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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
npctransport/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_npctransport
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
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):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
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"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
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__)
63 
64 
65 import weakref
66 
67 class IMP_NPCTRANSPORT_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_NPCTRANSPORT_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_npctransport.delete_IMP_NPCTRANSPORT_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
79  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator"""
83  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator"""
87  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_decr(self, n)
88 
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)
92 
93  def equal(self, x):
94  r"""equal(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
95  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator"""
99  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
103  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
107  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
111  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_previous(self)
112 
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)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
119  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
123  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___ne__(self, x)
124 
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)
128 
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)
132 
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)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator
140  __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_NPCTRANSPORT_SwigPyIterator in _IMP_npctransport:
147 _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_swigregister(IMP_NPCTRANSPORT_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_npctransport.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_npctransport.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_npctransport.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_npctransport.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_npctransport.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_npctransport.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_npctransport.IMP_MEMORY
167 
168 IMP_NONE = _IMP_npctransport.IMP_NONE
169 
170 IMP_USAGE = _IMP_npctransport.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_npctransport.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_npctransport.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_npctransport.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_npctransport.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_npctransport.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
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)
208  def cleanup(self):
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]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
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()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_npctransport._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_npctransport:
237 _IMP_npctransport._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
242 
243 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
246 
247 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
248 
249 IMP_BENCHMARK_HAS_NUMPY = _IMP_npctransport.IMP_BENCHMARK_HAS_NUMPY
250 
251 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
252 
253 import IMP.benchmark
254 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
255 
256 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
257 
258 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
259 
260 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
261 
262 IMP_CGAL_HAS_NUMPY = _IMP_npctransport.IMP_CGAL_HAS_NUMPY
263 
264 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
265 
266 import IMP.cgal
267 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
268 
269 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
270 
271 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
272 
273 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
274 
275 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
276 
277 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
278 
279 IMP_ALGEBRA_HAS_NUMPY = _IMP_npctransport.IMP_ALGEBRA_HAS_NUMPY
280 
281 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
282 
283 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
284 
285 import IMP.algebra
286 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
287 
288 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
289 
290 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
291 
292 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
293 
294 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
295 
296 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
297 
298 IMP_DISPLAY_HAS_NUMPY = _IMP_npctransport.IMP_DISPLAY_HAS_NUMPY
299 
300 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
301 
302 import IMP.display
303 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
304 
305 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
306 
307 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
308 
309 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
310 
311 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
312 
313 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
314 
315 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
316 
317 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_NUMPY
318 
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 
321 import IMP.score_functor
322 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
323 
324 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
325 
326 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
327 
328 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
329 
330 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
331 
332 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
333 
334 IMP_STATISTICS_HAS_NUMPY = _IMP_npctransport.IMP_STATISTICS_HAS_NUMPY
335 
336 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
337 
338 import IMP.statistics
339 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
340 
341 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
342 
343 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
344 
345 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
346 
347 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
348 
349 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
350 
351 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
352 
353 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
354 
355 IMP_CORE_HAS_NUMPY = _IMP_npctransport.IMP_CORE_HAS_NUMPY
356 
357 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
358 
359 import IMP.core
360 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
361 
362 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
363 
364 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
365 
366 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
367 
368 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
369 
370 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
371 
372 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
373 
374 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
375 
376 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
377 
378 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
379 
380 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
381 
382 IMP_CONTAINER_HAS_NUMPY = _IMP_npctransport.IMP_CONTAINER_HAS_NUMPY
383 
384 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
385 
386 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
387 
388 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
389 
390 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
391 
392 import IMP.container
393 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
394 
395 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
396 
397 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
398 
399 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
400 
401 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
402 
403 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
404 
405 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
406 
407 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
408 
409 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
410 
411 IMP_ATOM_HAS_NUMPY = _IMP_npctransport.IMP_ATOM_HAS_NUMPY
412 
413 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
414 
415 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
416 
417 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
418 
419 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
420 
421 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
422 
423 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
424 
425 import IMP.atom
426 IMP_EM_HAS_IMP_CGAL = _IMP_npctransport.IMP_EM_HAS_IMP_CGAL
427 
428 IMP_EM_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_EM_HAS_IMP_CONTAINER
429 
430 IMP_EM_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_EM_HAS_IMP_DISPLAY
431 
432 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_EM_HAS_IMP_SCORE_FUNCTOR
433 
434 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_FILESYSTEM
435 
436 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
437 
438 IMP_EM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_EM_HAS_BOOST_RANDOM
439 
440 IMP_EM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_EM_HAS_BOOST_REGEX
441 
442 IMP_EM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_SYSTEM
443 
444 IMP_EM_HAS_CGAL = _IMP_npctransport.IMP_EM_HAS_CGAL
445 
446 IMP_EM_HAS_HDF5 = _IMP_npctransport.IMP_EM_HAS_HDF5
447 
448 IMP_EM_HAS_NUMPY = _IMP_npctransport.IMP_EM_HAS_NUMPY
449 
450 IMP_EM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_EM_HAS_PYTHON_IHM
451 
452 IMPEM_SHOW_WARNINGS = _IMP_npctransport.IMPEM_SHOW_WARNINGS
453 
454 import IMP.em
455 IMP_SAXS_HAS_IMP_CGAL = _IMP_npctransport.IMP_SAXS_HAS_IMP_CGAL
456 
457 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_SAXS_HAS_IMP_CONTAINER
458 
459 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_SAXS_HAS_IMP_DISPLAY
460 
461 IMP_SAXS_HAS_IMP_KERNEL = _IMP_npctransport.IMP_SAXS_HAS_IMP_KERNEL
462 
463 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
464 
465 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_FILESYSTEM
466 
467 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
468 
469 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_RANDOM
470 
471 IMP_SAXS_HAS_BOOST_REGEX = _IMP_npctransport.IMP_SAXS_HAS_BOOST_REGEX
472 
473 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_SYSTEM
474 
475 IMP_SAXS_HAS_CGAL = _IMP_npctransport.IMP_SAXS_HAS_CGAL
476 
477 IMP_SAXS_HAS_HDF5 = _IMP_npctransport.IMP_SAXS_HAS_HDF5
478 
479 IMP_SAXS_HAS_NUMPY = _IMP_npctransport.IMP_SAXS_HAS_NUMPY
480 
481 IMP_SAXS_HAS_PYTHON_IHM = _IMP_npctransport.IMP_SAXS_HAS_PYTHON_IHM
482 
483 IMPSAXS_SHOW_WARNINGS = _IMP_npctransport.IMPSAXS_SHOW_WARNINGS
484 
485 import IMP.saxs
486 IMP_ISD_HAS_IMP_CGAL = _IMP_npctransport.IMP_ISD_HAS_IMP_CGAL
487 
488 IMP_ISD_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_ISD_HAS_IMP_DISPLAY
489 
490 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
491 
492 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_FILESYSTEM
493 
494 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
495 
496 IMP_ISD_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ISD_HAS_BOOST_RANDOM
497 
498 IMP_ISD_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ISD_HAS_BOOST_REGEX
499 
500 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_SYSTEM
501 
502 IMP_ISD_HAS_CGAL = _IMP_npctransport.IMP_ISD_HAS_CGAL
503 
504 IMP_ISD_HAS_HDF5 = _IMP_npctransport.IMP_ISD_HAS_HDF5
505 
506 IMP_ISD_HAS_NUMPY = _IMP_npctransport.IMP_ISD_HAS_NUMPY
507 
508 IMP_ISD_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ISD_HAS_PYTHON_IHM
509 
510 IMPISD_SHOW_WARNINGS = _IMP_npctransport.IMPISD_SHOW_WARNINGS
511 
512 import IMP.isd
513 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
514 
515 IMP_RMF_HAS_IMP_EM = _IMP_npctransport.IMP_RMF_HAS_IMP_EM
516 
517 IMP_RMF_HAS_IMP_SAXS = _IMP_npctransport.IMP_RMF_HAS_IMP_SAXS
518 
519 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
520 
521 IMP_RMF_HAS_IMP_STATISTICS = _IMP_npctransport.IMP_RMF_HAS_IMP_STATISTICS
522 
523 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
524 
525 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
526 
527 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
528 
529 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
530 
531 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
532 
533 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
534 
535 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
536 
537 IMP_RMF_HAS_NUMPY = _IMP_npctransport.IMP_RMF_HAS_NUMPY
538 
539 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
540 
541 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
542 
543 import IMP.rmf
544 import RMF
545 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
546 
547 IMP_NPCTRANSPORT_HAS_IMP_EM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_EM
548 
549 IMP_NPCTRANSPORT_HAS_IMP_ISD = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_ISD
550 
551 IMP_NPCTRANSPORT_HAS_IMP_SAXS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_SAXS
552 
553 IMP_NPCTRANSPORT_HAS_ABSEIL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_ABSEIL
554 
555 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
556 
557 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
558 
559 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
560 
561 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
562 
563 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
564 
565 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
566 
567 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
568 
569 IMP_NPCTRANSPORT_HAS_NUMPY = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_NUMPY
570 
571 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
572 
573 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
574 
575 
576 _object_types.append("SitesPairScore")
577 
578 
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)
582 
583 _object_types.append("Scoring")
584 
585 
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)
589 
590 _object_types.append("BrownianDynamicsTAMDWithSlabSupport")
591 
592 
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)
596 
597 _object_types.append("Statistics")
598 
599 
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)
603 
604 _object_types.append("SimulationData")
605 
606 
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)
610 
611 _object_types.append("SitesGeometry")
612 
613 
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)
617 
618 _object_types.append("TypedSitesGeometry")
619 
620 
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)
624 
625 _object_types.append("SlabWithCylindricalPorePairScore")
626 
627 
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)
631 
632 _object_types.append("SlabWithToroidalPorePairScore")
633 
634 
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)
638 
639 _object_types.append("PoreRadiusSingletonScore")
640 
641 
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)
645 
646 _object_types.append("ExcludeZRangeSingletonScore")
647 
648 
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)
652 
653 _object_types.append("ZBiasSingletonScore")
654 
655 
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)
659 
660 _object_types.append("SlabWithCylindricalPoreWireGeometry")
661 
662 
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)
666 
667 _object_types.append("SlabWithCylindricalPoreSurfaceGeometry")
668 
669 
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)
673 
674 _object_types.append("SlabWithToroidalPoreWireGeometry")
675 
676 
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)
680 
681 _object_types.append("LinearSoftSpherePairScore")
682 
683 
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)
687 
688 _object_types.append("FunctorLinearSoftSpherePairScore")
689 
690 
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)
694 
695 _object_types.append("LinearInteractionPairScore")
696 
697 
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)
701 
702 _object_types.append("FunctorLinearInteractionPairScore")
703 
704 
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)
708 
709 _object_types.append("LinearWellPairScore")
710 
711 
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)
715 
716 _object_types.append("HarmonicSpringSingletonScore")
717 
718 
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)
722 
723 _object_types.append("HierarchyWithSitesSaveLink")
724 
725 
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)
729 
730 _object_types.append("HierarchyWithSitesLoadLink")
731 
732 
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)
736 
737 _object_types.append("ChainStatisticsOptimizerState")
738 
739 
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)
743 
744 _object_types.append("BodyStatisticsOptimizerState")
745 
746 
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)
750 
751 _object_types.append("BipartitePairsStatisticsOptimizerState")
752 
753 
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)
757 
758 _object_types.append("ParticleTransportStatisticsOptimizerState")
759 
760 
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)
764 
765 _object_types.append("FGChain")
766 
767 
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)
771 
772 _object_types.append("ParticleFactory")
773 
774 
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)
778 
779 Avro2PBReaders=list
780 _plural_types.append("Avro2PBReaders")
781 _value_types.append("Avro2PBReader")
782 
783 
784 SitesPairScoreParametersList=list
785 _plural_types.append("SitesPairScoreParametersList")
786 _value_types.append("SitesPairScoreParameters")
787 
788 
789 def Transportings(l=[]):
790  return [Transporting(x) for x in l]
791 _plural_types.append("Transportings")
792 
793 
794 _value_types.append("Transporting")
795 
796 
797 def SlabWithPores(l=[]):
798  return [SlabWithPore(x) for x in l]
799 _plural_types.append("SlabWithPores")
800 
801 
802 _value_types.append("SlabWithPore")
803 
804 
805 def SlabWithCylindricalPores(l=[]):
806  return [SlabWithCylindricalPore(x) for x in l]
807 _plural_types.append("SlabWithCylindricalPores")
808 
809 
810 _value_types.append("SlabWithCylindricalPore")
811 
812 
813 def RelaxingSprings(l=[]):
814  return [RelaxingSpring(x) for x in l]
815 _plural_types.append("RelaxingSprings")
816 
817 
818 _value_types.append("RelaxingSpring")
819 
820 
821 def SlabWithToroidalPores(l=[]):
822  return [SlabWithToroidalPore(x) for x in l]
823 _plural_types.append("SlabWithToroidalPores")
824 
825 
826 _value_types.append("SlabWithToroidalPore")
827 
828 class _DoubleParameter(object):
829  r"""Proxy of C++ IMP::npctransport::Parameter< double > class."""
830 
831  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
832  __repr__ = _swig_repr
833 
834  def __init__(self, *args):
835  r"""
836  __init__(_DoubleParameter self) -> _DoubleParameter
837  __init__(_DoubleParameter self, double t) -> _DoubleParameter
838  """
839  _IMP_npctransport._DoubleParameter_swiginit(self, _IMP_npctransport.new__DoubleParameter(*args))
840 
841  def get_value(self):
842  r"""get_value(_DoubleParameter self) -> double"""
843  return _IMP_npctransport._DoubleParameter_get_value(self)
844 
845  def is_init(self):
846  r"""is_init(_DoubleParameter self) -> bool"""
847  return _IMP_npctransport._DoubleParameter_is_init(self)
848  __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
849 
850 # Register _DoubleParameter in _IMP_npctransport:
851 _IMP_npctransport._DoubleParameter_swigregister(_DoubleParameter)
852 class _IntParameter(object):
853  r"""Proxy of C++ IMP::npctransport::Parameter< int > class."""
854 
855  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
856  __repr__ = _swig_repr
857 
858  def __init__(self, *args):
859  r"""
860  __init__(_IntParameter self) -> _IntParameter
861  __init__(_IntParameter self, int t) -> _IntParameter
862  """
863  _IMP_npctransport._IntParameter_swiginit(self, _IMP_npctransport.new__IntParameter(*args))
864 
865  def get_value(self):
866  r"""get_value(_IntParameter self) -> int"""
867  return _IMP_npctransport._IntParameter_get_value(self)
868 
869  def is_init(self):
870  r"""is_init(_IntParameter self) -> bool"""
871  return _IMP_npctransport._IntParameter_is_init(self)
872  __swig_destroy__ = _IMP_npctransport.delete__IntParameter
873 
874 # Register _IntParameter in _IMP_npctransport:
875 _IMP_npctransport._IntParameter_swigregister(_IntParameter)
876 class _BoolParameter(object):
877  r"""Proxy of C++ IMP::npctransport::Parameter< bool > class."""
878 
879  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
880  __repr__ = _swig_repr
881 
882  def __init__(self, *args):
883  r"""
884  __init__(_BoolParameter self) -> _BoolParameter
885  __init__(_BoolParameter self, bool t) -> _BoolParameter
886  """
887  _IMP_npctransport._BoolParameter_swiginit(self, _IMP_npctransport.new__BoolParameter(*args))
888 
889  def get_value(self):
890  r"""get_value(_BoolParameter self) -> bool"""
891  return _IMP_npctransport._BoolParameter_get_value(self)
892 
893  def is_init(self):
894  r"""is_init(_BoolParameter self) -> bool"""
895  return _IMP_npctransport._BoolParameter_is_init(self)
896  __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
897 
898 # Register _BoolParameter in _IMP_npctransport:
899 _IMP_npctransport._BoolParameter_swigregister(_BoolParameter)
900 
902  r"""make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
903  return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
904 
906  r"""make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
907  return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
908 
910  r"""
911  make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
912  make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
913  """
914  return _IMP_npctransport.make_unordered_particle_index_pair(*args)
915 class LinearSoftSpherePairScore(IMP.PairScore):
916  r"""Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class."""
917 
918  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
919 
920  def __init__(self, *args):
921  r"""__init__(LinearSoftSpherePairScore self, double k, std::string name="LinearSSPairScore%1%") -> LinearSoftSpherePairScore"""
922  _IMP_npctransport.LinearSoftSpherePairScore_swiginit(self, _IMP_npctransport.new_LinearSoftSpherePairScore(*args))
923 
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)
927 
928  def get_k(self):
929  r"""get_k(LinearSoftSpherePairScore self) -> double"""
930  return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
931 
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
936 
937  def __str__(self):
938  r"""__str__(LinearSoftSpherePairScore self) -> std::string"""
939  return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
940 
941  def __repr__(self):
942  r"""__repr__(LinearSoftSpherePairScore self) -> std::string"""
943  return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
944 
945  @staticmethod
946  def get_from(o):
947  return _object_cast_to_LinearSoftSpherePairScore(o)
948 
949 
950 # Register LinearSoftSpherePairScore in _IMP_npctransport:
951 _IMP_npctransport.LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
952 class LinearInteractionPairScore(IMP.PairScore):
953  r"""Proxy of C++ IMP::npctransport::LinearInteractionPairScore class."""
954 
955  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
956 
957  def __init__(self, *args):
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))
960 
961  def evaluate_if_good_index(self, *args):
962  r"""
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
965  """
966  return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
967 
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)
971 
972  def get_range_attraction(self):
973  r"""get_range_attraction(LinearInteractionPairScore self) -> double"""
974  return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
975 
976  def get_k_attraction(self):
977  r"""get_k_attraction(LinearInteractionPairScore self) -> double"""
978  return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
979 
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)
983 
984  def get_k_repulsion(self):
985  r"""get_k_repulsion(LinearInteractionPairScore self) -> double"""
986  return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
987 
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)
991 
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
996 
997  def __str__(self):
998  r"""__str__(LinearInteractionPairScore self) -> std::string"""
999  return _IMP_npctransport.LinearInteractionPairScore___str__(self)
1000 
1001  def __repr__(self):
1002  r"""__repr__(LinearInteractionPairScore self) -> std::string"""
1003  return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
1004 
1005  @staticmethod
1006  def get_from(o):
1007  return _object_cast_to_LinearInteractionPairScore(o)
1008 
1009 
1010 # Register LinearInteractionPairScore in _IMP_npctransport:
1011 _IMP_npctransport.LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
1012 class LinearWellPairScore(IMP.PairScore):
1013  r"""Proxy of C++ IMP::npctransport::LinearWellPairScore class."""
1014 
1015  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1016 
1017  def __init__(self, *args):
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))
1020 
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)
1024 
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)
1028 
1029  def set_k(self, k):
1030  r"""set_k(LinearWellPairScore self, double k)"""
1031  return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
1032 
1033  def get_k(self):
1034  r"""get_k(LinearWellPairScore self) -> double"""
1035  return _IMP_npctransport.LinearWellPairScore_get_k(self)
1036 
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)
1040 
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
1045 
1046  def __str__(self):
1047  r"""__str__(LinearWellPairScore self) -> std::string"""
1048  return _IMP_npctransport.LinearWellPairScore___str__(self)
1049 
1050  def __repr__(self):
1051  r"""__repr__(LinearWellPairScore self) -> std::string"""
1052  return _IMP_npctransport.LinearWellPairScore___repr__(self)
1053 
1054  @staticmethod
1055  def get_from(o):
1056  return _object_cast_to_LinearWellPairScore(o)
1057 
1058 
1059 # Register LinearWellPairScore in _IMP_npctransport:
1060 _IMP_npctransport.LinearWellPairScore_swigregister(LinearWellPairScore)
1061 class RelaxingSpring(IMP.Decorator):
1062  r"""Proxy of C++ IMP::npctransport::RelaxingSpring class."""
1063 
1064  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1065 
1066  def __init__(self, *args):
1067  r"""
1068  __init__(RelaxingSpring self) -> RelaxingSpring
1069  __init__(RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
1070  __init__(RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
1071  """
1072  _IMP_npctransport.RelaxingSpring_swiginit(self, _IMP_npctransport.new_RelaxingSpring(*args))
1073 
1074  def show(self, *args):
1075  r"""show(RelaxingSpring self, _ostream out=std::cout)"""
1076  return _IMP_npctransport.RelaxingSpring_show(self, *args)
1077 
1078  @staticmethod
1079  def setup_particle(*args):
1080  r"""
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
1083  """
1084  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1085 
1086  @staticmethod
1087  def get_is_setup(*args):
1088  r"""
1089  get_is_setup(_ParticleAdaptor p) -> bool
1090  get_is_setup(Model m, ParticleIndex pi) -> bool
1091  """
1092  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1093 
1094  @staticmethod
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()
1098 
1099  @staticmethod
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()
1103 
1104  @staticmethod
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()
1108 
1109  @staticmethod
1110  def get_rest_length_key():
1111  r"""get_rest_length_key() -> FloatKey"""
1112  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1113 
1114  @staticmethod
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()
1118 
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)
1122 
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)
1126 
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)
1130 
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)
1134 
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)
1138 
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)
1142 
1143  def get_rest_length(self):
1144  r"""get_rest_length(RelaxingSpring self) -> IMP::Float"""
1145  return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1146 
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)
1150 
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)
1154 
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)
1158 
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)
1162 
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)
1166 
1167  def add_attribute(self, *args):
1168  r"""
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  """
1178  return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1179 
1180  def get_value(self, *args):
1181  r"""
1182  get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1183  get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1184  get_value(RelaxingSpring self, FloatsKey a0) -> IMP::Floats
1185  get_value(RelaxingSpring self, IntsKey a0) -> IMP::Ints
1186  get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1187  get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1188  get_value(RelaxingSpring self, ObjectKey a0) -> Object
1189  """
1190  return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1191 
1192  def set_value(self, *args):
1193  r"""
1194  set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1195  set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1196  set_value(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1197  set_value(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1198  set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1199  set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1200  set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1201  """
1202  return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1203 
1204  def remove_attribute(self, *args):
1205  r"""
1206  remove_attribute(RelaxingSpring self, FloatKey a0)
1207  remove_attribute(RelaxingSpring self, IntKey a0)
1208  remove_attribute(RelaxingSpring self, FloatsKey a0)
1209  remove_attribute(RelaxingSpring self, IntsKey a0)
1210  remove_attribute(RelaxingSpring self, StringKey a0)
1211  remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1212  remove_attribute(RelaxingSpring self, ObjectKey a0)
1213  """
1214  return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1215 
1216  def has_attribute(self, *args):
1217  r"""
1218  has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1219  has_attribute(RelaxingSpring self, IntKey a0) -> bool
1220  has_attribute(RelaxingSpring self, FloatsKey a0) -> bool
1221  has_attribute(RelaxingSpring self, IntsKey a0) -> bool
1222  has_attribute(RelaxingSpring self, StringKey a0) -> bool
1223  has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1224  has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1225  """
1226  return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1227 
1228  def get_derivative(self, a0):
1229  r"""get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1230  return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1231 
1232  def get_name(self):
1233  r"""get_name(RelaxingSpring self) -> std::string"""
1234  return _IMP_npctransport.RelaxingSpring_get_name(self)
1235 
1236  def clear_caches(self):
1237  r"""clear_caches(RelaxingSpring self)"""
1238  return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1239 
1240  def set_name(self, a0):
1241  r"""set_name(RelaxingSpring self, std::string a0)"""
1242  return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1243 
1244  def set_check_level(self, a0):
1245  r"""set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1246  return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1247 
1248  def add_to_derivative(self, a0, a1, a2):
1249  r"""add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1250  return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1251 
1252  def set_is_optimized(self, a0, a1):
1253  r"""set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1254  return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1255 
1256  def get_is_optimized(self, a0):
1257  r"""get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1258  return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1259 
1260  def get_check_level(self):
1261  r"""get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1262  return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1263 
1264  def __eq__(self, *args):
1265  r"""
1266  __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1267  __eq__(RelaxingSpring self, Particle d) -> bool
1268  """
1269  return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1270 
1271  def __ne__(self, *args):
1272  r"""
1273  __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1274  __ne__(RelaxingSpring self, Particle d) -> bool
1275  """
1276  return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1277 
1278  def __le__(self, *args):
1279  r"""
1280  __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1281  __le__(RelaxingSpring self, Particle d) -> bool
1282  """
1283  return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1284 
1285  def __lt__(self, *args):
1286  r"""
1287  __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1288  __lt__(RelaxingSpring self, Particle d) -> bool
1289  """
1290  return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1291 
1292  def __ge__(self, *args):
1293  r"""
1294  __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1295  __ge__(RelaxingSpring self, Particle d) -> bool
1296  """
1297  return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1298 
1299  def __gt__(self, *args):
1300  r"""
1301  __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1302  __gt__(RelaxingSpring self, Particle d) -> bool
1303  """
1304  return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1305 
1306  def __hash__(self):
1307  r"""__hash__(RelaxingSpring self) -> std::size_t"""
1308  return _IMP_npctransport.RelaxingSpring___hash__(self)
1309 
1310  def __str__(self):
1311  r"""__str__(RelaxingSpring self) -> std::string"""
1312  return _IMP_npctransport.RelaxingSpring___str__(self)
1313 
1314  def __repr__(self):
1315  r"""__repr__(RelaxingSpring self) -> std::string"""
1316  return _IMP_npctransport.RelaxingSpring___repr__(self)
1317 
1318  def _get_as_binary(self):
1319  r"""_get_as_binary(RelaxingSpring self) -> PyObject *"""
1320  return _IMP_npctransport.RelaxingSpring__get_as_binary(self)
1321 
1322  def _set_from_binary(self, p):
1323  r"""_set_from_binary(RelaxingSpring self, PyObject * p)"""
1324  return _IMP_npctransport.RelaxingSpring__set_from_binary(self, p)
1325 
1326  def __getstate__(self):
1327  p = self._get_as_binary()
1328  if len(self.__dict__) > 1:
1329  d = self.__dict__.copy()
1330  del d['this']
1331  p = (d, p)
1332  return p
1333 
1334  def __setstate__(self, p):
1335  if not hasattr(self, 'this'):
1336  self.__init__()
1337  if isinstance(p, tuple):
1338  d, p = p
1339  self.__dict__.update(d)
1340  return self._set_from_binary(p)
1341 
1342  __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1343 
1344 # Register RelaxingSpring in _IMP_npctransport:
1345 _IMP_npctransport.RelaxingSpring_swigregister(RelaxingSpring)
1346 class HarmonicSpringSingletonScore(IMP.SingletonScore):
1347  r"""Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1348 
1349  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1350 
1351  def __init__(self, *args):
1352  r"""__init__(HarmonicSpringSingletonScore self, double k1, double k2, std::string name="HarmonicSpringSingletonScore%1%") -> HarmonicSpringSingletonScore"""
1353  _IMP_npctransport.HarmonicSpringSingletonScore_swiginit(self, _IMP_npctransport.new_HarmonicSpringSingletonScore(*args))
1354 
1355  def set_k1(self, k1):
1356  r"""set_k1(HarmonicSpringSingletonScore self, double k1)"""
1357  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1358 
1359  def get_k1(self):
1360  r"""get_k1(HarmonicSpringSingletonScore self) -> double"""
1361  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1362 
1363  def set_k2(self, k2):
1364  r"""set_k2(HarmonicSpringSingletonScore self, double k2)"""
1365  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1366 
1367  def get_k2(self):
1368  r"""get_k2(HarmonicSpringSingletonScore self) -> double"""
1369  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1370 
1371  def do_get_inputs(self, m, pis):
1372  r"""do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1373  return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1374 
1375  def get_version_info(self):
1376  r"""get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1377  return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1378  __swig_destroy__ = _IMP_npctransport.delete_HarmonicSpringSingletonScore
1379 
1380  def __str__(self):
1381  r"""__str__(HarmonicSpringSingletonScore self) -> std::string"""
1382  return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1383 
1384  def __repr__(self):
1385  r"""__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1386  return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1387 
1388  @staticmethod
1389  def get_from(o):
1390  return _object_cast_to_HarmonicSpringSingletonScore(o)
1391 
1392 
1393 # Register HarmonicSpringSingletonScore in _IMP_npctransport:
1394 _IMP_npctransport.HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1395 class LinearInteraction(object):
1396  r"""Proxy of C++ IMP::npctransport::LinearInteraction class."""
1397 
1398  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1399  __repr__ = _swig_repr
1400 
1401  def __init__(self, *args):
1402  r"""
1403  __init__(LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction
1404  __init__(LinearInteraction self) -> LinearInteraction
1405  """
1406  _IMP_npctransport.LinearInteraction_swiginit(self, _IMP_npctransport.new_LinearInteraction(*args))
1407 
1408  def show(self, *args):
1409  r"""show(LinearInteraction self, _ostream out=std::cout)"""
1410  return _IMP_npctransport.LinearInteraction_show(self, *args)
1411  __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1412 
1413 # Register LinearInteraction in _IMP_npctransport:
1414 _IMP_npctransport.LinearInteraction_swigregister(LinearInteraction)
1415 class _DistancePairScoreForLinearSoftSphere(IMP.PairScore):
1416  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::npctransport::LinearSoftSphereScore > class."""
1417 
1418  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1419  __repr__ = _swig_repr
1420 
1421  def __init__(self, *args):
1422  r"""
1423  __init__(_DistancePairScoreForLinearSoftSphere self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _DistancePairScoreForLinearSoftSphere
1424  __init__(_DistancePairScoreForLinearSoftSphere self) -> _DistancePairScoreForLinearSoftSphere
1425  """
1426  _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swiginit(self, _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args))
1427 
1428  def do_get_inputs(self, m, pis):
1429  r"""do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1430  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1431 
1432  def get_score_functor(self):
1433  r"""get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1434  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1435 
1436  def get_version_info(self):
1437  r"""get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1438  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1439  __swig_destroy__ = _IMP_npctransport.delete__DistancePairScoreForLinearSoftSphere
1440 
1441 # Register _DistancePairScoreForLinearSoftSphere in _IMP_npctransport:
1442 _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1443 class _DistancePairScoreForLinearInteraction(IMP.PairScore):
1444  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::npctransport::LinearInteractionScore > class."""
1445 
1446  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1447  __repr__ = _swig_repr
1448 
1449  def __init__(self, *args):
1450  r"""
1451  __init__(_DistancePairScoreForLinearInteraction self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _DistancePairScoreForLinearInteraction
1452  __init__(_DistancePairScoreForLinearInteraction self) -> _DistancePairScoreForLinearInteraction
1453  """
1454  _IMP_npctransport._DistancePairScoreForLinearInteraction_swiginit(self, _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args))
1455 
1456  def do_get_inputs(self, m, pis):
1457  r"""do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1458  return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1459 
1460  def get_score_functor(self):
1461  r"""get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1462  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1463 
1464  def get_version_info(self):
1465  r"""get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1466  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1467  __swig_destroy__ = _IMP_npctransport.delete__DistancePairScoreForLinearInteraction
1468 
1469 # Register _DistancePairScoreForLinearInteraction in _IMP_npctransport:
1470 _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1471 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1472  r"""Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1473 
1474  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1475 
1476  def __init__(self, *args):
1477  r"""__init__(FunctorLinearSoftSpherePairScore self, double k, std::string name="LinearSSPairScore%1%") -> FunctorLinearSoftSpherePairScore"""
1478  _IMP_npctransport.FunctorLinearSoftSpherePairScore_swiginit(self, _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args))
1479  __swig_destroy__ = _IMP_npctransport.delete_FunctorLinearSoftSpherePairScore
1480 
1481  def __str__(self):
1482  r"""__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1483  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1484 
1485  def __repr__(self):
1486  r"""__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1487  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1488 
1489  @staticmethod
1490  def get_from(o):
1491  return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1492 
1493 
1494 # Register FunctorLinearSoftSpherePairScore in _IMP_npctransport:
1495 _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1496 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1497  r"""Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1498 
1499  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1500 
1501  def __init__(self, *args):
1502  r"""__init__(FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name="LinearSSPairScore%1%") -> FunctorLinearInteractionPairScore"""
1503  _IMP_npctransport.FunctorLinearInteractionPairScore_swiginit(self, _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args))
1504  __swig_destroy__ = _IMP_npctransport.delete_FunctorLinearInteractionPairScore
1505 
1506  def __str__(self):
1507  r"""__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1508  return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1509 
1510  def __repr__(self):
1511  r"""__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1512  return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1513 
1514  @staticmethod
1515  def get_from(o):
1516  return _object_cast_to_FunctorLinearInteractionPairScore(o)
1517 
1518 
1519 # Register FunctorLinearInteractionPairScore in _IMP_npctransport:
1520 _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1521 class BrownianDynamicsTAMDWithSlabSupport(IMP.atom.BrownianDynamicsTAMD):
1522  r"""Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1523 
1524  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1525 
1526  def __init__(self, *args):
1527  r"""__init__(BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name="BrownianDynamicsTAMDWithSlabSupport%1%", double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport"""
1528  _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swiginit(self, _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args))
1529 
1530  def __str__(self):
1531  r"""__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1532  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1533 
1534  def __repr__(self):
1535  r"""__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1536  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1537 
1538  @staticmethod
1539  def get_from(o):
1540  return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1541 
1542  __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1543 
1544 # Register BrownianDynamicsTAMDWithSlabSupport in _IMP_npctransport:
1545 _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1546 class SitesPairScoreParameters(object):
1547  r"""Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1548 
1549  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1550  r = property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set, doc=r"""r : double""")
1551  k = property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set, doc=r"""k : double""")
1552  r2 = property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set, doc=r"""r2 : double""")
1553  kr = property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set, doc=r"""kr : double""")
1554  kr2 = property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set, doc=r"""kr2 : double""")
1555  cosSigma1_max = property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set, doc=r"""cosSigma1_max : double""")
1556  cosSigma2_max = property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set, doc=r"""cosSigma2_max : double""")
1557  is_orientational = property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set, doc=r"""is_orientational : bool""")
1558 
1559  def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1560  r"""__init__(SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters"""
1561  _IMP_npctransport.SitesPairScoreParameters_swiginit(self, _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg))
1562 
1563  def set_range(self, r):
1564  r"""set_range(SitesPairScoreParameters self, double r)"""
1565  return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1566 
1567  def set_force_coefficient(self, k):
1568  r"""set_force_coefficient(SitesPairScoreParameters self, double k)"""
1569  return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1570 
1571  def set_sigma1_max(self, sigma1_max_deg):
1572  r"""set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1573  return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1574 
1575  def set_sigma2_max(self, sigma2_max_deg):
1576  r"""set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1577  return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1578 
1579  def update_is_orientational(self):
1580  r"""update_is_orientational(SitesPairScoreParameters self)"""
1581  return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1582 
1583  def show(self, *args):
1584  r"""show(SitesPairScoreParameters self, _ostream out=std::cout)"""
1585  return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1586 
1587  def __str__(self):
1588  r"""__str__(SitesPairScoreParameters self) -> std::string"""
1589  return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1590 
1591  def __repr__(self):
1592  r"""__repr__(SitesPairScoreParameters self) -> std::string"""
1593  return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1594  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1595 
1596 # Register SitesPairScoreParameters in _IMP_npctransport:
1597 _IMP_npctransport.SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1598 class SitesGeometry(IMP.core.XYZRGeometry):
1599  r"""Proxy of C++ IMP::npctransport::SitesGeometry class."""
1600 
1601  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1602 
1603  def __init__(self, p, sites):
1604  r"""__init__(SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1605  _IMP_npctransport.SitesGeometry_swiginit(self, _IMP_npctransport.new_SitesGeometry(p, sites))
1606  __swig_destroy__ = _IMP_npctransport.delete_SitesGeometry
1607 
1608  def __str__(self):
1609  r"""__str__(SitesGeometry self) -> std::string"""
1610  return _IMP_npctransport.SitesGeometry___str__(self)
1611 
1612  def __repr__(self):
1613  r"""__repr__(SitesGeometry self) -> std::string"""
1614  return _IMP_npctransport.SitesGeometry___repr__(self)
1615 
1616  @staticmethod
1617  def get_from(o):
1618  return _object_cast_to_SitesGeometry(o)
1619 
1620 
1621 # Register SitesGeometry in _IMP_npctransport:
1622 _IMP_npctransport.SitesGeometry_swigregister(SitesGeometry)
1623 class TypedSitesGeometry(IMP.display.SingletonsGeometry):
1624  r"""Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1625 
1626  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1627 
1628  def __init__(self, sc):
1629  r"""__init__(TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1630  _IMP_npctransport.TypedSitesGeometry_swiginit(self, _IMP_npctransport.new_TypedSitesGeometry(sc))
1631 
1632  def set_sites(self, t, s):
1633  r"""set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1634  return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1635 
1636  def get_version_info(self):
1637  r"""get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1638  return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1639  __swig_destroy__ = _IMP_npctransport.delete_TypedSitesGeometry
1640 
1641  def __str__(self):
1642  r"""__str__(TypedSitesGeometry self) -> std::string"""
1643  return _IMP_npctransport.TypedSitesGeometry___str__(self)
1644 
1645  def __repr__(self):
1646  r"""__repr__(TypedSitesGeometry self) -> std::string"""
1647  return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1648 
1649  @staticmethod
1650  def get_from(o):
1651  return _object_cast_to_TypedSitesGeometry(o)
1652 
1653 
1654 # Register TypedSitesGeometry in _IMP_npctransport:
1655 _IMP_npctransport.TypedSitesGeometry_swigregister(TypedSitesGeometry)
1656 class SitesPairScore(LinearInteractionPairScore):
1657  r"""Proxy of C++ IMP::npctransport::SitesPairScore class."""
1658 
1659  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1660 
1661  def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1662  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"""
1663  _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))
1664 
1665  def get_sites_range(self):
1666  r"""get_sites_range(SitesPairScore self) -> double"""
1667  return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1668 
1669  def get_sites_k(self):
1670  r"""get_sites_k(SitesPairScore self) -> double"""
1671  return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1672 
1673  def get_parameters(self):
1674  r"""get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1675  return _IMP_npctransport.SitesPairScore_get_parameters(self)
1676  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScore
1677 
1678  def set_sites(self, sites0, sites1):
1679  r"""set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1680  return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1681 
1682  def set_sites0(self, sites0):
1683  r"""set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1684  return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1685 
1686  def set_sites1(self, sites1):
1687  r"""set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1688  return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1689 
1690  def __str__(self):
1691  r"""__str__(SitesPairScore self) -> std::string"""
1692  return _IMP_npctransport.SitesPairScore___str__(self)
1693 
1694  def __repr__(self):
1695  r"""__repr__(SitesPairScore self) -> std::string"""
1696  return _IMP_npctransport.SitesPairScore___repr__(self)
1697 
1698  @staticmethod
1699  def get_from(o):
1700  return _object_cast_to_SitesPairScore(o)
1701 
1702 
1703 # Register SitesPairScore in _IMP_npctransport:
1704 _IMP_npctransport.SitesPairScore_swigregister(SitesPairScore)
1705 class FGChain(IMP.Object):
1706  r"""Proxy of C++ IMP::npctransport::FGChain class."""
1707 
1708  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1709 
1710  def __init__(self, *args):
1711  r"""__init__(FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name="chain %1%") -> FGChain"""
1712  _IMP_npctransport.FGChain_swiginit(self, _IMP_npctransport.new_FGChain(*args))
1713 
1714  def get_root(self):
1715  r"""get_root(FGChain self) -> Hierarchy"""
1716  return _IMP_npctransport.FGChain_get_root(self)
1717 
1718  def get_beads(self):
1719  r"""get_beads(FGChain self) -> IMP::ParticlesTemp"""
1720  return _IMP_npctransport.FGChain_get_beads(self)
1721 
1722  def get_bead(self, i):
1723  r"""get_bead(FGChain self, unsigned int i) -> Particle"""
1724  return _IMP_npctransport.FGChain_get_bead(self, i)
1725 
1726  def get_bead_index(self, i):
1727  r"""get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1728  return _IMP_npctransport.FGChain_get_bead_index(self, i)
1729 
1730  def get_number_of_beads(self):
1731  r"""get_number_of_beads(FGChain self) -> unsigned int"""
1732  return _IMP_npctransport.FGChain_get_number_of_beads(self)
1733 
1734  def get_chain_restraints(self, scoring_manager):
1735  r"""get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1736  return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1737 
1738  def set_rest_length_factor(self, rlf):
1739  r"""set_rest_length_factor(FGChain self, double rlf)"""
1740  return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1741 
1742  def set_backbone_k(self, k):
1743  r"""set_backbone_k(FGChain self, double k)"""
1744  return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1745 
1746  def get_rest_length_factor(self):
1747  r"""get_rest_length_factor(FGChain self) -> double"""
1748  return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1749 
1750  def get_backbone_k(self):
1751  r"""get_backbone_k(FGChain self) -> double"""
1752  return _IMP_npctransport.FGChain_get_backbone_k(self)
1753 
1754  def get_version_info(self):
1755  r"""get_version_info(FGChain self) -> VersionInfo"""
1756  return _IMP_npctransport.FGChain_get_version_info(self)
1757  __swig_destroy__ = _IMP_npctransport.delete_FGChain
1758 
1759  def __str__(self):
1760  r"""__str__(FGChain self) -> std::string"""
1761  return _IMP_npctransport.FGChain___str__(self)
1762 
1763  def __repr__(self):
1764  r"""__repr__(FGChain self) -> std::string"""
1765  return _IMP_npctransport.FGChain___repr__(self)
1766 
1767  @staticmethod
1768  def get_from(o):
1769  return _object_cast_to_FGChain(o)
1770 
1771 
1772 # Register FGChain in _IMP_npctransport:
1773 _IMP_npctransport.FGChain_swigregister(FGChain)
1774 
1775 def create_fg_chain(sd, parent, fg_data, c):
1776  r"""create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1777  return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1778 
1779 def get_fg_chain(*args):
1780  r"""
1781  get_fg_chain(Hierarchy root) -> FGChain
1782  get_fg_chain(Particle p_root) -> FGChain
1783  """
1784  return _IMP_npctransport.get_fg_chain(*args)
1785 class Scoring(IMP.Object):
1786  r"""Proxy of C++ IMP::npctransport::Scoring class."""
1787 
1788  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1789 
1790  def __init__(self, owner_sd, data):
1791  r"""__init__(Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1792  _IMP_npctransport.Scoring_swiginit(self, _IMP_npctransport.new_Scoring(owner_sd, data))
1793 
1794  def get_scoring_function(self, force_update=False):
1795  r"""get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction"""
1796  return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1797 
1798  def get_scoring_function_restraints(self, force_update=False):
1799  r"""get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints"""
1800  return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1801 
1802  def get_custom_scoring_function(self, *args):
1803  r"""
1804  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
1805  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
1806  """
1807  return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1808 
1809  def get_close_beads_container(self, update=False):
1810  r"""get_close_beads_container(Scoring self, bool update=False) -> PairContainer"""
1811  return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1812 
1813  def get_predicates_pair_restraint(self, update=False):
1814  r"""get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint"""
1815  return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1816 
1817  def get_bounding_volume_restraint(self, update=False):
1818  r"""get_bounding_volume_restraint(Scoring self, bool update=False) -> Restraint"""
1819  return _IMP_npctransport.Scoring_get_bounding_volume_restraint(self, update)
1820 
1821  def get_slab_restraint(self, update=False):
1822  r"""get_slab_restraint(Scoring self, bool update=False) -> Restraint"""
1823  return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1824 
1825  def add_interaction(self, idata):
1826  r"""add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1827  return _IMP_npctransport.Scoring_add_interaction(self, idata)
1828 
1829  def create_close_beads_container(self, *args):
1830  r"""
1831  create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1832  create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1833  """
1834  return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
1835 
1836  def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
1837  r"""create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint"""
1838  return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
1839 
1840  def create_bounding_volume_restraint(self, beads):
1841  r"""create_bounding_volume_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1842  return _IMP_npctransport.Scoring_create_bounding_volume_restraint(self, beads)
1843 
1844  def create_slab_restraint(self, beads):
1845  r"""create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1846  return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
1847 
1848  def get_model(self):
1849  r"""get_model(Scoring self) -> Model"""
1850  return _IMP_npctransport.Scoring_get_model(self)
1851 
1852  def get_sd(self):
1853  r"""get_sd(Scoring self) -> SimulationData"""
1854  return _IMP_npctransport.Scoring_get_sd(self)
1855 
1856  def get_has_bounding_box(self):
1857  r"""get_has_bounding_box(Scoring self) -> bool"""
1858  return _IMP_npctransport.Scoring_get_has_bounding_box(self)
1859 
1860  def get_has_bounding_sphere(self):
1861  r"""get_has_bounding_sphere(Scoring self) -> bool"""
1862  return _IMP_npctransport.Scoring_get_has_bounding_sphere(self)
1863 
1864  def get_has_bounding_volume(self):
1865  r"""get_has_bounding_volume(Scoring self) -> bool"""
1866  return _IMP_npctransport.Scoring_get_has_bounding_volume(self)
1867 
1868  def get_default_backbone_k(self):
1869  r"""get_default_backbone_k(Scoring self) -> double"""
1870  return _IMP_npctransport.Scoring_get_default_backbone_k(self)
1871 
1872  def get_is_backbone_harmonic(self):
1873  r"""get_is_backbone_harmonic(Scoring self) -> bool"""
1874  return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
1875 
1876  def get_excluded_volume_k(self):
1877  r"""get_excluded_volume_k(Scoring self) -> double"""
1878  return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
1879 
1880  def get_interaction_k(self):
1881  r"""get_interaction_k(Scoring self) -> double"""
1882  return _IMP_npctransport.Scoring_get_interaction_k(self)
1883 
1884  def get_predicate_pair_score(self, *args):
1885  r"""
1886  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1887  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1888  """
1889  return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
1890 
1891  def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
1892  r"""get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double"""
1893  return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
1894 
1895  def get_ordered_type_pair_predicate(self):
1896  r"""get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
1897  return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
1898 
1899  def add_chain_restraints(self, chain):
1900  r"""add_chain_restraints(Scoring self, FGChain chain)"""
1901  return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
1902 
1903  def get_chain_restraints_on(self, beads):
1904  r"""get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
1905  return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
1906 
1907  def get_all_chain_restraints(self):
1908  r"""get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
1909  return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
1910 
1911  def remove_particle_type(self, pt):
1912  r"""remove_particle_type(Scoring self, ParticleType pt)"""
1913  return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
1914 
1915  def add_z_bias_restraint(self, *args):
1916  r"""
1917  add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
1918  add_z_bias_restraint(Scoring self, Particle p, double k)
1919  """
1920  return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
1921 
1922  def get_z_bias_restraints(self):
1923  r"""get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
1924  return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
1925 
1926  def create_z_bias_restraint(self, ps, k):
1927  r"""create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
1928  return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
1929 
1930  def add_custom_restraint(self, r):
1931  r"""add_custom_restraint(Scoring self, Restraint r)"""
1932  return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
1933 
1934  def add_custom_restraints(self, R):
1935  r"""add_custom_restraints(Scoring self, IMP::Restraints R)"""
1936  return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
1937 
1938  def clear_custom_restraints(self):
1939  r"""clear_custom_restraints(Scoring self)"""
1940  return _IMP_npctransport.Scoring_clear_custom_restraints(self)
1941 
1942  def get_custom_restraints(self):
1943  r"""get_custom_restraints(Scoring self) -> IMP::Restraints"""
1944  return _IMP_npctransport.Scoring_get_custom_restraints(self)
1945 
1946  def add_restrained_anchor_bead(self, p):
1947  r"""add_restrained_anchor_bead(Scoring self, Particle p)"""
1948  return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
1949 
1950  def get_pore_radius_restraint(self):
1951  r"""get_pore_radius_restraint(Scoring self) -> Restraint"""
1952  return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
1953 
1954  def get_range(self):
1955  r"""get_range(Scoring self) -> double"""
1956  return _IMP_npctransport.Scoring_get_range(self)
1957 
1958  def set_interaction_range_factor(self, type, value):
1959  r"""set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
1960  return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
1961 
1962  def set_interaction_k_factor(self, type, value):
1963  r"""set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
1964  return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
1965 
1966  def get_version_info(self):
1967  r"""get_version_info(Scoring self) -> VersionInfo"""
1968  return _IMP_npctransport.Scoring_get_version_info(self)
1969  __swig_destroy__ = _IMP_npctransport.delete_Scoring
1970 
1971  def __str__(self):
1972  r"""__str__(Scoring self) -> std::string"""
1973  return _IMP_npctransport.Scoring___str__(self)
1974 
1975  def __repr__(self):
1976  r"""__repr__(Scoring self) -> std::string"""
1977  return _IMP_npctransport.Scoring___repr__(self)
1978 
1979  @staticmethod
1980  def get_from(o):
1981  return _object_cast_to_Scoring(o)
1982 
1983 
1984 # Register Scoring in _IMP_npctransport:
1985 _IMP_npctransport.Scoring_swigregister(Scoring)
1986 class SimpleTimer(object):
1987  r"""Proxy of C++ IMP::internal::SimpleTimer class."""
1988 
1989  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1990  __repr__ = _swig_repr
1991 
1992  def __init__(self):
1993  r"""__init__(SimpleTimer self) -> SimpleTimer"""
1994  _IMP_npctransport.SimpleTimer_swiginit(self, _IMP_npctransport.new_SimpleTimer())
1995  __swig_destroy__ = _IMP_npctransport.delete_SimpleTimer
1996 
1997 # Register SimpleTimer in _IMP_npctransport:
1998 _IMP_npctransport.SimpleTimer_swigregister(SimpleTimer)
1999 class Statistics(IMP.Object):
2000  r"""Proxy of C++ IMP::npctransport::Statistics class."""
2001 
2002  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2003 
2004  def remove_particle_type(self, pt):
2005  r"""remove_particle_type(Statistics self, ParticleType pt)"""
2006  return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2007 
2008  def __init__(self, sd, statistics_interval_frames, output_file_name):
2009  r"""__init__(Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2010  _IMP_npctransport.Statistics_swiginit(self, _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name))
2011 
2012  def add_fg_chain_stats(self, fg_chain):
2013  r"""add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2014  return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2015 
2016  def add_floater_stats(self, p):
2017  r"""add_floater_stats(Statistics self, Particle p)"""
2018  return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2019 
2020  def add_interaction_stats(self, type0, type1):
2021  r"""add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2022  return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2023 
2024  def add_optimizer_states(self, o=None):
2025  r"""add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates"""
2026  return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2027 
2028  def update_particle_type_zr_distribution_map(self, p):
2029  r"""update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2030  return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2031 
2032  def update_particle_type_xyz_distribution_map(self, p):
2033  r"""update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2034  return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2035 
2036  def update(self, timer, nf_new=1):
2037  r"""update(Statistics self, SimpleTimer timer, unsigned int nf_new=1)"""
2038  return _IMP_npctransport.Statistics_update(self, timer, nf_new)
2039 
2040  def reset_statistics_optimizer_states(self):
2041  r"""reset_statistics_optimizer_states(Statistics self)"""
2042  return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2043 
2044  def set_interrupted(self, tf):
2045  r"""set_interrupted(Statistics self, bool tf)"""
2046  return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2047 
2048  def get_model(self):
2049  r"""get_model(Statistics self) -> Model"""
2050  return _IMP_npctransport.Statistics_get_model(self)
2051 
2052  def get_sd(self):
2053  r"""get_sd(Statistics self) -> SimulationData"""
2054  return _IMP_npctransport.Statistics_get_sd(self)
2055 
2056  def get_is_activated(self):
2057  r"""get_is_activated(Statistics self) -> bool"""
2058  return _IMP_npctransport.Statistics_get_is_activated(self)
2059 
2060  def get_output_file_name(self):
2061  r"""get_output_file_name(Statistics self) -> std::string"""
2062  return _IMP_npctransport.Statistics_get_output_file_name(self)
2063 
2064  def get_version_info(self):
2065  r"""get_version_info(Statistics self) -> VersionInfo"""
2066  return _IMP_npctransport.Statistics_get_version_info(self)
2067  __swig_destroy__ = _IMP_npctransport.delete_Statistics
2068 
2069  def __str__(self):
2070  r"""__str__(Statistics self) -> std::string"""
2071  return _IMP_npctransport.Statistics___str__(self)
2072 
2073  def __repr__(self):
2074  r"""__repr__(Statistics self) -> std::string"""
2075  return _IMP_npctransport.Statistics___repr__(self)
2076 
2077  @staticmethod
2078  def get_from(o):
2079  return _object_cast_to_Statistics(o)
2080 
2081 
2082 # Register Statistics in _IMP_npctransport:
2083 _IMP_npctransport.Statistics_swigregister(Statistics)
2084 
2085 def create_boost_timer():
2086  r"""create_boost_timer() -> SimpleTimer"""
2087  return _IMP_npctransport.create_boost_timer()
2088 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2089 
2090 class SimulationData(IMP.Object):
2091  r"""Proxy of C++ IMP::npctransport::SimulationData class."""
2092 
2093  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2094 
2095  def get_output_npctransport_version(self):
2096  r"""get_output_npctransport_version(SimulationData self) -> double"""
2097  return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2098 
2099  def get_range(self):
2100  r"""get_range(SimulationData self) -> double"""
2101  return _IMP_npctransport.SimulationData_get_range(self)
2102 
2103  def get_output_statistics_interval_frames(self):
2104  r"""get_output_statistics_interval_frames(SimulationData self) -> int"""
2105  return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2106 
2107  def get_is_exclude_floaters_from_slab_initially(self):
2108  r"""get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2109  return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2110 
2111  def get_are_floaters_on_one_slab_side(self):
2112  r"""get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2113  return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2114 
2115  def get_is_xyz_hist_stats(self):
2116  r"""get_is_xyz_hist_stats(SimulationData self) -> bool"""
2117  return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2118 
2119  def get_angular_d_factor(self):
2120  r"""get_angular_d_factor(SimulationData self) -> double"""
2121  return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2122 
2123  def __init__(self, *args):
2124  r"""__init__(SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name=std::string(), std::string new_output_file="") -> SimulationData"""
2125  _IMP_npctransport.SimulationData_swiginit(self, _IMP_npctransport.new_SimulationData(*args))
2126 
2127  def get_model(self):
2128  r"""get_model(SimulationData self) -> Model"""
2129  return _IMP_npctransport.SimulationData_get_model(self)
2130 
2131  def get_scoring(self):
2132  r"""get_scoring(SimulationData self) -> Scoring"""
2133  return _IMP_npctransport.SimulationData_get_scoring(self)
2134 
2135  def get_statistics(self):
2136  r"""get_statistics(SimulationData self) -> Statistics"""
2137  return _IMP_npctransport.SimulationData_get_statistics(self)
2138 
2139  def get_bd(self, recreate=False):
2140  r"""get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics"""
2141  return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2142 
2143  def activate_statistics(self):
2144  r"""activate_statistics(SimulationData self)"""
2145  return _IMP_npctransport.SimulationData_activate_statistics(self)
2146 
2147  def get_statistics_fraction(self):
2148  r"""get_statistics_fraction(SimulationData self) -> double"""
2149  return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2150 
2151  def get_is_fg_bead(self, *args):
2152  r"""
2153  get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2154  get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2155  """
2156  return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2157 
2158  def get_is_fg_chain(self, *args):
2159  r"""
2160  get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2161  get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2162  """
2163  return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2164 
2165  def get_fg_bead_types(self):
2166  r"""get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2167  return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2168 
2169  def get_fg_chain_types(self):
2170  r"""get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2171  return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2172 
2173  def get_floater_types(self):
2174  r"""get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2175  return _IMP_npctransport.SimulationData_get_floater_types(self)
2176 
2177  def get_obstacle_types(self):
2178  r"""get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2179  return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2180 
2181  def get_fg_chain_roots(self):
2182  r"""get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2183  return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2184 
2185  def get_fg_chains(self):
2186  r"""get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2187  return _IMP_npctransport.SimulationData_get_fg_chains(self)
2188 
2189  def get_obstacle_particles(self):
2190  r"""get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2191  return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2192 
2193  def get_beads(self):
2194  r"""get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2195  return _IMP_npctransport.SimulationData_get_beads(self)
2196 
2197  def get_optimizable_beads(self):
2198  r"""get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2199  return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2200 
2201  def get_non_optimizable_beads(self):
2202  r"""get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2203  return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2204 
2205  def get_is_backbone_harmonic(self):
2206  r"""get_is_backbone_harmonic(SimulationData self) -> bool"""
2207  return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2208 
2209  def get_backbone_tau_ns(self):
2210  r"""get_backbone_tau_ns(SimulationData self) -> double"""
2211  return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2212 
2213  def get_temperature_k(self):
2214  r"""get_temperature_k(SimulationData self) -> double"""
2215  return _IMP_npctransport.SimulationData_get_temperature_k(self)
2216 
2217  def get_initial_simulation_time_ns(self):
2218  r"""get_initial_simulation_time_ns(SimulationData self) -> double"""
2219  return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2220 
2221  def get_site_centers(self, t0):
2222  r"""get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2223  return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2224 
2225  def get_sites(self, t0):
2226  r"""get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2227  return _IMP_npctransport.SimulationData_get_sites(self, t0)
2228 
2229  def set_sites(self, *args):
2230  r"""
2231  set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2232  set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2233  """
2234  return _IMP_npctransport.SimulationData_set_sites(self, *args)
2235 
2236  def get_site_display_radius(self, arg2):
2237  r"""get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2238  return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2239 
2240  def get_maximum_number_of_minutes(self):
2241  r"""get_maximum_number_of_minutes(SimulationData self) -> double"""
2242  return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2243 
2244  def remove_particle_type(self, pt):
2245  r"""remove_particle_type(SimulationData self, ParticleType pt)"""
2246  return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2247 
2248  def remove_fgs_with_prefix(self, s_fg_type):
2249  r"""remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2250  return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2251 
2252  def get_bounding_box(self):
2253  r"""get_bounding_box(SimulationData self) -> BoundingBox3D"""
2254  return _IMP_npctransport.SimulationData_get_bounding_box(self)
2255 
2256  def get_bounding_sphere(self):
2257  r"""get_bounding_sphere(SimulationData self) -> Sphere3D"""
2258  return _IMP_npctransport.SimulationData_get_bounding_sphere(self)
2259 
2260  def get_bounding_box_size(self):
2261  r"""get_bounding_box_size(SimulationData self) -> double"""
2262  return _IMP_npctransport.SimulationData_get_bounding_box_size(self)
2263 
2264  def set_bounding_box_size(self, box_size):
2265  r"""set_bounding_box_size(SimulationData self, double box_size)"""
2266  return _IMP_npctransport.SimulationData_set_bounding_box_size(self, box_size)
2267 
2268  def get_bounding_sphere_radius(self):
2269  r"""get_bounding_sphere_radius(SimulationData self) -> double"""
2270  return _IMP_npctransport.SimulationData_get_bounding_sphere_radius(self)
2271 
2272  def set_bounding_sphere_radius(self, sphere_radius):
2273  r"""set_bounding_sphere_radius(SimulationData self, double sphere_radius)"""
2274  return _IMP_npctransport.SimulationData_set_bounding_sphere_radius(self, sphere_radius)
2275 
2276  def get_bounding_volume(self):
2277  r"""get_bounding_volume(SimulationData self) -> double"""
2278  return _IMP_npctransport.SimulationData_get_bounding_volume(self)
2279 
2280  def set_bounding_volume(self, volume_A3):
2281  r"""set_bounding_volume(SimulationData self, double volume_A3)"""
2282  return _IMP_npctransport.SimulationData_set_bounding_volume(self, volume_A3)
2283 
2284  def get_has_slab(self):
2285  r"""get_has_slab(SimulationData self) -> bool"""
2286  return _IMP_npctransport.SimulationData_get_has_slab(self)
2287 
2288  def get_is_slab_with_cylindrical_pore(self):
2289  r"""get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2290  return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2291 
2292  def get_is_slab_with_toroidal_pore(self):
2293  r"""get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2294  return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2295 
2296  def get_slab_particle(self):
2297  r"""get_slab_particle(SimulationData self) -> Particle"""
2298  return _IMP_npctransport.SimulationData_get_slab_particle(self)
2299 
2300  def get_cylinder(self):
2301  r"""get_cylinder(SimulationData self) -> Cylinder3D"""
2302  return _IMP_npctransport.SimulationData_get_cylinder(self)
2303 
2304  def get_has_bounding_box(self):
2305  r"""get_has_bounding_box(SimulationData self) -> bool"""
2306  return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2307 
2308  def get_has_bounding_sphere(self):
2309  r"""get_has_bounding_sphere(SimulationData self) -> bool"""
2310  return _IMP_npctransport.SimulationData_get_has_bounding_sphere(self)
2311 
2312  def get_has_bounding_volume(self):
2313  r"""get_has_bounding_volume(SimulationData self) -> bool"""
2314  return _IMP_npctransport.SimulationData_get_has_bounding_volume(self)
2315 
2316  def initialize_positions_from_rmf(self, fh, frame_number=-1):
2317  r"""initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)"""
2318  return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2319 
2320  def link_rmf_file_handle(self, fh, is_restraints=True):
2321  r"""link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)"""
2322  return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2323 
2324  def get_rmf_sos_writer(self):
2325  r"""get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2326  return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2327 
2328  def reset_rmf(self):
2329  r"""reset_rmf(SimulationData self)"""
2330  return _IMP_npctransport.SimulationData_reset_rmf(self)
2331 
2332  def switch_suspend_rmf(self, suspend):
2333  r"""switch_suspend_rmf(SimulationData self, bool suspend)"""
2334  return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2335 
2336  def write_geometry(self, out):
2337  r"""write_geometry(SimulationData self, std::string out)"""
2338  return _IMP_npctransport.SimulationData_write_geometry(self, out)
2339 
2340  def dump_geometry(self):
2341  r"""dump_geometry(SimulationData self)"""
2342  return _IMP_npctransport.SimulationData_dump_geometry(self)
2343 
2344  def get_root_of_type(self, type):
2345  r"""get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2346  return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2347 
2348  def get_number_of_frames(self):
2349  r"""get_number_of_frames(SimulationData self) -> unsigned int"""
2350  return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2351 
2352  def get_number_of_trials(self):
2353  r"""get_number_of_trials(SimulationData self) -> unsigned int"""
2354  return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2355 
2356  def get_root(self):
2357  r"""get_root(SimulationData self) -> Hierarchy"""
2358  return _IMP_npctransport.SimulationData_get_root(self)
2359 
2360  def get_slab_thickness(self):
2361  r"""get_slab_thickness(SimulationData self) -> double"""
2362  return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2363 
2364  def get_tunnel_radius(self):
2365  r"""get_tunnel_radius(SimulationData self) -> double"""
2366  return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2367 
2368  def get_pore_radius(self):
2369  r"""get_pore_radius(SimulationData self) -> double"""
2370  return _IMP_npctransport.SimulationData_get_pore_radius(self)
2371 
2372  def get_tunnel_radius_k(self):
2373  r"""get_tunnel_radius_k(SimulationData self) -> double"""
2374  return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2375 
2376  def get_pore_radius_k(self):
2377  r"""get_pore_radius_k(SimulationData self) -> double"""
2378  return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2379 
2380  def get_is_pore_radius_dynamic(self):
2381  r"""get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2382  return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2383 
2384  def get_pore_anchored_beads_k(self):
2385  r"""get_pore_anchored_beads_k(SimulationData self) -> double"""
2386  return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2387 
2388  def get_static_geometry(self):
2389  r"""get_static_geometry(SimulationData self) -> Geometry"""
2390  return _IMP_npctransport.SimulationData_get_static_geometry(self)
2391 
2392  def get_rmf_dump_interval_frames(self):
2393  r"""get_rmf_dump_interval_frames(SimulationData self) -> int"""
2394  return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2395 
2396  def get_rmf_file_name(self):
2397  r"""get_rmf_file_name(SimulationData self) -> std::string"""
2398  return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2399 
2400  def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2401  r"""set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)"""
2402  return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2403 
2404  def get_version_info(self):
2405  r"""get_version_info(SimulationData self) -> VersionInfo"""
2406  return _IMP_npctransport.SimulationData_get_version_info(self)
2407  __swig_destroy__ = _IMP_npctransport.delete_SimulationData
2408 
2409  def __str__(self):
2410  r"""__str__(SimulationData self) -> std::string"""
2411  return _IMP_npctransport.SimulationData___str__(self)
2412 
2413  def __repr__(self):
2414  r"""__repr__(SimulationData self) -> std::string"""
2415  return _IMP_npctransport.SimulationData___repr__(self)
2416 
2417  @staticmethod
2418  def get_from(o):
2419  return _object_cast_to_SimulationData(o)
2420 
2421 
2422 # Register SimulationData in _IMP_npctransport:
2423 _IMP_npctransport.SimulationData_swigregister(SimulationData)
2424 
2425 def get_simulation_data_key():
2426  r"""get_simulation_data_key() -> IMP::WeakObjectKey"""
2427  return _IMP_npctransport.get_simulation_data_key()
2428 
2429 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2430  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)"""
2431  return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2432 class ParticleFactory(IMP.Object):
2433  r"""Proxy of C++ IMP::npctransport::ParticleFactory class."""
2434 
2435  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2436  sd_ = property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set, doc=r"""sd_ : IMP::WeakPointer<(IMP::npctransport::SimulationData)>""")
2437  radius_ = property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set, doc=r"""radius_ : double""")
2438  D_factor_ = property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set, doc=r"""D_factor_ : double""")
2439  angular_D_factor_ = property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set, doc=r"""angular_D_factor_ : double""")
2440  color_ = property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set, doc=r"""color_ : IMP::display::Color""")
2441  type_ = property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set, doc=r"""type_ : IMP::core::ParticleType""")
2442 
2443  def __init__(self, *args):
2444  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"""
2445  _IMP_npctransport.ParticleFactory_swiginit(self, _IMP_npctransport.new_ParticleFactory(*args))
2446 
2447  def create(self, *args):
2448  r"""create(ParticleFactory self, std::string name="") -> Particle"""
2449  return _IMP_npctransport.ParticleFactory_create(self, *args)
2450 
2451  def get_model(self):
2452  r"""get_model(ParticleFactory self) -> Model"""
2453  return _IMP_npctransport.ParticleFactory_get_model(self)
2454 
2455  def get_simulation_data(self):
2456  r"""get_simulation_data(ParticleFactory self) -> SimulationData"""
2457  return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2458 
2459  def get_radius(self):
2460  r"""get_radius(ParticleFactory self) -> double"""
2461  return _IMP_npctransport.ParticleFactory_get_radius(self)
2462 
2463  def get_version_info(self):
2464  r"""get_version_info(ParticleFactory self) -> VersionInfo"""
2465  return _IMP_npctransport.ParticleFactory_get_version_info(self)
2466  __swig_destroy__ = _IMP_npctransport.delete_ParticleFactory
2467 
2468  def __str__(self):
2469  r"""__str__(ParticleFactory self) -> std::string"""
2470  return _IMP_npctransport.ParticleFactory___str__(self)
2471 
2472  def __repr__(self):
2473  r"""__repr__(ParticleFactory self) -> std::string"""
2474  return _IMP_npctransport.ParticleFactory___repr__(self)
2475 
2476  @staticmethod
2477  def get_from(o):
2478  return _object_cast_to_ParticleFactory(o)
2479 
2480 
2481 # Register ParticleFactory in _IMP_npctransport:
2482 _IMP_npctransport.ParticleFactory_swigregister(ParticleFactory)
2483 class HierarchyWithSitesLoadLink(IMP.rmf.HierarchyLoadLink):
2484  r"""Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2485 
2486  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2487 
2488  def __init__(self, fh):
2489  r"""__init__(HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2490  _IMP_npctransport.HierarchyWithSitesLoadLink_swiginit(self, _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh))
2491 
2492  @staticmethod
2493  def get_name():
2494  r"""get_name() -> char const *"""
2495  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2496 
2497  def __str__(self):
2498  r"""__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2499  return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2500 
2501  def __repr__(self):
2502  r"""__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2503  return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2504 
2505  @staticmethod
2506  def get_from(o):
2507  return _object_cast_to_HierarchyWithSitesLoadLink(o)
2508 
2509  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2510 
2511 # Register HierarchyWithSitesLoadLink in _IMP_npctransport:
2512 _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2513 class HierarchyWithSitesSaveLink(IMP.rmf.HierarchySaveLink):
2514  r"""Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2515 
2516  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2517 
2518  def __init__(self, fh):
2519  r"""__init__(HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2520  _IMP_npctransport.HierarchyWithSitesSaveLink_swiginit(self, _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh))
2521 
2522  @staticmethod
2523  def get_name():
2524  r"""get_name() -> char const *"""
2525  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2526 
2527  def __str__(self):
2528  r"""__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2529  return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2530 
2531  def __repr__(self):
2532  r"""__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2533  return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2534 
2535  @staticmethod
2536  def get_from(o):
2537  return _object_cast_to_HierarchyWithSitesSaveLink(o)
2538 
2539  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2540 
2541 # Register HierarchyWithSitesSaveLink in _IMP_npctransport:
2542 _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2543 
2544 def add_test_sites(*args):
2545  r"""
2546  add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2547  add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2548  """
2549  return _IMP_npctransport.add_test_sites(*args)
2550 
2551 def add_hierarchies_with_sites(*args):
2552  r"""
2553  add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2554  add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2555  """
2556  return _IMP_npctransport.add_hierarchies_with_sites(*args)
2557 
2558 def add_hierarchy_with_sites(fh, hs):
2559  r"""add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2560  return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2561 
2563  r"""create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2564  return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2565 
2566 def link_hierarchies_with_sites(fh, hs):
2567  r"""link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2568  return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2569 class Transporting(IMP.Decorator):
2570  r"""Proxy of C++ IMP::npctransport::Transporting class."""
2571 
2572  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2573 
2574  def __init__(self, *args):
2575  r"""
2576  __init__(Transporting self) -> Transporting
2577  __init__(Transporting self, Model m, ParticleIndex id) -> Transporting
2578  __init__(Transporting self, _ParticleAdaptor d) -> Transporting
2579  """
2580  _IMP_npctransport.Transporting_swiginit(self, _IMP_npctransport.new_Transporting(*args))
2581 
2582  def show(self, *args):
2583  r"""show(Transporting self, _ostream out=std::cout)"""
2584  return _IMP_npctransport.Transporting_show(self, *args)
2585 
2586  @staticmethod
2587  def setup_particle(*args):
2588  r"""
2589  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2590  setup_particle(_ParticleAdaptor pa, bool is_last_entry_from_top=False) -> Transporting
2591  """
2592  return _IMP_npctransport.Transporting_setup_particle(*args)
2593 
2594  @staticmethod
2595  def get_is_setup(*args):
2596  r"""
2597  get_is_setup(_ParticleAdaptor p) -> bool
2598  get_is_setup(Model m, ParticleIndex pi) -> bool
2599  """
2600  return _IMP_npctransport.Transporting_get_is_setup(*args)
2601 
2602  def set_is_last_entry_from_top(self, is_last_entry_from_top):
2603  r"""set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2604  return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2605 
2606  def get_is_last_entry_from_top(self):
2607  r"""get_is_last_entry_from_top(Transporting self) -> bool"""
2608  return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2609 
2610  @staticmethod
2611  def get_is_last_entry_from_top_key():
2612  r"""get_is_last_entry_from_top_key() -> IntKey"""
2613  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
2614 
2615  def set_last_tracked_z(self, last_tracked_z):
2616  r"""set_last_tracked_z(Transporting self, double last_tracked_z)"""
2617  return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
2618 
2619  def get_last_tracked_z(self):
2620  r"""get_last_tracked_z(Transporting self) -> double"""
2621  return _IMP_npctransport.Transporting_get_last_tracked_z(self)
2622 
2623  @staticmethod
2624  def get_last_tracked_z_key():
2625  r"""get_last_tracked_z_key() -> FloatKey"""
2626  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
2627 
2628  def set_n_entries_bottom(self, n):
2629  r"""set_n_entries_bottom(Transporting self, int n)"""
2630  return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
2631 
2632  def get_n_entries_bottom(self):
2633  r"""get_n_entries_bottom(Transporting self) -> int"""
2634  return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
2635 
2636  @staticmethod
2637  def get_n_entries_bottom_key():
2638  r"""get_n_entries_bottom_key() -> IntKey"""
2639  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
2640 
2641  def set_n_entries_top(self, n):
2642  r"""set_n_entries_top(Transporting self, int n)"""
2643  return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
2644 
2645  def get_n_entries_top(self):
2646  r"""get_n_entries_top(Transporting self) -> int"""
2647  return _IMP_npctransport.Transporting_get_n_entries_top(self)
2648 
2649  @staticmethod
2650  def get_n_entries_top_key():
2651  r"""get_n_entries_top_key() -> IntKey"""
2652  return _IMP_npctransport.Transporting_get_n_entries_top_key()
2653 
2654  def add_attribute(self, *args):
2655  r"""
2656  add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
2657  add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
2658  add_attribute(Transporting self, IntKey a0, IMP::Int a1)
2659  add_attribute(Transporting self, FloatsKey a0, IMP::Floats a1)
2660  add_attribute(Transporting self, IntsKey a0, IMP::Ints a1)
2661  add_attribute(Transporting self, StringKey a0, IMP::String a1)
2662  add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
2663  add_attribute(Transporting self, ObjectKey a0, Object a1)
2664  """
2665  return _IMP_npctransport.Transporting_add_attribute(self, *args)
2666 
2667  def get_value(self, *args):
2668  r"""
2669  get_value(Transporting self, FloatKey a0) -> IMP::Float
2670  get_value(Transporting self, IntKey a0) -> IMP::Int
2671  get_value(Transporting self, FloatsKey a0) -> IMP::Floats
2672  get_value(Transporting self, IntsKey a0) -> IMP::Ints
2673  get_value(Transporting self, StringKey a0) -> IMP::String
2674  get_value(Transporting self, ParticleIndexKey a0) -> Particle
2675  get_value(Transporting self, ObjectKey a0) -> Object
2676  """
2677  return _IMP_npctransport.Transporting_get_value(self, *args)
2678 
2679  def set_value(self, *args):
2680  r"""
2681  set_value(Transporting self, FloatKey a0, IMP::Float a1)
2682  set_value(Transporting self, IntKey a0, IMP::Int a1)
2683  set_value(Transporting self, FloatsKey a0, IMP::Floats a1)
2684  set_value(Transporting self, IntsKey a0, IMP::Ints a1)
2685  set_value(Transporting self, StringKey a0, IMP::String a1)
2686  set_value(Transporting self, ParticleIndexKey a0, Particle a1)
2687  set_value(Transporting self, ObjectKey a0, Object a1)
2688  """
2689  return _IMP_npctransport.Transporting_set_value(self, *args)
2690 
2691  def remove_attribute(self, *args):
2692  r"""
2693  remove_attribute(Transporting self, FloatKey a0)
2694  remove_attribute(Transporting self, IntKey a0)
2695  remove_attribute(Transporting self, FloatsKey a0)
2696  remove_attribute(Transporting self, IntsKey a0)
2697  remove_attribute(Transporting self, StringKey a0)
2698  remove_attribute(Transporting self, ParticleIndexKey a0)
2699  remove_attribute(Transporting self, ObjectKey a0)
2700  """
2701  return _IMP_npctransport.Transporting_remove_attribute(self, *args)
2702 
2703  def has_attribute(self, *args):
2704  r"""
2705  has_attribute(Transporting self, FloatKey a0) -> bool
2706  has_attribute(Transporting self, IntKey a0) -> bool
2707  has_attribute(Transporting self, FloatsKey a0) -> bool
2708  has_attribute(Transporting self, IntsKey a0) -> bool
2709  has_attribute(Transporting self, StringKey a0) -> bool
2710  has_attribute(Transporting self, ParticleIndexKey a0) -> bool
2711  has_attribute(Transporting self, ObjectKey a0) -> bool
2712  """
2713  return _IMP_npctransport.Transporting_has_attribute(self, *args)
2714 
2715  def get_derivative(self, a0):
2716  r"""get_derivative(Transporting self, FloatKey a0) -> double"""
2717  return _IMP_npctransport.Transporting_get_derivative(self, a0)
2718 
2719  def get_name(self):
2720  r"""get_name(Transporting self) -> std::string"""
2721  return _IMP_npctransport.Transporting_get_name(self)
2722 
2723  def clear_caches(self):
2724  r"""clear_caches(Transporting self)"""
2725  return _IMP_npctransport.Transporting_clear_caches(self)
2726 
2727  def set_name(self, a0):
2728  r"""set_name(Transporting self, std::string a0)"""
2729  return _IMP_npctransport.Transporting_set_name(self, a0)
2730 
2731  def set_check_level(self, a0):
2732  r"""set_check_level(Transporting self, IMP::CheckLevel a0)"""
2733  return _IMP_npctransport.Transporting_set_check_level(self, a0)
2734 
2735  def add_to_derivative(self, a0, a1, a2):
2736  r"""add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2737  return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
2738 
2739  def set_is_optimized(self, a0, a1):
2740  r"""set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
2741  return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
2742 
2743  def get_is_optimized(self, a0):
2744  r"""get_is_optimized(Transporting self, FloatKey a0) -> bool"""
2745  return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
2746 
2747  def get_check_level(self):
2748  r"""get_check_level(Transporting self) -> IMP::CheckLevel"""
2749  return _IMP_npctransport.Transporting_get_check_level(self)
2750 
2751  def __eq__(self, *args):
2752  r"""
2753  __eq__(Transporting self, Transporting o) -> bool
2754  __eq__(Transporting self, Particle d) -> bool
2755  """
2756  return _IMP_npctransport.Transporting___eq__(self, *args)
2757 
2758  def __ne__(self, *args):
2759  r"""
2760  __ne__(Transporting self, Transporting o) -> bool
2761  __ne__(Transporting self, Particle d) -> bool
2762  """
2763  return _IMP_npctransport.Transporting___ne__(self, *args)
2764 
2765  def __le__(self, *args):
2766  r"""
2767  __le__(Transporting self, Transporting o) -> bool
2768  __le__(Transporting self, Particle d) -> bool
2769  """
2770  return _IMP_npctransport.Transporting___le__(self, *args)
2771 
2772  def __lt__(self, *args):
2773  r"""
2774  __lt__(Transporting self, Transporting o) -> bool
2775  __lt__(Transporting self, Particle d) -> bool
2776  """
2777  return _IMP_npctransport.Transporting___lt__(self, *args)
2778 
2779  def __ge__(self, *args):
2780  r"""
2781  __ge__(Transporting self, Transporting o) -> bool
2782  __ge__(Transporting self, Particle d) -> bool
2783  """
2784  return _IMP_npctransport.Transporting___ge__(self, *args)
2785 
2786  def __gt__(self, *args):
2787  r"""
2788  __gt__(Transporting self, Transporting o) -> bool
2789  __gt__(Transporting self, Particle d) -> bool
2790  """
2791  return _IMP_npctransport.Transporting___gt__(self, *args)
2792 
2793  def __hash__(self):
2794  r"""__hash__(Transporting self) -> std::size_t"""
2795  return _IMP_npctransport.Transporting___hash__(self)
2796 
2797  def __str__(self):
2798  r"""__str__(Transporting self) -> std::string"""
2799  return _IMP_npctransport.Transporting___str__(self)
2800 
2801  def __repr__(self):
2802  r"""__repr__(Transporting self) -> std::string"""
2803  return _IMP_npctransport.Transporting___repr__(self)
2804 
2805  def _get_as_binary(self):
2806  r"""_get_as_binary(Transporting self) -> PyObject *"""
2807  return _IMP_npctransport.Transporting__get_as_binary(self)
2808 
2809  def _set_from_binary(self, p):
2810  r"""_set_from_binary(Transporting self, PyObject * p)"""
2811  return _IMP_npctransport.Transporting__set_from_binary(self, p)
2812 
2813  def __getstate__(self):
2814  p = self._get_as_binary()
2815  if len(self.__dict__) > 1:
2816  d = self.__dict__.copy()
2817  del d['this']
2818  p = (d, p)
2819  return p
2820 
2821  def __setstate__(self, p):
2822  if not hasattr(self, 'this'):
2823  self.__init__()
2824  if isinstance(p, tuple):
2825  d, p = p
2826  self.__dict__.update(d)
2827  return self._set_from_binary(p)
2828 
2829  __swig_destroy__ = _IMP_npctransport.delete_Transporting
2830 
2831 # Register Transporting in _IMP_npctransport:
2832 _IMP_npctransport.Transporting_swigregister(Transporting)
2833 
2834 def show_ranges(fname):
2835  r"""show_ranges(std::string fname)"""
2836  return _IMP_npctransport.show_ranges(fname)
2837 
2838 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
2839  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"""
2840  return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
2841 
2842 def get_number_of_work_units(configuration_file):
2843  r"""get_number_of_work_units(std::string configuration_file) -> int"""
2844  return _IMP_npctransport.get_number_of_work_units(configuration_file)
2845 class SlabWithPore(IMP.Decorator):
2846  r"""Proxy of C++ IMP::npctransport::SlabWithPore class."""
2847 
2848  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2849 
2850  def __init__(self, *args):
2851  r"""
2852  __init__(SlabWithPore self) -> SlabWithPore
2853  __init__(SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
2854  __init__(SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
2855  """
2856  _IMP_npctransport.SlabWithPore_swiginit(self, _IMP_npctransport.new_SlabWithPore(*args))
2857 
2858  def show(self, *args):
2859  r"""show(SlabWithPore self, _ostream out=std::cout)"""
2860  return _IMP_npctransport.SlabWithPore_show(self, *args)
2861 
2862  @staticmethod
2863  def setup_particle(*args):
2864  r"""
2865  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
2866  setup_particle(_ParticleAdaptor pa, double thickness, double pore_radius) -> SlabWithPore
2867  """
2868  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
2869 
2870  @staticmethod
2871  def get_is_setup(*args):
2872  r"""
2873  get_is_setup(_ParticleAdaptor p) -> bool
2874  get_is_setup(Model m, ParticleIndex pi) -> bool
2875  """
2876  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
2877 
2878  def set_thickness(self, thickness):
2879  r"""set_thickness(SlabWithPore self, double thickness)"""
2880  return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
2881 
2882  def get_thickness(self):
2883  r"""get_thickness(SlabWithPore self) -> IMP::Float"""
2884  return _IMP_npctransport.SlabWithPore_get_thickness(self)
2885 
2886  def get_pore_radius(self):
2887  r"""get_pore_radius(SlabWithPore self) -> IMP::Float"""
2888  return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
2889 
2890  def set_pore_radius(self, r):
2891  r"""set_pore_radius(SlabWithPore self, double r)"""
2892  return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
2893 
2894  def add_to_pore_radius_derivative(self, v, d):
2895  r"""add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
2896  return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
2897 
2898  def get_pore_radius_is_optimized(self):
2899  r"""get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
2900  return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
2901 
2902  def set_pore_radius_is_optimized(self, tf):
2903  r"""set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
2904  return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
2905 
2906  @staticmethod
2907  def get_thickness_key():
2908  r"""get_thickness_key() -> FloatKey"""
2909  return _IMP_npctransport.SlabWithPore_get_thickness_key()
2910 
2911  @staticmethod
2912  def get_pore_radius_key():
2913  r"""get_pore_radius_key() -> FloatKey"""
2914  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
2915 
2916  def add_attribute(self, *args):
2917  r"""
2918  add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
2919  add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
2920  add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
2921  add_attribute(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
2922  add_attribute(SlabWithPore self, IntsKey a0, IMP::Ints a1)
2923  add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
2924  add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
2925  add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
2926  """
2927  return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
2928 
2929  def get_value(self, *args):
2930  r"""
2931  get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
2932  get_value(SlabWithPore self, IntKey a0) -> IMP::Int
2933  get_value(SlabWithPore self, FloatsKey a0) -> IMP::Floats
2934  get_value(SlabWithPore self, IntsKey a0) -> IMP::Ints
2935  get_value(SlabWithPore self, StringKey a0) -> IMP::String
2936  get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
2937  get_value(SlabWithPore self, ObjectKey a0) -> Object
2938  """
2939  return _IMP_npctransport.SlabWithPore_get_value(self, *args)
2940 
2941  def set_value(self, *args):
2942  r"""
2943  set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
2944  set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
2945  set_value(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
2946  set_value(SlabWithPore self, IntsKey a0, IMP::Ints a1)
2947  set_value(SlabWithPore self, StringKey a0, IMP::String a1)
2948  set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
2949  set_value(SlabWithPore self, ObjectKey a0, Object a1)
2950  """
2951  return _IMP_npctransport.SlabWithPore_set_value(self, *args)
2952 
2953  def remove_attribute(self, *args):
2954  r"""
2955  remove_attribute(SlabWithPore self, FloatKey a0)
2956  remove_attribute(SlabWithPore self, IntKey a0)
2957  remove_attribute(SlabWithPore self, FloatsKey a0)
2958  remove_attribute(SlabWithPore self, IntsKey a0)
2959  remove_attribute(SlabWithPore self, StringKey a0)
2960  remove_attribute(SlabWithPore self, ParticleIndexKey a0)
2961  remove_attribute(SlabWithPore self, ObjectKey a0)
2962  """
2963  return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
2964 
2965  def has_attribute(self, *args):
2966  r"""
2967  has_attribute(SlabWithPore self, FloatKey a0) -> bool
2968  has_attribute(SlabWithPore self, IntKey a0) -> bool
2969  has_attribute(SlabWithPore self, FloatsKey a0) -> bool
2970  has_attribute(SlabWithPore self, IntsKey a0) -> bool
2971  has_attribute(SlabWithPore self, StringKey a0) -> bool
2972  has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
2973  has_attribute(SlabWithPore self, ObjectKey a0) -> bool
2974  """
2975  return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
2976 
2977  def get_derivative(self, a0):
2978  r"""get_derivative(SlabWithPore self, FloatKey a0) -> double"""
2979  return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
2980 
2981  def get_name(self):
2982  r"""get_name(SlabWithPore self) -> std::string"""
2983  return _IMP_npctransport.SlabWithPore_get_name(self)
2984 
2985  def clear_caches(self):
2986  r"""clear_caches(SlabWithPore self)"""
2987  return _IMP_npctransport.SlabWithPore_clear_caches(self)
2988 
2989  def set_name(self, a0):
2990  r"""set_name(SlabWithPore self, std::string a0)"""
2991  return _IMP_npctransport.SlabWithPore_set_name(self, a0)
2992 
2993  def set_check_level(self, a0):
2994  r"""set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
2995  return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
2996 
2997  def add_to_derivative(self, a0, a1, a2):
2998  r"""add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2999  return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3000 
3001  def set_is_optimized(self, a0, a1):
3002  r"""set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3003  return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3004 
3005  def get_is_optimized(self, a0):
3006  r"""get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3007  return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3008 
3009  def get_check_level(self):
3010  r"""get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3011  return _IMP_npctransport.SlabWithPore_get_check_level(self)
3012 
3013  def __eq__(self, *args):
3014  r"""
3015  __eq__(SlabWithPore self, SlabWithPore o) -> bool
3016  __eq__(SlabWithPore self, Particle d) -> bool
3017  """
3018  return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3019 
3020  def __ne__(self, *args):
3021  r"""
3022  __ne__(SlabWithPore self, SlabWithPore o) -> bool
3023  __ne__(SlabWithPore self, Particle d) -> bool
3024  """
3025  return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3026 
3027  def __le__(self, *args):
3028  r"""
3029  __le__(SlabWithPore self, SlabWithPore o) -> bool
3030  __le__(SlabWithPore self, Particle d) -> bool
3031  """
3032  return _IMP_npctransport.SlabWithPore___le__(self, *args)
3033 
3034  def __lt__(self, *args):
3035  r"""
3036  __lt__(SlabWithPore self, SlabWithPore o) -> bool
3037  __lt__(SlabWithPore self, Particle d) -> bool
3038  """
3039  return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3040 
3041  def __ge__(self, *args):
3042  r"""
3043  __ge__(SlabWithPore self, SlabWithPore o) -> bool
3044  __ge__(SlabWithPore self, Particle d) -> bool
3045  """
3046  return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3047 
3048  def __gt__(self, *args):
3049  r"""
3050  __gt__(SlabWithPore self, SlabWithPore o) -> bool
3051  __gt__(SlabWithPore self, Particle d) -> bool
3052  """
3053  return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3054 
3055  def __hash__(self):
3056  r"""__hash__(SlabWithPore self) -> std::size_t"""
3057  return _IMP_npctransport.SlabWithPore___hash__(self)
3058 
3059  def __str__(self):
3060  r"""__str__(SlabWithPore self) -> std::string"""
3061  return _IMP_npctransport.SlabWithPore___str__(self)
3062 
3063  def __repr__(self):
3064  r"""__repr__(SlabWithPore self) -> std::string"""
3065  return _IMP_npctransport.SlabWithPore___repr__(self)
3066 
3067  def _get_as_binary(self):
3068  r"""_get_as_binary(SlabWithPore self) -> PyObject *"""
3069  return _IMP_npctransport.SlabWithPore__get_as_binary(self)
3070 
3071  def _set_from_binary(self, p):
3072  r"""_set_from_binary(SlabWithPore self, PyObject * p)"""
3073  return _IMP_npctransport.SlabWithPore__set_from_binary(self, p)
3074 
3075  def __getstate__(self):
3076  p = self._get_as_binary()
3077  if len(self.__dict__) > 1:
3078  d = self.__dict__.copy()
3079  del d['this']
3080  p = (d, p)
3081  return p
3082 
3083  def __setstate__(self, p):
3084  if not hasattr(self, 'this'):
3085  self.__init__()
3086  if isinstance(p, tuple):
3087  d, p = p
3088  self.__dict__.update(d)
3089  return self._set_from_binary(p)
3090 
3091  __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3092 
3093 # Register SlabWithPore in _IMP_npctransport:
3094 _IMP_npctransport.SlabWithPore_swigregister(SlabWithPore)
3095 class SlabWithCylindricalPore(SlabWithPore):
3096  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3097 
3098  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3099 
3100  def __init__(self, *args):
3101  r"""
3102  __init__(SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3103  __init__(SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3104  __init__(SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3105  """
3106  _IMP_npctransport.SlabWithCylindricalPore_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPore(*args))
3107 
3108  def show(self, *args):
3109  r"""show(SlabWithCylindricalPore self, _ostream out=std::cout)"""
3110  return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3111 
3112  @staticmethod
3113  def setup_particle(*args):
3114  r"""
3115  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3116  setup_particle(_ParticleAdaptor pa, double thickness, double radius) -> SlabWithCylindricalPore
3117  """
3118  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3119 
3120  @staticmethod
3121  def get_is_setup(*args):
3122  r"""
3123  get_is_setup(_ParticleAdaptor p) -> bool
3124  get_is_setup(Model m, ParticleIndex pi) -> bool
3125  """
3126  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3127 
3128  @staticmethod
3129  def get_cylindrical_pore_key():
3130  r"""get_cylindrical_pore_key() -> IntKey"""
3131  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3132 
3133  def add_attribute(self, *args):
3134  r"""
3135  add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3136  add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3137  add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3138  add_attribute(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3139  add_attribute(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3140  add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3141  add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3142  add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3143  """
3144  return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3145 
3146  def get_value(self, *args):
3147  r"""
3148  get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3149  get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3150  get_value(SlabWithCylindricalPore self, FloatsKey a0) -> IMP::Floats
3151  get_value(SlabWithCylindricalPore self, IntsKey a0) -> IMP::Ints
3152  get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3153  get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3154  get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3155  """
3156  return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3157 
3158  def set_value(self, *args):
3159  r"""
3160  set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3161  set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3162  set_value(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3163  set_value(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3164  set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3165  set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3166  set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3167  """
3168  return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3169 
3170  def remove_attribute(self, *args):
3171  r"""
3172  remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3173  remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3174  remove_attribute(SlabWithCylindricalPore self, FloatsKey a0)
3175  remove_attribute(SlabWithCylindricalPore self, IntsKey a0)
3176  remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3177  remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3178  remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3179  """
3180  return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3181 
3182  def has_attribute(self, *args):
3183  r"""
3184  has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3185  has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3186  has_attribute(SlabWithCylindricalPore self, FloatsKey a0) -> bool
3187  has_attribute(SlabWithCylindricalPore self, IntsKey a0) -> bool
3188  has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3189  has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3190  has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3191  """
3192  return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3193 
3194  def get_derivative(self, a0):
3195  r"""get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3196  return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3197 
3198  def get_name(self):
3199  r"""get_name(SlabWithCylindricalPore self) -> std::string"""
3200  return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3201 
3202  def clear_caches(self):
3203  r"""clear_caches(SlabWithCylindricalPore self)"""
3204  return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3205 
3206  def set_name(self, a0):
3207  r"""set_name(SlabWithCylindricalPore self, std::string a0)"""
3208  return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3209 
3210  def set_check_level(self, a0):
3211  r"""set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3212  return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3213 
3214  def add_to_derivative(self, a0, a1, a2):
3215  r"""add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3216  return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3217 
3218  def set_is_optimized(self, a0, a1):
3219  r"""set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3220  return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3221 
3222  def get_is_optimized(self, a0):
3223  r"""get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3224  return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3225 
3226  def get_check_level(self):
3227  r"""get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3228  return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3229 
3230  def __eq__(self, *args):
3231  r"""
3232  __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3233  __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3234  """
3235  return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3236 
3237  def __ne__(self, *args):
3238  r"""
3239  __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3240  __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3241  """
3242  return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3243 
3244  def __le__(self, *args):
3245  r"""
3246  __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3247  __le__(SlabWithCylindricalPore self, Particle d) -> bool
3248  """
3249  return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3250 
3251  def __lt__(self, *args):
3252  r"""
3253  __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3254  __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3255  """
3256  return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3257 
3258  def __ge__(self, *args):
3259  r"""
3260  __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3261  __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3262  """
3263  return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3264 
3265  def __gt__(self, *args):
3266  r"""
3267  __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3268  __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3269  """
3270  return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3271 
3272  def __hash__(self):
3273  r"""__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3274  return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3275 
3276  def __str__(self):
3277  r"""__str__(SlabWithCylindricalPore self) -> std::string"""
3278  return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3279 
3280  def __repr__(self):
3281  r"""__repr__(SlabWithCylindricalPore self) -> std::string"""
3282  return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3283 
3284  def _get_as_binary(self):
3285  r"""_get_as_binary(SlabWithCylindricalPore self) -> PyObject *"""
3286  return _IMP_npctransport.SlabWithCylindricalPore__get_as_binary(self)
3287 
3288  def _set_from_binary(self, p):
3289  r"""_set_from_binary(SlabWithCylindricalPore self, PyObject * p)"""
3290  return _IMP_npctransport.SlabWithCylindricalPore__set_from_binary(self, p)
3291 
3292  def __getstate__(self):
3293  p = self._get_as_binary()
3294  if len(self.__dict__) > 1:
3295  d = self.__dict__.copy()
3296  del d['this']
3297  p = (d, p)
3298  return p
3299 
3300  def __setstate__(self, p):
3301  if not hasattr(self, 'this'):
3302  self.__init__()
3303  if isinstance(p, tuple):
3304  d, p = p
3305  self.__dict__.update(d)
3306  return self._set_from_binary(p)
3307 
3308  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3309 
3310 # Register SlabWithCylindricalPore in _IMP_npctransport:
3311 _IMP_npctransport.SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3312 class SlabWithToroidalPore(SlabWithPore):
3313  r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3314 
3315  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3316 
3317  def __init__(self, *args):
3318  r"""
3319  __init__(SlabWithToroidalPore self) -> SlabWithToroidalPore
3320  __init__(SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3321  __init__(SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3322  """
3323  _IMP_npctransport.SlabWithToroidalPore_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPore(*args))
3324 
3325  def show(self, *args):
3326  r"""show(SlabWithToroidalPore self, _ostream out=std::cout)"""
3327  return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3328 
3329  @staticmethod
3330  def setup_particle(*args):
3331  r"""
3332  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3333  setup_particle(_ParticleAdaptor pa, double thickness, double major_radius) -> SlabWithToroidalPore
3334  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3335  setup_particle(_ParticleAdaptor pa, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3336  """
3337  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3338 
3339  @staticmethod
3340  def get_is_setup(*args):
3341  r"""
3342  get_is_setup(_ParticleAdaptor p) -> bool
3343  get_is_setup(Model m, ParticleIndex pi) -> bool
3344  """
3345  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3346 
3347  def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3348  r"""set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3349  return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3350 
3351  def get_minor_radius_h2v_aspect_ratio(self):
3352  r"""get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3353  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3354 
3355  def get_vertical_minor_radius(self):
3356  r"""get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3357  return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3358 
3359  def set_vertical_minor_radius(self, rv):
3360  r"""set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3361  return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3362 
3363  def get_horizontal_minor_radius(self):
3364  r"""get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3365  return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3366 
3367  def set_horizontal_minor_radius(self, rh):
3368  r"""set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3369  return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3370 
3371  @staticmethod
3372  def get_minor_radius_h2v_aspect_ratio_key():
3373  r"""get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3374  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3375 
3376  @staticmethod
3377  def get_toroidal_pore_key():
3378  r"""get_toroidal_pore_key() -> IntKey"""
3379  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3380 
3381  def add_attribute(self, *args):
3382  r"""
3383  add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3384  add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3385  add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3386  add_attribute(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3387  add_attribute(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3388  add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3389  add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3390  add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3391  """
3392  return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3393 
3394  def get_value(self, *args):
3395  r"""
3396  get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3397  get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3398  get_value(SlabWithToroidalPore self, FloatsKey a0) -> IMP::Floats
3399  get_value(SlabWithToroidalPore self, IntsKey a0) -> IMP::Ints
3400  get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3401  get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3402  get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3403  """
3404  return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3405 
3406  def set_value(self, *args):
3407  r"""
3408  set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3409  set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3410  set_value(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3411  set_value(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3412  set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3413  set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3414  set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3415  """
3416  return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3417 
3418  def remove_attribute(self, *args):
3419  r"""
3420  remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3421  remove_attribute(SlabWithToroidalPore self, IntKey a0)
3422  remove_attribute(SlabWithToroidalPore self, FloatsKey a0)
3423  remove_attribute(SlabWithToroidalPore self, IntsKey a0)
3424  remove_attribute(SlabWithToroidalPore self, StringKey a0)
3425  remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3426  remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3427  """
3428  return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3429 
3430  def has_attribute(self, *args):
3431  r"""
3432  has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3433  has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3434  has_attribute(SlabWithToroidalPore self, FloatsKey a0) -> bool
3435  has_attribute(SlabWithToroidalPore self, IntsKey a0) -> bool
3436  has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3437  has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3438  has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3439  """
3440  return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3441 
3442  def get_derivative(self, a0):
3443  r"""get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3444  return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3445 
3446  def get_name(self):
3447  r"""get_name(SlabWithToroidalPore self) -> std::string"""
3448  return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3449 
3450  def clear_caches(self):
3451  r"""clear_caches(SlabWithToroidalPore self)"""
3452  return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3453 
3454  def set_name(self, a0):
3455  r"""set_name(SlabWithToroidalPore self, std::string a0)"""
3456  return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3457 
3458  def set_check_level(self, a0):
3459  r"""set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3460  return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3461 
3462  def add_to_derivative(self, a0, a1, a2):
3463  r"""add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3464  return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3465 
3466  def set_is_optimized(self, a0, a1):
3467  r"""set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3468  return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3469 
3470  def get_is_optimized(self, a0):
3471  r"""get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3472  return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
3473 
3474  def get_check_level(self):
3475  r"""get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
3476  return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
3477 
3478  def __eq__(self, *args):
3479  r"""
3480  __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3481  __eq__(SlabWithToroidalPore self, Particle d) -> bool
3482  """
3483  return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
3484 
3485  def __ne__(self, *args):
3486  r"""
3487  __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3488  __ne__(SlabWithToroidalPore self, Particle d) -> bool
3489  """
3490  return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
3491 
3492  def __le__(self, *args):
3493  r"""
3494  __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3495  __le__(SlabWithToroidalPore self, Particle d) -> bool
3496  """
3497  return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
3498 
3499  def __lt__(self, *args):
3500  r"""
3501  __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3502  __lt__(SlabWithToroidalPore self, Particle d) -> bool
3503  """
3504  return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
3505 
3506  def __ge__(self, *args):
3507  r"""
3508  __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3509  __ge__(SlabWithToroidalPore self, Particle d) -> bool
3510  """
3511  return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
3512 
3513  def __gt__(self, *args):
3514  r"""
3515  __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3516  __gt__(SlabWithToroidalPore self, Particle d) -> bool
3517  """
3518  return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
3519 
3520  def __hash__(self):
3521  r"""__hash__(SlabWithToroidalPore self) -> std::size_t"""
3522  return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
3523 
3524  def __str__(self):
3525  r"""__str__(SlabWithToroidalPore self) -> std::string"""
3526  return _IMP_npctransport.SlabWithToroidalPore___str__(self)
3527 
3528  def __repr__(self):
3529  r"""__repr__(SlabWithToroidalPore self) -> std::string"""
3530  return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
3531 
3532  def _get_as_binary(self):
3533  r"""_get_as_binary(SlabWithToroidalPore self) -> PyObject *"""
3534  return _IMP_npctransport.SlabWithToroidalPore__get_as_binary(self)
3535 
3536  def _set_from_binary(self, p):
3537  r"""_set_from_binary(SlabWithToroidalPore self, PyObject * p)"""
3538  return _IMP_npctransport.SlabWithToroidalPore__set_from_binary(self, p)
3539 
3540  def __getstate__(self):
3541  p = self._get_as_binary()
3542  if len(self.__dict__) > 1:
3543  d = self.__dict__.copy()
3544  del d['this']
3545  p = (d, p)
3546  return p
3547 
3548  def __setstate__(self, p):
3549  if not hasattr(self, 'this'):
3550  self.__init__()
3551  if isinstance(p, tuple):
3552  d, p = p
3553  self.__dict__.update(d)
3554  return self._set_from_binary(p)
3555 
3556  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
3557 
3558 # Register SlabWithToroidalPore in _IMP_npctransport:
3559 _IMP_npctransport.SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
3560 
3561 def __lshift__(*args):
3562  r"""
3563  __lshift__(_ostream out, RelaxingSpring n) -> _ostream
3564  __lshift__(_ostream out, Transporting n) -> _ostream
3565  __lshift__(_ostream out, SlabWithPore n) -> _ostream
3566  __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
3567  __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
3568  """
3569  return _IMP_npctransport.__lshift__(*args)
3570 class SlabWithCylindricalPorePairScore(IMP.PairScore):
3571  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
3572 
3573  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3574 
3575  def __init__(self, k):
3576  r"""__init__(SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
3577  _IMP_npctransport.SlabWithCylindricalPorePairScore_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k))
3578 
3579  def get_displacement_direction(self, slab, v):
3580  r"""get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
3581  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
3582 
3583  def get_displacement_magnitude(self, slab, v):
3584  r"""get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
3585  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
3586 
3587  def do_get_inputs(self, m, pis):
3588  r"""do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3589  return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
3590 
3591  def get_version_info(self):
3592  r"""get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
3593  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
3594  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPorePairScore
3595 
3596  def __str__(self):
3597  r"""__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
3598  return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
3599 
3600  def __repr__(self):
3601  r"""__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
3602  return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
3603 
3604  @staticmethod
3605  def get_from(o):
3606  return _object_cast_to_SlabWithCylindricalPorePairScore(o)
3607 
3608 
3609 # Register SlabWithCylindricalPorePairScore in _IMP_npctransport:
3610 _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
3611 class SlabWithToroidalPorePairScore(IMP.PairScore):
3612  r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
3613 
3614  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3615 
3616  def __init__(self, k):
3617  r"""__init__(SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
3618  _IMP_npctransport.SlabWithToroidalPorePairScore_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPorePairScore(k))
3619 
3620  def do_get_inputs(self, m, pis):
3621  r"""do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3622  return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
3623 
3624  def get_version_info(self):
3625  r"""get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
3626  return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
3627  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPorePairScore
3628 
3629  def __str__(self):
3630  r"""__str__(SlabWithToroidalPorePairScore self) -> std::string"""
3631  return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
3632 
3633  def __repr__(self):
3634  r"""__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
3635  return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
3636 
3637  @staticmethod
3638  def get_from(o):
3639  return _object_cast_to_SlabWithToroidalPorePairScore(o)
3640 
3641 
3642 # Register SlabWithToroidalPorePairScore in _IMP_npctransport:
3643 _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
3644 class SlabWithCylindricalPoreWireGeometry(IMP.display.Geometry):
3645  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
3646 
3647  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3648 
3649  def __init__(self, height, radius, length):
3650  r"""__init__(SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
3651  _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length))
3652 
3653  def get_version_info(self):
3654  r"""get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
3655  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
3656  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreWireGeometry
3657 
3658  def __str__(self):
3659  r"""__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
3660  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
3661 
3662  def __repr__(self):
3663  r"""__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
3664  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
3665 
3666  @staticmethod
3667  def get_from(o):
3668  return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
3669 
3670 
3671 # Register SlabWithCylindricalPoreWireGeometry in _IMP_npctransport:
3672 _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
3673 class SlabWithCylindricalPoreSurfaceGeometry(IMP.display.SurfaceMeshGeometry):
3674  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
3675 
3676  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3677 
3678  def __init__(self, height, radius, length):
3679  r"""__init__(SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
3680  _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length))
3681 
3682  def __str__(self):
3683  r"""__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
3684  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
3685 
3686  def __repr__(self):
3687  r"""__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
3688  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
3689 
3690  @staticmethod
3691  def get_from(o):
3692  return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
3693 
3694  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
3695 
3696 # Register SlabWithCylindricalPoreSurfaceGeometry in _IMP_npctransport:
3697 _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
3698 class SlabWithToroidalPoreWireGeometry(IMP.display.Geometry):
3699  r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
3700 
3701  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3702 
3703  def __init__(self, *args):
3704  r"""
3705  __init__(SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
3706  __init__(SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
3707  """
3708  _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args))
3709 
3710  def get_version_info(self):
3711  r"""get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
3712  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
3713  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPoreWireGeometry
3714 
3715  def __str__(self):
3716  r"""__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
3717  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
3718 
3719  def __repr__(self):
3720  r"""__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
3721  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
3722 
3723  @staticmethod
3724  def get_from(o):
3725  return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
3726 
3727 
3728 # Register SlabWithToroidalPoreWireGeometry in _IMP_npctransport:
3729 _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
3730 class _GenericAttributeSingletonScoreForPoreRadus(IMP.SingletonScore):
3731  r"""Proxy of C++ IMP::core::GenericAttributeSingletonScore< IMP::core::Harmonic > class."""
3732 
3733  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3734  __repr__ = _swig_repr
3735 
3736  def __init__(self, f, k):
3737  r"""__init__(_GenericAttributeSingletonScoreForPoreRadus self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
3738  _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swiginit(self, _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k))
3739 
3740  def do_get_inputs(self, m, pis):
3741  r"""do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3742  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
3743 
3744  def get_unary_function(self):
3745  r"""get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
3746  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
3747 
3748  def get_version_info(self):
3749  r"""get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
3750  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
3751  __swig_destroy__ = _IMP_npctransport.delete__GenericAttributeSingletonScoreForPoreRadus
3752 
3753 # Register _GenericAttributeSingletonScoreForPoreRadus in _IMP_npctransport:
3754 _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
3755 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
3756  r"""Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
3757 
3758  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3759 
3760  def __init__(self, mean, k):
3761  r"""__init__(PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
3762  _IMP_npctransport.PoreRadiusSingletonScore_swiginit(self, _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k))
3763 
3764  def set_k(self, k):
3765  r"""set_k(PoreRadiusSingletonScore self, double k)"""
3766  return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
3767  __swig_destroy__ = _IMP_npctransport.delete_PoreRadiusSingletonScore
3768 
3769  def __str__(self):
3770  r"""__str__(PoreRadiusSingletonScore self) -> std::string"""
3771  return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
3772 
3773  def __repr__(self):
3774  r"""__repr__(PoreRadiusSingletonScore self) -> std::string"""
3775  return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
3776 
3777  @staticmethod
3778  def get_from(o):
3779  return _object_cast_to_PoreRadiusSingletonScore(o)
3780 
3781 
3782 # Register PoreRadiusSingletonScore in _IMP_npctransport:
3783 _IMP_npctransport.PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
3784 class ExcludeZRangeSingletonScore(IMP.SingletonScore):
3785  r"""Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
3786 
3787  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3788 
3789  def __init__(self, bottom, top, k):
3790  r"""__init__(ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
3791  _IMP_npctransport.ExcludeZRangeSingletonScore_swiginit(self, _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k))
3792 
3793  def get_bottom_z(self):
3794  r"""get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
3795  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
3796 
3797  def get_top_z(self):
3798  r"""get_top_z(ExcludeZRangeSingletonScore self) -> double"""
3799  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
3800 
3801  def get_k(self):
3802  r"""get_k(ExcludeZRangeSingletonScore self) -> double"""
3803  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
3804 
3805  def do_get_inputs(self, m, pis):
3806  r"""do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3807  return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
3808 
3809  def get_version_info(self):
3810  r"""get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
3811  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
3812  __swig_destroy__ = _IMP_npctransport.delete_ExcludeZRangeSingletonScore
3813 
3814  def __str__(self):
3815  r"""__str__(ExcludeZRangeSingletonScore self) -> std::string"""
3816  return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
3817 
3818  def __repr__(self):
3819  r"""__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
3820  return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
3821 
3822  @staticmethod
3823  def get_from(o):
3824  return _object_cast_to_ExcludeZRangeSingletonScore(o)
3825 
3826 
3827 # Register ExcludeZRangeSingletonScore in _IMP_npctransport:
3828 _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
3829 class ZBiasSingletonScore(IMP.SingletonScore):
3830  r"""Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
3831 
3832  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3833 
3834  def __init__(self, *args):
3835  r"""__init__(ZBiasSingletonScore self, double k, double max_r=HALF_SQRT_MAX_DOUBLE) -> ZBiasSingletonScore"""
3836  _IMP_npctransport.ZBiasSingletonScore_swiginit(self, _IMP_npctransport.new_ZBiasSingletonScore(*args))
3837 
3838  def get_k(self):
3839  r"""get_k(ZBiasSingletonScore self) -> double"""
3840  return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
3841 
3842  def set_k(self, k):
3843  r"""set_k(ZBiasSingletonScore self, double k)"""
3844  return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
3845 
3846  def do_get_inputs(self, m, pis):
3847  r"""do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3848  return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
3849 
3850  def get_version_info(self):
3851  r"""get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
3852  return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
3853  __swig_destroy__ = _IMP_npctransport.delete_ZBiasSingletonScore
3854 
3855  def __str__(self):
3856  r"""__str__(ZBiasSingletonScore self) -> std::string"""
3857  return _IMP_npctransport.ZBiasSingletonScore___str__(self)
3858 
3859  def __repr__(self):
3860  r"""__repr__(ZBiasSingletonScore self) -> std::string"""
3861  return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
3862 
3863  @staticmethod
3864  def get_from(o):
3865  return _object_cast_to_ZBiasSingletonScore(o)
3866 
3867 
3868 # Register ZBiasSingletonScore in _IMP_npctransport:
3869 _IMP_npctransport.ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
3870 class BodyStatisticsOptimizerState(IMP.OptimizerState):
3871  r"""Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
3872 
3873  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3874 
3875  def __init__(self, p, statistics_manager=None, periodicity=1):
3876  r"""__init__(BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState"""
3877  _IMP_npctransport.BodyStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity))
3878 
3879  def get_correlation_time(self):
3880  r"""get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
3881  return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
3882 
3883  def get_diffusion_coefficient(self):
3884  r"""get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
3885  return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
3886 
3887  def update_particle_type_zr_distribution_map(self):
3888  r"""update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
3889  return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
3890 
3891  def do_update(self, call_num):
3892  r"""do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
3893  return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
3894 
3895  def get_version_info(self):
3896  r"""get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
3897  return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
3898  __swig_destroy__ = _IMP_npctransport.delete_BodyStatisticsOptimizerState
3899 
3900  def __str__(self):
3901  r"""__str__(BodyStatisticsOptimizerState self) -> std::string"""
3902  return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
3903 
3904  def __repr__(self):
3905  r"""__repr__(BodyStatisticsOptimizerState self) -> std::string"""
3906  return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
3907 
3908  @staticmethod
3909  def get_from(o):
3910  return _object_cast_to_BodyStatisticsOptimizerState(o)
3911 
3912 
3913 # Register BodyStatisticsOptimizerState in _IMP_npctransport:
3914 _IMP_npctransport.BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
3915 class ParticleTransportStatisticsOptimizerState(IMP.OptimizerState):
3916  r"""Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
3917 
3918  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3919 
3920  def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
3921  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"""
3922  _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner))
3923 
3924  def set_owner(self, owner):
3925  r"""set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
3926  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
3927 
3928  def get_owner(self):
3929  r"""get_owner(ParticleTransportStatisticsOptimizerState self) -> Simulator"""
3930  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
3931 
3932  def get_n_transports_up(self):
3933  r"""get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
3934  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
3935 
3936  def get_n_transports_down(self):
3937  r"""get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
3938  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
3939 
3940  def get_total_n_transports(self):
3941  r"""get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
3942  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
3943 
3944  def get_transport_time_points_in_ns(self):
3945  r"""get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
3946  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
3947 
3948  def do_update(self, call_num):
3949  r"""do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
3950  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
3951 
3952  def get_version_info(self):
3953  r"""get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
3954  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
3955  __swig_destroy__ = _IMP_npctransport.delete_ParticleTransportStatisticsOptimizerState
3956 
3957  def __str__(self):
3958  r"""__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
3959  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
3960 
3961  def __repr__(self):
3962  r"""__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
3963  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
3964 
3965  @staticmethod
3966  def get_from(o):
3967  return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
3968 
3969 
3970 # Register ParticleTransportStatisticsOptimizerState in _IMP_npctransport:
3971 _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
3972 class ChainStatisticsOptimizerState(IMP.OptimizerState):
3973  r"""Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
3974 
3975  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3976 
3977  def __init__(self, ps, periodicity=1):
3978  r"""__init__(ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState"""
3979  _IMP_npctransport.ChainStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity))
3980 
3981  def get_correlation_time(self):
3982  r"""get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
3983  return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
3984 
3985  def get_local_diffusion_coefficients(self):
3986  r"""get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
3987  return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
3988 
3989  def get_diffusion_coefficient(self):
3990  r"""get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
3991  return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
3992 
3993  def get_mean_radius_of_gyration(self):
3994  r"""get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
3995  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
3996 
3997  def get_mean_square_radius_of_gyration(self):
3998  r"""get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
3999  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4000 
4001  def get_mean_end_to_end_distance(self):
4002  r"""get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4003  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4004 
4005  def get_mean_square_end_to_end_distance(self):
4006  r"""get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4007  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4008 
4009  def get_mean_bond_distance(self):
4010  r"""get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4011  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4012 
4013  def get_mean_square_bond_distance(self):
4014  r"""get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4015  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4016 
4017  def do_update(self, call_num):
4018  r"""do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4019  return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4020 
4021  def get_version_info(self):
4022  r"""get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4023  return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4024  __swig_destroy__ = _IMP_npctransport.delete_ChainStatisticsOptimizerState
4025 
4026  def __str__(self):
4027  r"""__str__(ChainStatisticsOptimizerState self) -> std::string"""
4028  return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4029 
4030  def __repr__(self):
4031  r"""__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4032  return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4033 
4034  @staticmethod
4035  def get_from(o):
4036  return _object_cast_to_ChainStatisticsOptimizerState(o)
4037 
4038 
4039 # Register ChainStatisticsOptimizerState in _IMP_npctransport:
4040 _IMP_npctransport.ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4041 class BipartitePairsStatisticsOptimizerState(IMP.OptimizerState):
4042  r"""Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4043 
4044  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4045 
4046  def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4047  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"""
4048  _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack))
4049 
4050  def get_interaction_type(self):
4051  r"""get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4052  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4053 
4054  def get_average_number_of_contacts(self):
4055  r"""get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4056  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4057 
4058  def get_average_off_per_contact_per_ns(self):
4059  r"""get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4060  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4061 
4062  def get_average_off_per_bound_I_per_ns(self):
4063  r"""get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4064  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4065 
4066  def get_average_off_per_bound_II_per_ns(self):
4067  r"""get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4068  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4069 
4070  def get_average_on_per_missing_contact_per_ns(self):
4071  r"""get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4072  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4073 
4074  def get_average_on_per_unbound_I_per_ns(self):
4075  r"""get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4076  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4077 
4078  def get_average_on_per_unbound_II_per_ns(self):
4079  r"""get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4080  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4081 
4082  def get_average_fraction_bound_particles_I(self):
4083  r"""get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4084  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4085 
4086  def get_average_fraction_bound_particles_II(self):
4087  r"""get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4088  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4089 
4090  def get_average_fraction_bound_particle_sites_I(self):
4091  r"""get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4092  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4093 
4094  def get_average_fraction_bound_particle_sites_II(self):
4095  r"""get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4096  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4097 
4098  def get_average_fraction_nonspecific_interactions_I(self):
4099  r"""get_average_fraction_nonspecific_interactions_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4100  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_I(self)
4101 
4102  def get_average_fraction_nonspecific_interactions_II(self):
4103  r"""get_average_fraction_nonspecific_interactions_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4104  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_II(self)
4105 
4106  def get_number_of_particles_1(self):
4107  r"""get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4108  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4109 
4110  def get_number_of_particles_2(self):
4111  r"""get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4112  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4113 
4114  def get_misc_stats_period_ns(self):
4115  r"""get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4116  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4117 
4118  def get_off_stats_period_ns(self):
4119  r"""get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4120  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4121 
4122  def get_off_I_stats_period_ns(self):
4123  r"""get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4124  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4125 
4126  def get_off_II_stats_period_ns(self):
4127  r"""get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4128  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4129 
4130  def get_on_stats_period_ns(self):
4131  r"""get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4132  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4133 
4134  def get_on_I_stats_period_ns(self):
4135  r"""get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4136  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4137 
4138  def get_on_II_stats_period_ns(self):
4139  r"""get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4140  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4141 
4142  def get_version_info(self):
4143  r"""get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4144  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4145  __swig_destroy__ = _IMP_npctransport.delete_BipartitePairsStatisticsOptimizerState
4146 
4147  def __str__(self):
4148  r"""__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4149  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4150 
4151  def __repr__(self):
4152  r"""__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4153  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4154 
4155  @staticmethod
4156  def get_from(o):
4157  return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4158 
4159 
4160 # Register BipartitePairsStatisticsOptimizerState in _IMP_npctransport:
4161 _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4162 
4163 def get_close_pairs_range(*args):
4164  r"""
4165  get_close_pairs_range(double max_range, double max_range_factor) -> double
4166  get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4167  """
4168  return _IMP_npctransport.get_close_pairs_range(*args)
4169 
4170 def get_time_step(*args):
4171  r"""
4172  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
4173  get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4174  """
4175  return _IMP_npctransport.get_time_step(*args)
4176 
4177 def get_frames_from_ns(ns, time_step):
4178  r"""get_frames_from_ns(double ns, double time_step) -> int"""
4179  return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4180 
4181 def get_number_of_frames(config, time_step):
4182  r"""get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4183  return _IMP_npctransport.get_number_of_frames(config, time_step)
4184 
4185 def get_dump_interval_in_frames(config, time_step):
4186  r"""get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4187  return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4188 
4189 def get_statistics_interval_in_frames(assign, time_step, default_value_ns=0.1):
4190  r"""get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int"""
4191  return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4192 
4193 def get_output_statistics_interval_in_frames(assign, time_step, default_value_ns=1.0):
4194  r"""get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int"""
4195  return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4196 
4197 def initialize_positions(*args):
4198  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)"""
4199  return _IMP_npctransport.initialize_positions(*args)
4200 class Avro2PBReader(object):
4201  r"""Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4202 
4203  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4204 
4205  def __init__(self, *args):
4206  r"""
4207  __init__(Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4208  __init__(Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4209  """
4210  _IMP_npctransport.Avro2PBReader_swiginit(self, _IMP_npctransport.new_Avro2PBReader(*args))
4211  __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4212 
4213  def read_next(self):
4214  r"""read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4215  return _IMP_npctransport.Avro2PBReader_read_next(self)
4216 
4217  def get_is_valid(self):
4218  r"""get_is_valid(Avro2PBReader self) -> bool"""
4219  return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4220 
4221  def get_cur_file_name(self):
4222  r"""get_cur_file_name(Avro2PBReader self) -> std::string"""
4223  return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4224 
4225  def show(self, *args):
4226  r"""show(Avro2PBReader self, _ostream out=std::cout)"""
4227  return _IMP_npctransport.Avro2PBReader_show(self, *args)
4228 
4229  def __str__(self):
4230  r"""__str__(Avro2PBReader self) -> std::string"""
4231  return _IMP_npctransport.Avro2PBReader___str__(self)
4232 
4233  def __repr__(self):
4234  r"""__repr__(Avro2PBReader self) -> std::string"""
4235  return _IMP_npctransport.Avro2PBReader___repr__(self)
4236 
4237 # Register Avro2PBReader in _IMP_npctransport:
4238 _IMP_npctransport.Avro2PBReader_swigregister(Avro2PBReader)
4239 
4240 def get_optimizable_particles(particles):
4241  r"""get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4242  return _IMP_npctransport.get_optimizable_particles(particles)
4243 
4244 def get_non_optimizable_particles(particles):
4245  r"""get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4246  return _IMP_npctransport.get_non_optimizable_particles(particles)
4247 
4248 def get_particle_indexes(particles):
4249  r"""get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4250  return _IMP_npctransport.get_particle_indexes(particles)
4251 
4252 def get_protobuf_configuration_from_text(config_txt, config_pb):
4253  r"""get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4254  return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4255 
4256 def get_spheres_from_vectors(vs, radius):
4257  r"""get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4258  return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4259 
4260 def get_spheres_centers(spheres):
4261  r"""get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4262  return _IMP_npctransport.get_spheres_centers(spheres)
4263 
4265  r"""copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4266  return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4267 
4269  r"""copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4270  return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4271 
4272 def copy_FGs_coordinates(src_sd, trg_sd):
4273  r"""copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4274  return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4275 
4276 try:
4277  from .npctransport_pb2 import *
4278  import google.protobuf
4279 except ImportError:
4280  print("no protobuf support in python")
4281 from ._configuration import *
4282 
4283 timer = SimpleTimer
4284 
4285 
4286 def get_module_version():
4287  r"""get_module_version() -> std::string const"""
4288  return _IMP_npctransport.get_module_version()
4289 
4290 def get_example_path(fname):
4291  r"""get_example_path(std::string fname) -> std::string"""
4292  return _IMP_npctransport.get_example_path(fname)
4293 
4294 def get_data_path(fname):
4295  r"""get_data_path(std::string fname) -> std::string"""
4296  return _IMP_npctransport.get_data_path(fname)
4297 
4298 from . import _version_check
4299 _version_check.check_version(get_module_version())
4300 __version__ = get_module_version()
4301 
4302 
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:44
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:80
FGChain * create_fg_chain(IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
Various classes to hold sets of particles.
int assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed)
The base class for geometry.
int get_output_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
Definition: typedefs.h:45
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.
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.
Definition: Object.h:111
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 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)
Definition: Decorator.h:119
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)
Definition: typedefs.h:35
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
Definition: typedefs.h:26
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.
Definition: exception.h:72
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:151
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
Definition: util.h:169