithCylindricalPore self, PyObject * p)"""
3390 return _IMP_npctransport.SlabWithCylindricalPore__set_from_binary(self, p)
3392 def __getstate__(self):
3393 p = self._get_as_binary()
3394 if len(self.__dict__) > 1:
3395 d = self.__dict__.copy()
3400 def __setstate__(self, p):
3401 if not hasattr(self,
'this'):
3403 if isinstance(p, tuple):
3405 self.__dict__.update(d)
3406 return self._set_from_binary(p)
3408 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3411 _IMP_npctransport.SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3412 class SlabWithToroidalPore(SlabWithPore):
3413 r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3415 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3419 __init__(SlabWithToroidalPore self) -> SlabWithToroidalPore
3420 __init__(SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3421 __init__(SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3423 _IMP_npctransport.SlabWithToroidalPore_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPore(*args))
3425 def show(self, *args):
3426 r"""show(SlabWithToroidalPore self, _ostream out=std::cout)"""
3427 return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3430 def setup_particle(*args):
3432 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3433 setup_particle(_ParticleAdaptor pa, double thickness, double major_radius) -> SlabWithToroidalPore
3434 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3435 setup_particle(_ParticleAdaptor pa, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3437 return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3440 def get_is_setup(*args):
3442 get_is_setup(_ParticleAdaptor p) -> bool
3443 get_is_setup(Model m, ParticleIndex pi) -> bool
3445 return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3447 def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3448 r"""set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3449 return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3451 def get_minor_radius_h2v_aspect_ratio(self):
3452 r"""get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3453 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3455 def get_vertical_minor_radius(self):
3456 r"""get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3457 return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3459 def set_vertical_minor_radius(self, rv):
3460 r"""set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3461 return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3463 def get_horizontal_minor_radius(self):
3464 r"""get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3465 return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3467 def set_horizontal_minor_radius(self, rh):
3468 r"""set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3469 return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3472 def get_minor_radius_h2v_aspect_ratio_key():
3473 r"""get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3474 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3477 def get_toroidal_pore_key():
3478 r"""get_toroidal_pore_key() -> IntKey"""
3479 return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3481 def add_attribute(self, *args):
3483 add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3484 add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3485 add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3486 add_attribute(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3487 add_attribute(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3488 add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3489 add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3490 add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3491 add_attribute(SlabWithToroidalPore self, SparseFloatKey a0, IMP::Float a1)
3492 add_attribute(SlabWithToroidalPore self, SparseIntKey a0, IMP::Int a1)
3493 add_attribute(SlabWithToroidalPore self, SparseStringKey a0, IMP::String a1)
3494 add_attribute(SlabWithToroidalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3496 return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3498 def get_value(self, *args):
3500 get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3501 get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3502 get_value(SlabWithToroidalPore self, FloatsKey a0) -> IMP::Floats
3503 get_value(SlabWithToroidalPore self, IntsKey a0) -> IMP::Ints
3504 get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3505 get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3506 get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3507 get_value(SlabWithToroidalPore self, SparseFloatKey a0) -> IMP::Float
3508 get_value(SlabWithToroidalPore self, SparseIntKey a0) -> IMP::Int
3509 get_value(SlabWithToroidalPore self, SparseStringKey a0) -> IMP::String
3510 get_value(SlabWithToroidalPore self, SparseParticleIndexKey a0) -> ParticleIndex
3512 return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3514 def set_value(self, *args):
3516 set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3517 set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3518 set_value(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3519 set_value(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3520 set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3521 set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3522 set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3523 set_value(SlabWithToroidalPore self, SparseFloatKey a0, IMP::Float a1)
3524 set_value(SlabWithToroidalPore self, SparseIntKey a0, IMP::Int a1)
3525 set_value(SlabWithToroidalPore self, SparseStringKey a0, IMP::String a1)
3526 set_value(SlabWithToroidalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3528 return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3530 def remove_attribute(self, *args):
3532 remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3533 remove_attribute(SlabWithToroidalPore self, IntKey a0)
3534 remove_attribute(SlabWithToroidalPore self, FloatsKey a0)
3535 remove_attribute(SlabWithToroidalPore self, IntsKey a0)
3536 remove_attribute(SlabWithToroidalPore self, StringKey a0)
3537 remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3538 remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3539 remove_attribute(SlabWithToroidalPore self, SparseFloatKey a0)
3540 remove_attribute(SlabWithToroidalPore self, SparseIntKey a0)
3541 remove_attribute(SlabWithToroidalPore self, SparseStringKey a0)
3542 remove_attribute(SlabWithToroidalPore self, SparseParticleIndexKey a0)
3544 return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3546 def has_attribute(self, *args):
3548 has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3549 has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3550 has_attribute(SlabWithToroidalPore self, FloatsKey a0) -> bool
3551 has_attribute(SlabWithToroidalPore self, IntsKey a0) -> bool
3552 has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3553 has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3554 has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3555 has_attribute(SlabWithToroidalPore self, SparseFloatKey a0) -> bool
3556 has_attribute(SlabWithToroidalPore self, SparseIntKey a0) -> bool
3557 has_attribute(SlabWithToroidalPore self, SparseStringKey a0) -> bool
3558 has_attribute(SlabWithToroidalPore self, SparseParticleIndexKey a0) -> bool
3560 return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3562 def get_derivative(self, a0):
3563 r"""get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3564 return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3567 r"""get_name(SlabWithToroidalPore self) -> std::string"""
3568 return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3570 def clear_caches(self):
3571 r"""clear_caches(SlabWithToroidalPore self)"""
3572 return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3574 def set_name(self, a0):
3575 r"""set_name(SlabWithToroidalPore self, std::string a0)"""
3576 return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3579 r"""set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3580 return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3582 def add_to_derivative(self, a0, a1, a2):
3583 r"""add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3584 return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3586 def set_is_optimized(self, a0, a1):
3587 r"""set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3588 return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3590 def get_is_optimized(self, a0):
3591 r"""get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3592 return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
3595 r"""get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
3596 return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
3598 def __eq__(self, *args):
3600 __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3601 __eq__(SlabWithToroidalPore self, Particle d) -> bool
3603 return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
3605 def __ne__(self, *args):
3607 __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3608 __ne__(SlabWithToroidalPore self, Particle d) -> bool
3610 return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
3612 def __le__(self, *args):
3614 __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3615 __le__(SlabWithToroidalPore self, Particle d) -> bool
3617 return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
3619 def __lt__(self, *args):
3621 __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3622 __lt__(SlabWithToroidalPore self, Particle d) -> bool
3624 return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
3626 def __ge__(self, *args):
3628 __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3629 __ge__(SlabWithToroidalPore self, Particle d) -> bool
3631 return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
3633 def __gt__(self, *args):
3635 __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3636 __gt__(SlabWithToroidalPore self, Particle d) -> bool
3638 return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
3641 r"""__hash__(SlabWithToroidalPore self) -> std::size_t"""
3642 return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
3645 r"""__str__(SlabWithToroidalPore self) -> std::string"""
3646 return _IMP_npctransport.SlabWithToroidalPore___str__(self)
3649 r"""__repr__(SlabWithToroidalPore self) -> std::string"""
3650 return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
3652 def _get_as_binary(self):
3653 r"""_get_as_binary(SlabWithToroidalPore self) -> PyObject *"""
3654 return _IMP_npctransport.SlabWithToroidalPore__get_as_binary(self)
3656 def _set_from_binary(self, p):
3657 r"""_set_from_binary(SlabWithToroidalPore self, PyObject * p)"""
3658 return _IMP_npctransport.SlabWithToroidalPore__set_from_binary(self, p)
3660 def __getstate__(self):
3661 p = self._get_as_binary()
3662 if len(self.__dict__) > 1:
3663 d = self.__dict__.copy()
3668 def __setstate__(self, p):
3669 if not hasattr(self,
'this'):
3671 if isinstance(p, tuple):
3673 self.__dict__.update(d)
3674 return self._set_from_binary(p)
3676 __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
3679 _IMP_npctransport.SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
3681 def __lshift__(*args):
3683 __lshift__(_ostream out, RelaxingSpring n) -> _ostream
3684 __lshift__(_ostream out, Transporting n) -> _ostream
3685 __lshift__(_ostream out, SlabWithPore n) -> _ostream
3686 __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
3687 __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
3689 return _IMP_npctransport.__lshift__(*args)
3691 r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
3693 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3696 r"""__init__(SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
3697 _IMP_npctransport.SlabWithCylindricalPorePairScore_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k))
3699 def get_displacement_direction(self, slab, v):
3700 r"""get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
3701 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
3703 def get_displacement_magnitude(self, slab, v):
3704 r"""get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
3705 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
3707 def do_get_inputs(self, m, pis):
3708 r"""do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3709 return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
3711 def get_version_info(self):
3712 r"""get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
3713 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
3714 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPorePairScore
3717 r"""__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
3718 return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
3721 r"""__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
3722 return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
3726 return _object_cast_to_SlabWithCylindricalPorePairScore(o)
3730 _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
3732 r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
3734 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3737 r"""__init__(SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
3738 _IMP_npctransport.SlabWithToroidalPorePairScore_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPorePairScore(k))
3740 def do_get_inputs(self, m, pis):
3741 r"""do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3742 return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
3744 def get_version_info(self):
3745 r"""get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
3746 return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
3747 __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPorePairScore
3750 r"""__str__(SlabWithToroidalPorePairScore self) -> std::string"""
3751 return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
3754 r"""__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
3755 return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
3759 return _object_cast_to_SlabWithToroidalPorePairScore(o)
3763 _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
3765 r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
3767 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3769 def __init__(self, height, radius, length):
3770 r"""__init__(SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
3771 _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length))
3773 def get_version_info(self):
3774 r"""get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
3775 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
3776 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreWireGeometry
3779 r"""__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
3780 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
3783 r"""__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
3784 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
3788 return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
3792 _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
3794 r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
3796 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3798 def __init__(self, height, radius, length):
3799 r"""__init__(SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
3800 _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length))
3803 r"""__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
3804 return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
3807 r"""__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
3808 return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
3812 return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
3814 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
3817 _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
3819 r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
3821 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3825 __init__(SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
3826 __init__(SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
3828 _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args))
3830 def get_version_info(self):
3831 r"""get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
3832 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
3833 __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPoreWireGeometry
3836 r"""__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
3837 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
3840 r"""__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
3841 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
3845 return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
3849 _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
3851 r"""Proxy of C++ IMP::core::GenericAttributeSingletonScore< IMP::core::Harmonic > class."""
3853 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3854 __repr__ = _swig_repr
3857 r"""__init__(_GenericAttributeSingletonScoreForPoreRadus self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
3858 _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swiginit(self, _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k))
3860 def do_get_inputs(self, m, pis):
3861 r"""do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3862 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
3864 def get_unary_function(self):
3865 r"""get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
3866 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
3868 def get_version_info(self):
3869 r"""get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
3870 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
3871 __swig_destroy__ = _IMP_npctransport.delete__GenericAttributeSingletonScoreForPoreRadus
3874 _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
3875 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
3876 r"""Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
3878 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3881 r"""__init__(PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
3882 _IMP_npctransport.PoreRadiusSingletonScore_swiginit(self, _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k))
3885 r"""set_k(PoreRadiusSingletonScore self, double k)"""
3886 return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
3887 __swig_destroy__ = _IMP_npctransport.delete_PoreRadiusSingletonScore
3890 r"""__str__(PoreRadiusSingletonScore self) -> std::string"""
3891 return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
3894 r"""__repr__(PoreRadiusSingletonScore self) -> std::string"""
3895 return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
3899 return _object_cast_to_PoreRadiusSingletonScore(o)
3903 _IMP_npctransport.PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
3905 r"""Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
3907 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3909 def __init__(self, bottom, top, k):
3910 r"""__init__(ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
3911 _IMP_npctransport.ExcludeZRangeSingletonScore_swiginit(self, _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k))
3913 def get_bottom_z(self):
3914 r"""get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
3915 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
3917 def get_top_z(self):
3918 r"""get_top_z(ExcludeZRangeSingletonScore self) -> double"""
3919 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
3922 r"""get_k(ExcludeZRangeSingletonScore self) -> double"""
3923 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
3925 def do_get_inputs(self, m, pis):
3926 r"""do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3927 return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
3929 def get_version_info(self):
3930 r"""get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
3931 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
3932 __swig_destroy__ = _IMP_npctransport.delete_ExcludeZRangeSingletonScore
3935 r"""__str__(ExcludeZRangeSingletonScore self) -> std::string"""
3936 return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
3939 r"""__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
3940 return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
3944 return _object_cast_to_ExcludeZRangeSingletonScore(o)
3948 _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
3950 r"""Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
3952 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3955 r"""__init__(ZBiasSingletonScore self, double k, double max_r=HALF_SQRT_MAX_DOUBLE) -> ZBiasSingletonScore"""
3956 _IMP_npctransport.ZBiasSingletonScore_swiginit(self, _IMP_npctransport.new_ZBiasSingletonScore(*args))
3959 r"""get_k(ZBiasSingletonScore self) -> double"""
3960 return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
3963 r"""set_k(ZBiasSingletonScore self, double k)"""
3964 return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
3966 def do_get_inputs(self, m, pis):
3967 r"""do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3968 return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
3970 def get_version_info(self):
3971 r"""get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
3972 return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
3973 __swig_destroy__ = _IMP_npctransport.delete_ZBiasSingletonScore
3976 r"""__str__(ZBiasSingletonScore self) -> std::string"""
3977 return _IMP_npctransport.ZBiasSingletonScore___str__(self)
3980 r"""__repr__(ZBiasSingletonScore self) -> std::string"""
3981 return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
3985 return _object_cast_to_ZBiasSingletonScore(o)
3989 _IMP_npctransport.ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
3991 r"""Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
3993 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3995 def __init__(self, p, statistics_manager=None, periodicity=1):
3996 r"""__init__(BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState"""
3997 _IMP_npctransport.BodyStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity))
3999 def get_correlation_time(self):
4000 r"""get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4001 return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4004 r"""get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4005 return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4007 def update_particle_type_zr_distribution_map(self):
4008 r"""update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4009 return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4011 def do_update(self, call_num):
4012 r"""do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4013 return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4015 def get_version_info(self):
4016 r"""get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4017 return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4018 __swig_destroy__ = _IMP_npctransport.delete_BodyStatisticsOptimizerState
4021 r"""__str__(BodyStatisticsOptimizerState self) -> std::string"""
4022 return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4025 r"""__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4026 return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4030 return _object_cast_to_BodyStatisticsOptimizerState(o)
4034 _IMP_npctransport.BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4036 r"""Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
4038 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4040 def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4041 r"""__init__(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"""
4042 _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner))
4044 def set_owner(self, owner):
4045 r"""set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4046 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4048 def get_owner(self):
4049 r"""get_owner(ParticleTransportStatisticsOptimizerState self) -> Simulator"""
4050 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4052 def get_n_transports_up(self):
4053 r"""get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4054 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4056 def get_n_transports_down(self):
4057 r"""get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4058 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4060 def get_total_n_transports(self):
4061 r"""get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4062 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4064 def get_transport_time_points_in_ns(self):
4065 r"""get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4066 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4068 def do_update(self, call_num):
4069 r"""do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4070 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4072 def get_version_info(self):
4073 r"""get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4074 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4075 __swig_destroy__ = _IMP_npctransport.delete_ParticleTransportStatisticsOptimizerState
4078 r"""__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4079 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4082 r"""__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4083 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4087 return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4091 _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4093 r"""Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
4095 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4097 def __init__(self, ps, periodicity=1):
4098 r"""__init__(ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState"""
4099 _IMP_npctransport.ChainStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity))
4101 def get_correlation_time(self):
4102 r"""get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4103 return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4105 def get_local_diffusion_coefficients(self):
4106 r"""get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4107 return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4110 r"""get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
4111 return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
4113 def get_mean_radius_of_gyration(self):
4114 r"""get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4115 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
4117 def get_mean_square_radius_of_gyration(self):
4118 r"""get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4119 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4121 def get_mean_end_to_end_distance(self):
4122 r"""get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4123 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4125 def get_mean_square_end_to_end_distance(self):
4126 r"""get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4127 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4129 def get_mean_bond_distance(self):
4130 r"""get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4131 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4133 def get_mean_square_bond_distance(self):
4134 r"""get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4135 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4137 def do_update(self, call_num):
4138 r"""do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4139 return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4141 def get_version_info(self):
4142 r"""get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4143 return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4144 __swig_destroy__ = _IMP_npctransport.delete_ChainStatisticsOptimizerState
4147 r"""__str__(ChainStatisticsOptimizerState self) -> std::string"""
4148 return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4151 r"""__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4152 return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4156 return _object_cast_to_ChainStatisticsOptimizerState(o)
4160 _IMP_npctransport.ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4162 r"""Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4164 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4166 def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4167 r"""__init__(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"""
4168 _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack))
4170 def get_interaction_type(self):
4171 r"""get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4172 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4174 def get_average_number_of_contacts(self):
4175 r"""get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4176 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4178 def get_average_off_per_contact_per_ns(self):
4179 r"""get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4180 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4182 def get_average_off_per_bound_I_per_ns(self):
4183 r"""get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4184 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4186 def get_average_off_per_bound_II_per_ns(self):
4187 r"""get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4188 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4190 def get_average_on_per_missing_contact_per_ns(self):
4191 r"""get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4192 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4194 def get_average_on_per_unbound_I_per_ns(self):
4195 r"""get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4196 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4198 def get_average_on_per_unbound_II_per_ns(self):
4199 r"""get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4200 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4202 def get_average_fraction_bound_particles_I(self):
4203 r"""get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4204 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4206 def get_average_fraction_bound_particles_II(self):
4207 r"""get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4208 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4210 def get_average_fraction_bound_particle_sites_I(self):
4211 r"""get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4212 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4214 def get_average_fraction_bound_particle_sites_II(self):
4215 r"""get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4216 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4218 def get_average_fraction_nonspecific_interactions_I(self):
4219 r"""get_average_fraction_nonspecific_interactions_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4220 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_I(self)
4222 def get_average_fraction_nonspecific_interactions_II(self):
4223 r"""get_average_fraction_nonspecific_interactions_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4224 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_II(self)
4226 def get_number_of_particles_1(self):
4227 r"""get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4228 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4230 def get_number_of_particles_2(self):
4231 r"""get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4232 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4234 def get_misc_stats_period_ns(self):
4235 r"""get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4236 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4238 def get_off_stats_period_ns(self):
4239 r"""get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4240 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4242 def get_off_I_stats_period_ns(self):
4243 r"""get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4244 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4246 def get_off_II_stats_period_ns(self):
4247 r"""get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4248 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4250 def get_on_stats_period_ns(self):
4251 r"""get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4252 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4254 def get_on_I_stats_period_ns(self):
4255 r"""get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4256 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4258 def get_on_II_stats_period_ns(self):
4259 r"""get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4260 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4262 def get_version_info(self):
4263 r"""get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4264 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4265 __swig_destroy__ = _IMP_npctransport.delete_BipartitePairsStatisticsOptimizerState
4268 r"""__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4269 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4272 r"""__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4273 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4277 return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4281 _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4283 def get_close_pairs_range(*args):
4285 get_close_pairs_range(double max_range, double max_range_factor) -> double
4286 get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4288 return _IMP_npctransport.get_close_pairs_range(*args)
4292 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
4293 get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4295 return _IMP_npctransport.get_time_step(*args)
4298 r"""get_frames_from_ns(double ns, double time_step) -> int"""
4299 return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4302 r"""get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4303 return _IMP_npctransport.get_number_of_frames(config, time_step)
4306 r"""get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4307 return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4310 r"""get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int"""
4311 return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4314 r"""get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int"""
4315 return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4318 r"""initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints=IMP::RestraintsTemp(), bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False, bool are_fgs_pre_initialized=False)"""
4319 return _IMP_npctransport.initialize_positions(*args)
4322 r"""get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4323 return _IMP_npctransport.get_optimizable_particles(particles)
4326 r"""get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4327 return _IMP_npctransport.get_non_optimizable_particles(particles)
4330 r"""get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4331 return _IMP_npctransport.get_particle_indexes(particles)
4334 r"""get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4335 return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4338 r"""get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4339 return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4341 def get_spheres_centers(spheres):
4342 r"""get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4343 return _IMP_npctransport.get_spheres_centers(spheres)
4346 r"""copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4347 return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4350 r"""copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4351 return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4354 r"""copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4355 return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4356 class Avro2PBReader(object):
4357 r"""Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4359 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4363 __init__(Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4364 __init__(Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4366 _IMP_npctransport.Avro2PBReader_swiginit(self, _IMP_npctransport.new_Avro2PBReader(*args))
4367 __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4369 def read_next(self):
4370 r"""read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4371 return _IMP_npctransport.Avro2PBReader_read_next(self)
4373 def get_is_valid(self):
4374 r"""get_is_valid(Avro2PBReader self) -> bool"""
4375 return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4377 def get_cur_file_name(self):
4378 r"""get_cur_file_name(Avro2PBReader self) -> std::string"""
4379 return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4381 def show(self, *args):
4382 r"""show(Avro2PBReader self, _ostream out=std::cout)"""
4383 return _IMP_npctransport.Avro2PBReader_show(self, *args)
4386 r"""__str__(Avro2PBReader self) -> std::string"""
4387 return _IMP_npctransport.Avro2PBReader___str__(self)
4390 r"""__repr__(Avro2PBReader self) -> std::string"""
4391 return _IMP_npctransport.Avro2PBReader___repr__(self)
4394 _IMP_npctransport.Avro2PBReader_swigregister(Avro2PBReader)
4397 r"""startup(int argc) -> SimulationData"""
4398 return _IMP_npctransport.startup(argc)
4401 r"""remove_Nup42(SimulationData sd)"""
4402 return _IMP_npctransport.remove_Nup42(sd)
4405 r"""inflate_floater(SimulationData sd, std::string const floater_name, float const new_radius)"""
4406 return _IMP_npctransport.inflate_floater(sd, floater_name, new_radius)
4409 r"""reset_box_size(SimulationData sd, double box_size)"""
4410 return _IMP_npctransport.reset_box_size(sd, box_size)
4413 r"""do_main_loop(SimulationData sd, IMP::RestraintsTemp const & init_restraints)"""
4414 return _IMP_npctransport.do_main_loop(sd, init_restraints)
4417 from .npctransport_pb2
import *
4418 import google.protobuf
4420 print(
"no protobuf support in python")
4421 from ._configuration
import *
4427 r"""get_module_version() -> std::string const"""
4428 return _IMP_npctransport.get_module_version()
4431 r"""get_example_path(std::string fname) -> std::string"""
4432 return _IMP_npctransport.get_example_path(fname)
4435 r"""get_data_path(std::string fname) -> std::string"""
4436 return _IMP_npctransport.get_data_path(fname)
4438 from .
import _version_check
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)
void remove_Nup42(SimulationData *sd)
remove nup42 and its anchors (also from obstacles)
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)
IMP::npctransport::SimulationData * startup(int argc, char *argv[])
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_module_version()
Return the version of this module, as a string.
void do_main_loop(SimulationData *sd, const RestraintsTemp &init_restraints)
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)
Basic utilities for handling cryo-electron microscopy 3D density maps.
void inflate_floater(SimulationData *sd, const std::string floater_name, const float new_radius)
inflate floater of specified type to new_radius
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)
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)
void reset_box_size(SimulationData *sd, double box_size)
change box size sd to specified box size and update output file
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.
Support for small angle X-ray scattering (SAXS) data.
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)
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
algebra::Sphere3Ds get_spheres_from_vectors(V3iter first, V3iter last, double radius)
convert vectors to spheres of passed radius