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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
npctransport/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.2.1
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 2007-2024 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  add_attribute(RelaxingSpring self, SparseFloatKey a0, IMP::Float a1)
1178  add_attribute(RelaxingSpring self, SparseIntKey a0, IMP::Int a1)
1179  add_attribute(RelaxingSpring self, SparseStringKey a0, IMP::String a1)
1180  add_attribute(RelaxingSpring self, SparseParticleIndexKey a0, ParticleIndex a1)
1181  """
1182  return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1183 
1184  def get_value(self, *args):
1185  r"""
1186  get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1187  get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1188  get_value(RelaxingSpring self, FloatsKey a0) -> IMP::Floats
1189  get_value(RelaxingSpring self, IntsKey a0) -> IMP::Ints
1190  get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1191  get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1192  get_value(RelaxingSpring self, ObjectKey a0) -> Object
1193  get_value(RelaxingSpring self, SparseFloatKey a0) -> IMP::Float
1194  get_value(RelaxingSpring self, SparseIntKey a0) -> IMP::Int
1195  get_value(RelaxingSpring self, SparseStringKey a0) -> IMP::String
1196  get_value(RelaxingSpring self, SparseParticleIndexKey a0) -> ParticleIndex
1197  """
1198  return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1199 
1200  def set_value(self, *args):
1201  r"""
1202  set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1203  set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1204  set_value(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1205  set_value(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1206  set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1207  set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1208  set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1209  set_value(RelaxingSpring self, SparseFloatKey a0, IMP::Float a1)
1210  set_value(RelaxingSpring self, SparseIntKey a0, IMP::Int a1)
1211  set_value(RelaxingSpring self, SparseStringKey a0, IMP::String a1)
1212  set_value(RelaxingSpring self, SparseParticleIndexKey a0, ParticleIndex a1)
1213  """
1214  return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1215 
1216  def remove_attribute(self, *args):
1217  r"""
1218  remove_attribute(RelaxingSpring self, FloatKey a0)
1219  remove_attribute(RelaxingSpring self, IntKey a0)
1220  remove_attribute(RelaxingSpring self, FloatsKey a0)
1221  remove_attribute(RelaxingSpring self, IntsKey a0)
1222  remove_attribute(RelaxingSpring self, StringKey a0)
1223  remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1224  remove_attribute(RelaxingSpring self, ObjectKey a0)
1225  remove_attribute(RelaxingSpring self, SparseFloatKey a0)
1226  remove_attribute(RelaxingSpring self, SparseIntKey a0)
1227  remove_attribute(RelaxingSpring self, SparseStringKey a0)
1228  remove_attribute(RelaxingSpring self, SparseParticleIndexKey a0)
1229  """
1230  return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1231 
1232  def has_attribute(self, *args):
1233  r"""
1234  has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1235  has_attribute(RelaxingSpring self, IntKey a0) -> bool
1236  has_attribute(RelaxingSpring self, FloatsKey a0) -> bool
1237  has_attribute(RelaxingSpring self, IntsKey a0) -> bool
1238  has_attribute(RelaxingSpring self, StringKey a0) -> bool
1239  has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1240  has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1241  has_attribute(RelaxingSpring self, SparseFloatKey a0) -> bool
1242  has_attribute(RelaxingSpring self, SparseIntKey a0) -> bool
1243  has_attribute(RelaxingSpring self, SparseStringKey a0) -> bool
1244  has_attribute(RelaxingSpring self, SparseParticleIndexKey a0) -> bool
1245  """
1246  return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1247 
1248  def get_derivative(self, a0):
1249  r"""get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1250  return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1251 
1252  def get_name(self):
1253  r"""get_name(RelaxingSpring self) -> std::string"""
1254  return _IMP_npctransport.RelaxingSpring_get_name(self)
1255 
1256  def clear_caches(self):
1257  r"""clear_caches(RelaxingSpring self)"""
1258  return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1259 
1260  def set_name(self, a0):
1261  r"""set_name(RelaxingSpring self, std::string a0)"""
1262  return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1263 
1264  def set_check_level(self, a0):
1265  r"""set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1266  return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1267 
1268  def add_to_derivative(self, a0, a1, a2):
1269  r"""add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1270  return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1271 
1272  def set_is_optimized(self, a0, a1):
1273  r"""set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1274  return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1275 
1276  def get_is_optimized(self, a0):
1277  r"""get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1278  return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1279 
1280  def get_check_level(self):
1281  r"""get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1282  return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1283 
1284  def __eq__(self, *args):
1285  r"""
1286  __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1287  __eq__(RelaxingSpring self, Particle d) -> bool
1288  """
1289  return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1290 
1291  def __ne__(self, *args):
1292  r"""
1293  __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1294  __ne__(RelaxingSpring self, Particle d) -> bool
1295  """
1296  return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1297 
1298  def __le__(self, *args):
1299  r"""
1300  __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1301  __le__(RelaxingSpring self, Particle d) -> bool
1302  """
1303  return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1304 
1305  def __lt__(self, *args):
1306  r"""
1307  __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1308  __lt__(RelaxingSpring self, Particle d) -> bool
1309  """
1310  return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1311 
1312  def __ge__(self, *args):
1313  r"""
1314  __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1315  __ge__(RelaxingSpring self, Particle d) -> bool
1316  """
1317  return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1318 
1319  def __gt__(self, *args):
1320  r"""
1321  __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1322  __gt__(RelaxingSpring self, Particle d) -> bool
1323  """
1324  return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1325 
1326  def __hash__(self):
1327  r"""__hash__(RelaxingSpring self) -> std::size_t"""
1328  return _IMP_npctransport.RelaxingSpring___hash__(self)
1329 
1330  def __str__(self):
1331  r"""__str__(RelaxingSpring self) -> std::string"""
1332  return _IMP_npctransport.RelaxingSpring___str__(self)
1333 
1334  def __repr__(self):
1335  r"""__repr__(RelaxingSpring self) -> std::string"""
1336  return _IMP_npctransport.RelaxingSpring___repr__(self)
1337 
1338  def _get_as_binary(self):
1339  r"""_get_as_binary(RelaxingSpring self) -> PyObject *"""
1340  return _IMP_npctransport.RelaxingSpring__get_as_binary(self)
1341 
1342  def _set_from_binary(self, p):
1343  r"""_set_from_binary(RelaxingSpring self, PyObject * p)"""
1344  return _IMP_npctransport.RelaxingSpring__set_from_binary(self, p)
1345 
1346  def __getstate__(self):
1347  p = self._get_as_binary()
1348  if len(self.__dict__) > 1:
1349  d = self.__dict__.copy()
1350  del d['this']
1351  p = (d, p)
1352  return p
1353 
1354  def __setstate__(self, p):
1355  if not hasattr(self, 'this'):
1356  self.__init__()
1357  if isinstance(p, tuple):
1358  d, p = p
1359  self.__dict__.update(d)
1360  return self._set_from_binary(p)
1361 
1362  __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1363 
1364 # Register RelaxingSpring in _IMP_npctransport:
1365 _IMP_npctransport.RelaxingSpring_swigregister(RelaxingSpring)
1366 class HarmonicSpringSingletonScore(IMP.SingletonScore):
1367  r"""Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1368 
1369  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1370 
1371  def __init__(self, *args):
1372  r"""__init__(HarmonicSpringSingletonScore self, double k1, double k2, std::string name="HarmonicSpringSingletonScore%1%") -> HarmonicSpringSingletonScore"""
1373  _IMP_npctransport.HarmonicSpringSingletonScore_swiginit(self, _IMP_npctransport.new_HarmonicSpringSingletonScore(*args))
1374 
1375  def set_k1(self, k1):
1376  r"""set_k1(HarmonicSpringSingletonScore self, double k1)"""
1377  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1378 
1379  def get_k1(self):
1380  r"""get_k1(HarmonicSpringSingletonScore self) -> double"""
1381  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1382 
1383  def set_k2(self, k2):
1384  r"""set_k2(HarmonicSpringSingletonScore self, double k2)"""
1385  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1386 
1387  def get_k2(self):
1388  r"""get_k2(HarmonicSpringSingletonScore self) -> double"""
1389  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1390 
1391  def do_get_inputs(self, m, pis):
1392  r"""do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1393  return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1394 
1395  def get_version_info(self):
1396  r"""get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1397  return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1398  __swig_destroy__ = _IMP_npctransport.delete_HarmonicSpringSingletonScore
1399 
1400  def __str__(self):
1401  r"""__str__(HarmonicSpringSingletonScore self) -> std::string"""
1402  return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1403 
1404  def __repr__(self):
1405  r"""__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1406  return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1407 
1408  @staticmethod
1409  def get_from(o):
1410  return _object_cast_to_HarmonicSpringSingletonScore(o)
1411 
1412 
1413 # Register HarmonicSpringSingletonScore in _IMP_npctransport:
1414 _IMP_npctransport.HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1415 class LinearInteraction(object):
1416  r"""Proxy of C++ IMP::npctransport::LinearInteraction 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__(LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction
1424  __init__(LinearInteraction self) -> LinearInteraction
1425  """
1426  _IMP_npctransport.LinearInteraction_swiginit(self, _IMP_npctransport.new_LinearInteraction(*args))
1427 
1428  def show(self, *args):
1429  r"""show(LinearInteraction self, _ostream out=std::cout)"""
1430  return _IMP_npctransport.LinearInteraction_show(self, *args)
1431  __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1432 
1433 # Register LinearInteraction in _IMP_npctransport:
1434 _IMP_npctransport.LinearInteraction_swigregister(LinearInteraction)
1435 class _DistancePairScoreForLinearSoftSphere(IMP.PairScore):
1436  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::npctransport::LinearSoftSphereScore > class."""
1437 
1438  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1439  __repr__ = _swig_repr
1440 
1441  def __init__(self, *args):
1442  r"""
1443  __init__(_DistancePairScoreForLinearSoftSphere self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _DistancePairScoreForLinearSoftSphere
1444  __init__(_DistancePairScoreForLinearSoftSphere self) -> _DistancePairScoreForLinearSoftSphere
1445  """
1446  _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swiginit(self, _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args))
1447 
1448  def do_get_inputs(self, m, pis):
1449  r"""do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1450  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1451 
1452  def get_score_functor(self):
1453  r"""get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1454  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1455 
1456  def get_version_info(self):
1457  r"""get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1458  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1459  __swig_destroy__ = _IMP_npctransport.delete__DistancePairScoreForLinearSoftSphere
1460 
1461 # Register _DistancePairScoreForLinearSoftSphere in _IMP_npctransport:
1462 _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1463 class _DistancePairScoreForLinearInteraction(IMP.PairScore):
1464  r"""Proxy of C++ IMP::score_functor::DistancePairScore< IMP::npctransport::LinearInteractionScore > class."""
1465 
1466  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1467  __repr__ = _swig_repr
1468 
1469  def __init__(self, *args):
1470  r"""
1471  __init__(_DistancePairScoreForLinearInteraction self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name="FunctorDistancePairScore %1%") -> _DistancePairScoreForLinearInteraction
1472  __init__(_DistancePairScoreForLinearInteraction self) -> _DistancePairScoreForLinearInteraction
1473  """
1474  _IMP_npctransport._DistancePairScoreForLinearInteraction_swiginit(self, _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args))
1475 
1476  def do_get_inputs(self, m, pis):
1477  r"""do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1478  return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1479 
1480  def get_score_functor(self):
1481  r"""get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1482  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1483 
1484  def get_version_info(self):
1485  r"""get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1486  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1487  __swig_destroy__ = _IMP_npctransport.delete__DistancePairScoreForLinearInteraction
1488 
1489 # Register _DistancePairScoreForLinearInteraction in _IMP_npctransport:
1490 _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1491 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1492  r"""Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1493 
1494  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1495 
1496  def __init__(self, *args):
1497  r"""__init__(FunctorLinearSoftSpherePairScore self, double k, std::string name="LinearSSPairScore%1%") -> FunctorLinearSoftSpherePairScore"""
1498  _IMP_npctransport.FunctorLinearSoftSpherePairScore_swiginit(self, _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args))
1499  __swig_destroy__ = _IMP_npctransport.delete_FunctorLinearSoftSpherePairScore
1500 
1501  def __str__(self):
1502  r"""__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1503  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1504 
1505  def __repr__(self):
1506  r"""__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1507  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1508 
1509  @staticmethod
1510  def get_from(o):
1511  return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1512 
1513 
1514 # Register FunctorLinearSoftSpherePairScore in _IMP_npctransport:
1515 _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1516 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1517  r"""Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1518 
1519  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1520 
1521  def __init__(self, *args):
1522  r"""__init__(FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name="LinearSSPairScore%1%") -> FunctorLinearInteractionPairScore"""
1523  _IMP_npctransport.FunctorLinearInteractionPairScore_swiginit(self, _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args))
1524  __swig_destroy__ = _IMP_npctransport.delete_FunctorLinearInteractionPairScore
1525 
1526  def __str__(self):
1527  r"""__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1528  return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1529 
1530  def __repr__(self):
1531  r"""__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1532  return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1533 
1534  @staticmethod
1535  def get_from(o):
1536  return _object_cast_to_FunctorLinearInteractionPairScore(o)
1537 
1538 
1539 # Register FunctorLinearInteractionPairScore in _IMP_npctransport:
1540 _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1541 class BrownianDynamicsTAMDWithSlabSupport(IMP.atom.BrownianDynamicsTAMD):
1542  r"""Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1543 
1544  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1545 
1546  def __init__(self, *args):
1547  r"""__init__(BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name="BrownianDynamicsTAMDWithSlabSupport%1%", double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport"""
1548  _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swiginit(self, _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args))
1549 
1550  def __str__(self):
1551  r"""__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1552  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1553 
1554  def __repr__(self):
1555  r"""__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1556  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1557 
1558  @staticmethod
1559  def get_from(o):
1560  return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1561 
1562  __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1563 
1564 # Register BrownianDynamicsTAMDWithSlabSupport in _IMP_npctransport:
1565 _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1566 class SitesPairScoreParameters(object):
1567  r"""Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1568 
1569  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1570  r = property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set, doc=r"""r : double""")
1571  k = property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set, doc=r"""k : double""")
1572  r2 = property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set, doc=r"""r2 : double""")
1573  kr = property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set, doc=r"""kr : double""")
1574  kr2 = property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set, doc=r"""kr2 : double""")
1575  cosSigma1_max = property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set, doc=r"""cosSigma1_max : double""")
1576  cosSigma2_max = property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set, doc=r"""cosSigma2_max : double""")
1577  is_orientational = property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set, doc=r"""is_orientational : bool""")
1578 
1579  def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1580  r"""__init__(SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters"""
1581  _IMP_npctransport.SitesPairScoreParameters_swiginit(self, _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg))
1582 
1583  def set_range(self, r):
1584  r"""set_range(SitesPairScoreParameters self, double r)"""
1585  return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1586 
1587  def set_force_coefficient(self, k):
1588  r"""set_force_coefficient(SitesPairScoreParameters self, double k)"""
1589  return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1590 
1591  def set_sigma1_max(self, sigma1_max_deg):
1592  r"""set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1593  return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1594 
1595  def set_sigma2_max(self, sigma2_max_deg):
1596  r"""set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1597  return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1598 
1599  def update_is_orientational(self):
1600  r"""update_is_orientational(SitesPairScoreParameters self)"""
1601  return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1602 
1603  def show(self, *args):
1604  r"""show(SitesPairScoreParameters self, _ostream out=std::cout)"""
1605  return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1606 
1607  def __str__(self):
1608  r"""__str__(SitesPairScoreParameters self) -> std::string"""
1609  return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1610 
1611  def __repr__(self):
1612  r"""__repr__(SitesPairScoreParameters self) -> std::string"""
1613  return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1614  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1615 
1616 # Register SitesPairScoreParameters in _IMP_npctransport:
1617 _IMP_npctransport.SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1618 class SitesGeometry(IMP.core.XYZRGeometry):
1619  r"""Proxy of C++ IMP::npctransport::SitesGeometry class."""
1620 
1621  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1622 
1623  def __init__(self, p, sites):
1624  r"""__init__(SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1625  _IMP_npctransport.SitesGeometry_swiginit(self, _IMP_npctransport.new_SitesGeometry(p, sites))
1626  __swig_destroy__ = _IMP_npctransport.delete_SitesGeometry
1627 
1628  def __str__(self):
1629  r"""__str__(SitesGeometry self) -> std::string"""
1630  return _IMP_npctransport.SitesGeometry___str__(self)
1631 
1632  def __repr__(self):
1633  r"""__repr__(SitesGeometry self) -> std::string"""
1634  return _IMP_npctransport.SitesGeometry___repr__(self)
1635 
1636  @staticmethod
1637  def get_from(o):
1638  return _object_cast_to_SitesGeometry(o)
1639 
1640 
1641 # Register SitesGeometry in _IMP_npctransport:
1642 _IMP_npctransport.SitesGeometry_swigregister(SitesGeometry)
1643 class TypedSitesGeometry(IMP.display.SingletonsGeometry):
1644  r"""Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1645 
1646  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1647 
1648  def __init__(self, sc):
1649  r"""__init__(TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1650  _IMP_npctransport.TypedSitesGeometry_swiginit(self, _IMP_npctransport.new_TypedSitesGeometry(sc))
1651 
1652  def set_sites(self, t, s):
1653  r"""set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1654  return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1655 
1656  def get_version_info(self):
1657  r"""get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1658  return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1659  __swig_destroy__ = _IMP_npctransport.delete_TypedSitesGeometry
1660 
1661  def __str__(self):
1662  r"""__str__(TypedSitesGeometry self) -> std::string"""
1663  return _IMP_npctransport.TypedSitesGeometry___str__(self)
1664 
1665  def __repr__(self):
1666  r"""__repr__(TypedSitesGeometry self) -> std::string"""
1667  return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1668 
1669  @staticmethod
1670  def get_from(o):
1671  return _object_cast_to_TypedSitesGeometry(o)
1672 
1673 
1674 # Register TypedSitesGeometry in _IMP_npctransport:
1675 _IMP_npctransport.TypedSitesGeometry_swigregister(TypedSitesGeometry)
1676 class SitesPairScore(LinearInteractionPairScore):
1677  r"""Proxy of C++ IMP::npctransport::SitesPairScore class."""
1678 
1679  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1680 
1681  def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1682  r"""__init__(SitesPairScore self, double range, double k, double sigma0_deg, double sigma1_deg, double range_nonspec_attraction, double k_nonspec_attraction, double k_nonspec_repulsion, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1) -> SitesPairScore"""
1683  _IMP_npctransport.SitesPairScore_swiginit(self, _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1))
1684 
1685  def get_sites_range(self):
1686  r"""get_sites_range(SitesPairScore self) -> double"""
1687  return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1688 
1689  def get_sites_k(self):
1690  r"""get_sites_k(SitesPairScore self) -> double"""
1691  return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1692 
1693  def get_parameters(self):
1694  r"""get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1695  return _IMP_npctransport.SitesPairScore_get_parameters(self)
1696  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScore
1697 
1698  def set_sites(self, sites0, sites1):
1699  r"""set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1700  return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1701 
1702  def set_sites0(self, sites0):
1703  r"""set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1704  return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1705 
1706  def set_sites1(self, sites1):
1707  r"""set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1708  return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1709 
1710  def __str__(self):
1711  r"""__str__(SitesPairScore self) -> std::string"""
1712  return _IMP_npctransport.SitesPairScore___str__(self)
1713 
1714  def __repr__(self):
1715  r"""__repr__(SitesPairScore self) -> std::string"""
1716  return _IMP_npctransport.SitesPairScore___repr__(self)
1717 
1718  @staticmethod
1719  def get_from(o):
1720  return _object_cast_to_SitesPairScore(o)
1721 
1722 
1723 # Register SitesPairScore in _IMP_npctransport:
1724 _IMP_npctransport.SitesPairScore_swigregister(SitesPairScore)
1725 class FGChain(IMP.Object):
1726  r"""Proxy of C++ IMP::npctransport::FGChain class."""
1727 
1728  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1729 
1730  def __init__(self, *args):
1731  r"""__init__(FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name="chain %1%") -> FGChain"""
1732  _IMP_npctransport.FGChain_swiginit(self, _IMP_npctransport.new_FGChain(*args))
1733 
1734  def get_root(self):
1735  r"""get_root(FGChain self) -> Hierarchy"""
1736  return _IMP_npctransport.FGChain_get_root(self)
1737 
1738  def get_beads(self):
1739  r"""get_beads(FGChain self) -> IMP::ParticlesTemp"""
1740  return _IMP_npctransport.FGChain_get_beads(self)
1741 
1742  def get_bead(self, i):
1743  r"""get_bead(FGChain self, unsigned int i) -> Particle"""
1744  return _IMP_npctransport.FGChain_get_bead(self, i)
1745 
1746  def get_bead_index(self, i):
1747  r"""get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1748  return _IMP_npctransport.FGChain_get_bead_index(self, i)
1749 
1750  def get_number_of_beads(self):
1751  r"""get_number_of_beads(FGChain self) -> unsigned int"""
1752  return _IMP_npctransport.FGChain_get_number_of_beads(self)
1753 
1754  def get_chain_restraints(self, scoring_manager):
1755  r"""get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1756  return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1757 
1758  def set_rest_length_factor(self, rlf):
1759  r"""set_rest_length_factor(FGChain self, double rlf)"""
1760  return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1761 
1762  def set_backbone_k(self, k):
1763  r"""set_backbone_k(FGChain self, double k)"""
1764  return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1765 
1766  def get_rest_length_factor(self):
1767  r"""get_rest_length_factor(FGChain self) -> double"""
1768  return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1769 
1770  def get_backbone_k(self):
1771  r"""get_backbone_k(FGChain self) -> double"""
1772  return _IMP_npctransport.FGChain_get_backbone_k(self)
1773 
1774  def get_version_info(self):
1775  r"""get_version_info(FGChain self) -> VersionInfo"""
1776  return _IMP_npctransport.FGChain_get_version_info(self)
1777  __swig_destroy__ = _IMP_npctransport.delete_FGChain
1778 
1779  def __str__(self):
1780  r"""__str__(FGChain self) -> std::string"""
1781  return _IMP_npctransport.FGChain___str__(self)
1782 
1783  def __repr__(self):
1784  r"""__repr__(FGChain self) -> std::string"""
1785  return _IMP_npctransport.FGChain___repr__(self)
1786 
1787  @staticmethod
1788  def get_from(o):
1789  return _object_cast_to_FGChain(o)
1790 
1791 
1792 # Register FGChain in _IMP_npctransport:
1793 _IMP_npctransport.FGChain_swigregister(FGChain)
1794 
1795 def create_fg_chain(sd, parent, fg_data, c):
1796  r"""create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1797  return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1798 
1799 def get_fg_chain(*args):
1800  r"""
1801  get_fg_chain(Hierarchy root) -> FGChain
1802  get_fg_chain(Particle p_root) -> FGChain
1803  """
1804  return _IMP_npctransport.get_fg_chain(*args)
1805 class Scoring(IMP.Object):
1806  r"""Proxy of C++ IMP::npctransport::Scoring class."""
1807 
1808  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1809 
1810  def __init__(self, owner_sd, data):
1811  r"""__init__(Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1812  _IMP_npctransport.Scoring_swiginit(self, _IMP_npctransport.new_Scoring(owner_sd, data))
1813 
1814  def get_scoring_function(self, force_update=False):
1815  r"""get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction"""
1816  return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1817 
1818  def get_scoring_function_restraints(self, force_update=False):
1819  r"""get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints"""
1820  return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1821 
1822  def get_custom_scoring_function(self, *args):
1823  r"""
1824  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1825  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1826  """
1827  return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1828 
1829  def get_close_beads_container(self, update=False):
1830  r"""get_close_beads_container(Scoring self, bool update=False) -> PairContainer"""
1831  return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1832 
1833  def get_predicates_pair_restraint(self, update=False):
1834  r"""get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint"""
1835  return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1836 
1837  def get_bounding_volume_restraint(self, update=False):
1838  r"""get_bounding_volume_restraint(Scoring self, bool update=False) -> Restraint"""
1839  return _IMP_npctransport.Scoring_get_bounding_volume_restraint(self, update)
1840 
1841  def get_slab_restraint(self, update=False):
1842  r"""get_slab_restraint(Scoring self, bool update=False) -> Restraint"""
1843  return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1844 
1845  def add_interaction(self, idata):
1846  r"""add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1847  return _IMP_npctransport.Scoring_add_interaction(self, idata)
1848 
1849  def create_close_beads_container(self, *args):
1850  r"""
1851  create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1852  create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1853  """
1854  return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
1855 
1856  def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
1857  r"""create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint"""
1858  return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
1859 
1860  def create_bounding_volume_restraint(self, beads):
1861  r"""create_bounding_volume_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1862  return _IMP_npctransport.Scoring_create_bounding_volume_restraint(self, beads)
1863 
1864  def create_slab_restraint(self, beads):
1865  r"""create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1866  return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
1867 
1868  def get_model(self):
1869  r"""get_model(Scoring self) -> Model"""
1870  return _IMP_npctransport.Scoring_get_model(self)
1871 
1872  def get_sd(self):
1873  r"""get_sd(Scoring self) -> SimulationData"""
1874  return _IMP_npctransport.Scoring_get_sd(self)
1875 
1876  def get_has_bounding_box(self):
1877  r"""get_has_bounding_box(Scoring self) -> bool"""
1878  return _IMP_npctransport.Scoring_get_has_bounding_box(self)
1879 
1880  def get_has_bounding_sphere(self):
1881  r"""get_has_bounding_sphere(Scoring self) -> bool"""
1882  return _IMP_npctransport.Scoring_get_has_bounding_sphere(self)
1883 
1884  def get_has_bounding_volume(self):
1885  r"""get_has_bounding_volume(Scoring self) -> bool"""
1886  return _IMP_npctransport.Scoring_get_has_bounding_volume(self)
1887 
1888  def get_default_backbone_k(self):
1889  r"""get_default_backbone_k(Scoring self) -> double"""
1890  return _IMP_npctransport.Scoring_get_default_backbone_k(self)
1891 
1892  def get_is_backbone_harmonic(self):
1893  r"""get_is_backbone_harmonic(Scoring self) -> bool"""
1894  return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
1895 
1896  def get_excluded_volume_k(self):
1897  r"""get_excluded_volume_k(Scoring self) -> double"""
1898  return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
1899 
1900  def get_interaction_k(self):
1901  r"""get_interaction_k(Scoring self) -> double"""
1902  return _IMP_npctransport.Scoring_get_interaction_k(self)
1903 
1904  def get_predicate_pair_score(self, *args):
1905  r"""
1906  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1907  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1908  """
1909  return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
1910 
1911  def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
1912  r"""get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double"""
1913  return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
1914 
1915  def get_ordered_type_pair_predicate(self):
1916  r"""get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
1917  return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
1918 
1919  def add_chain_restraints(self, chain):
1920  r"""add_chain_restraints(Scoring self, FGChain chain)"""
1921  return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
1922 
1923  def get_chain_restraints_on(self, beads):
1924  r"""get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
1925  return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
1926 
1927  def get_all_chain_restraints(self):
1928  r"""get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
1929  return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
1930 
1931  def remove_particle_type(self, pt):
1932  r"""remove_particle_type(Scoring self, ParticleType pt)"""
1933  return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
1934 
1935  def add_z_bias_restraint(self, *args):
1936  r"""
1937  add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
1938  add_z_bias_restraint(Scoring self, Particle p, double k)
1939  """
1940  return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
1941 
1942  def get_z_bias_restraints(self):
1943  r"""get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
1944  return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
1945 
1946  def create_z_bias_restraint(self, ps, k):
1947  r"""create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
1948  return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
1949 
1950  def add_custom_restraint(self, r):
1951  r"""add_custom_restraint(Scoring self, Restraint r)"""
1952  return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
1953 
1954  def add_custom_restraints(self, R):
1955  r"""add_custom_restraints(Scoring self, IMP::Restraints R)"""
1956  return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
1957 
1958  def clear_custom_restraints(self):
1959  r"""clear_custom_restraints(Scoring self)"""
1960  return _IMP_npctransport.Scoring_clear_custom_restraints(self)
1961 
1962  def get_custom_restraints(self):
1963  r"""get_custom_restraints(Scoring self) -> IMP::Restraints"""
1964  return _IMP_npctransport.Scoring_get_custom_restraints(self)
1965 
1966  def add_restrained_anchor_bead(self, p):
1967  r"""add_restrained_anchor_bead(Scoring self, Particle p)"""
1968  return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
1969 
1970  def get_pore_radius_restraint(self):
1971  r"""get_pore_radius_restraint(Scoring self) -> Restraint"""
1972  return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
1973 
1974  def get_range(self):
1975  r"""get_range(Scoring self) -> double"""
1976  return _IMP_npctransport.Scoring_get_range(self)
1977 
1978  def set_interaction_range_factor(self, type, value):
1979  r"""set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
1980  return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
1981 
1982  def set_interaction_k_factor(self, type, value):
1983  r"""set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
1984  return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
1985 
1986  def get_version_info(self):
1987  r"""get_version_info(Scoring self) -> VersionInfo"""
1988  return _IMP_npctransport.Scoring_get_version_info(self)
1989  __swig_destroy__ = _IMP_npctransport.delete_Scoring
1990 
1991  def __str__(self):
1992  r"""__str__(Scoring self) -> std::string"""
1993  return _IMP_npctransport.Scoring___str__(self)
1994 
1995  def __repr__(self):
1996  r"""__repr__(Scoring self) -> std::string"""
1997  return _IMP_npctransport.Scoring___repr__(self)
1998 
1999  @staticmethod
2000  def get_from(o):
2001  return _object_cast_to_Scoring(o)
2002 
2003 
2004 # Register Scoring in _IMP_npctransport:
2005 _IMP_npctransport.Scoring_swigregister(Scoring)
2006 class SimpleTimer(object):
2007  r"""Proxy of C++ IMP::internal::SimpleTimer class."""
2008 
2009  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2010  __repr__ = _swig_repr
2011 
2012  def __init__(self):
2013  r"""__init__(SimpleTimer self) -> SimpleTimer"""
2014  _IMP_npctransport.SimpleTimer_swiginit(self, _IMP_npctransport.new_SimpleTimer())
2015  __swig_destroy__ = _IMP_npctransport.delete_SimpleTimer
2016 
2017 # Register SimpleTimer in _IMP_npctransport:
2018 _IMP_npctransport.SimpleTimer_swigregister(SimpleTimer)
2019 class Statistics(IMP.Object):
2020  r"""Proxy of C++ IMP::npctransport::Statistics class."""
2021 
2022  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2023 
2024  def remove_particle_type(self, pt):
2025  r"""remove_particle_type(Statistics self, ParticleType pt)"""
2026  return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2027 
2028  def __init__(self, sd, statistics_interval_frames, output_file_name):
2029  r"""__init__(Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2030  _IMP_npctransport.Statistics_swiginit(self, _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name))
2031 
2032  def add_fg_chain_stats(self, fg_chain):
2033  r"""add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2034  return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2035 
2036  def add_floater_stats(self, p):
2037  r"""add_floater_stats(Statistics self, Particle p)"""
2038  return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2039 
2040  def add_interaction_stats(self, type0, type1):
2041  r"""add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2042  return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2043 
2044  def add_optimizer_states(self, o=None):
2045  r"""add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates"""
2046  return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2047 
2048  def update_particle_type_zr_distribution_map(self, p):
2049  r"""update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2050  return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2051 
2052  def update_particle_type_xyz_distribution_map(self, p):
2053  r"""update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2054  return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2055 
2056  def update(self, timer, nf_new=1, force_full_output=False):
2057  r"""update(Statistics self, SimpleTimer timer, unsigned int nf_new=1, bool force_full_output=False)"""
2058  return _IMP_npctransport.Statistics_update(self, timer, nf_new, force_full_output)
2059 
2060  def reset_statistics_optimizer_states(self):
2061  r"""reset_statistics_optimizer_states(Statistics self)"""
2062  return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2063 
2064  def set_interrupted(self, tf):
2065  r"""set_interrupted(Statistics self, bool tf)"""
2066  return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2067 
2068  def get_model(self):
2069  r"""get_model(Statistics self) -> Model"""
2070  return _IMP_npctransport.Statistics_get_model(self)
2071 
2072  def get_sd(self):
2073  r"""get_sd(Statistics self) -> SimulationData"""
2074  return _IMP_npctransport.Statistics_get_sd(self)
2075 
2076  def get_is_activated(self):
2077  r"""get_is_activated(Statistics self) -> bool"""
2078  return _IMP_npctransport.Statistics_get_is_activated(self)
2079 
2080  def get_output_file_name(self):
2081  r"""get_output_file_name(Statistics self) -> std::string"""
2082  return _IMP_npctransport.Statistics_get_output_file_name(self)
2083 
2084  def get_version_info(self):
2085  r"""get_version_info(Statistics self) -> VersionInfo"""
2086  return _IMP_npctransport.Statistics_get_version_info(self)
2087  __swig_destroy__ = _IMP_npctransport.delete_Statistics
2088 
2089  def __str__(self):
2090  r"""__str__(Statistics self) -> std::string"""
2091  return _IMP_npctransport.Statistics___str__(self)
2092 
2093  def __repr__(self):
2094  r"""__repr__(Statistics self) -> std::string"""
2095  return _IMP_npctransport.Statistics___repr__(self)
2096 
2097  @staticmethod
2098  def get_from(o):
2099  return _object_cast_to_Statistics(o)
2100 
2101 
2102 # Register Statistics in _IMP_npctransport:
2103 _IMP_npctransport.Statistics_swigregister(Statistics)
2104 
2105 def create_boost_timer():
2106  r"""create_boost_timer() -> SimpleTimer"""
2107  return _IMP_npctransport.create_boost_timer()
2108 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2109 
2110 class SimulationData(IMP.Object):
2111  r"""Proxy of C++ IMP::npctransport::SimulationData class."""
2112 
2113  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2114 
2115  def get_output_npctransport_version(self):
2116  r"""get_output_npctransport_version(SimulationData self) -> double"""
2117  return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2118 
2119  def get_range(self):
2120  r"""get_range(SimulationData self) -> double"""
2121  return _IMP_npctransport.SimulationData_get_range(self)
2122 
2123  def get_output_statistics_interval_frames(self):
2124  r"""get_output_statistics_interval_frames(SimulationData self) -> int"""
2125  return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2126 
2127  def get_full_output_statistics_interval_factor(self):
2128  r"""get_full_output_statistics_interval_factor(SimulationData self) -> int"""
2129  return _IMP_npctransport.SimulationData_get_full_output_statistics_interval_factor(self)
2130 
2131  def get_is_multiple_hdf5s(self):
2132  r"""get_is_multiple_hdf5s(SimulationData self) -> bool"""
2133  return _IMP_npctransport.SimulationData_get_is_multiple_hdf5s(self)
2134 
2135  def get_is_exclude_floaters_from_slab_initially(self):
2136  r"""get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2137  return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2138 
2139  def get_are_floaters_on_one_slab_side(self):
2140  r"""get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2141  return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2142 
2143  def get_is_xyz_hist_stats(self):
2144  r"""get_is_xyz_hist_stats(SimulationData self) -> bool"""
2145  return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2146 
2147  def get_xyz_stats_crop_factor(self):
2148  r"""get_xyz_stats_crop_factor(SimulationData self) -> double"""
2149  return _IMP_npctransport.SimulationData_get_xyz_stats_crop_factor(self)
2150 
2151  def get_xyz_stats_voxel_size_A(self):
2152  r"""get_xyz_stats_voxel_size_A(SimulationData self) -> double"""
2153  return _IMP_npctransport.SimulationData_get_xyz_stats_voxel_size_A(self)
2154 
2155  def get_xyz_stats_max_box_size_A(self):
2156  r"""get_xyz_stats_max_box_size_A(SimulationData self) -> double"""
2157  return _IMP_npctransport.SimulationData_get_xyz_stats_max_box_size_A(self)
2158 
2159  def get_angular_d_factor(self):
2160  r"""get_angular_d_factor(SimulationData self) -> double"""
2161  return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2162 
2163  def __init__(self, *args):
2164  r"""__init__(SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name=std::string(), std::string new_output_file="") -> SimulationData"""
2165  _IMP_npctransport.SimulationData_swiginit(self, _IMP_npctransport.new_SimulationData(*args))
2166 
2167  def get_model(self):
2168  r"""get_model(SimulationData self) -> Model"""
2169  return _IMP_npctransport.SimulationData_get_model(self)
2170 
2171  def get_scoring(self):
2172  r"""get_scoring(SimulationData self) -> Scoring"""
2173  return _IMP_npctransport.SimulationData_get_scoring(self)
2174 
2175  def get_statistics(self):
2176  r"""get_statistics(SimulationData self) -> Statistics"""
2177  return _IMP_npctransport.SimulationData_get_statistics(self)
2178 
2179  def get_bd(self, recreate=False):
2180  r"""get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics"""
2181  return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2182 
2183  def activate_statistics(self):
2184  r"""activate_statistics(SimulationData self)"""
2185  return _IMP_npctransport.SimulationData_activate_statistics(self)
2186 
2187  def get_statistics_fraction(self):
2188  r"""get_statistics_fraction(SimulationData self) -> double"""
2189  return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2190 
2191  def get_is_fg_bead(self, *args):
2192  r"""
2193  get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2194  get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2195  """
2196  return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2197 
2198  def get_is_fg_chain(self, *args):
2199  r"""
2200  get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2201  get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2202  """
2203  return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2204 
2205  def get_fg_bead_types(self):
2206  r"""get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2207  return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2208 
2209  def get_fg_chain_types(self):
2210  r"""get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2211  return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2212 
2213  def get_floater_types(self):
2214  r"""get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2215  return _IMP_npctransport.SimulationData_get_floater_types(self)
2216 
2217  def get_obstacle_types(self):
2218  r"""get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2219  return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2220 
2221  def get_fg_chain_roots(self):
2222  r"""get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2223  return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2224 
2225  def get_fg_chains(self):
2226  r"""get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2227  return _IMP_npctransport.SimulationData_get_fg_chains(self)
2228 
2229  def get_obstacle_particles(self):
2230  r"""get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2231  return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2232 
2233  def get_beads(self):
2234  r"""get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2235  return _IMP_npctransport.SimulationData_get_beads(self)
2236 
2237  def get_optimizable_beads(self):
2238  r"""get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2239  return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2240 
2241  def get_non_optimizable_beads(self):
2242  r"""get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2243  return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2244 
2245  def get_is_backbone_harmonic(self):
2246  r"""get_is_backbone_harmonic(SimulationData self) -> bool"""
2247  return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2248 
2249  def get_backbone_tau_ns(self):
2250  r"""get_backbone_tau_ns(SimulationData self) -> double"""
2251  return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2252 
2253  def get_temperature_k(self):
2254  r"""get_temperature_k(SimulationData self) -> double"""
2255  return _IMP_npctransport.SimulationData_get_temperature_k(self)
2256 
2257  def get_initial_simulation_time_ns(self):
2258  r"""get_initial_simulation_time_ns(SimulationData self) -> double"""
2259  return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2260 
2261  def get_site_centers(self, t0):
2262  r"""get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2263  return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2264 
2265  def get_sites(self, t0):
2266  r"""get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2267  return _IMP_npctransport.SimulationData_get_sites(self, t0)
2268 
2269  def set_sites(self, *args):
2270  r"""
2271  set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2272  set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2273  """
2274  return _IMP_npctransport.SimulationData_set_sites(self, *args)
2275 
2276  def get_site_display_radius(self, arg2):
2277  r"""get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2278  return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2279 
2280  def get_maximum_number_of_minutes(self):
2281  r"""get_maximum_number_of_minutes(SimulationData self) -> double"""
2282  return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2283 
2284  def remove_particle_type(self, pt):
2285  r"""remove_particle_type(SimulationData self, ParticleType pt)"""
2286  return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2287 
2288  def remove_fgs_with_prefix(self, s_fg_type):
2289  r"""remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2290  return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2291 
2292  def get_bounding_box(self):
2293  r"""get_bounding_box(SimulationData self) -> BoundingBox3D"""
2294  return _IMP_npctransport.SimulationData_get_bounding_box(self)
2295 
2296  def get_bounding_sphere(self):
2297  r"""get_bounding_sphere(SimulationData self) -> Sphere3D"""
2298  return _IMP_npctransport.SimulationData_get_bounding_sphere(self)
2299 
2300  def get_bounding_box_size(self):
2301  r"""get_bounding_box_size(SimulationData self) -> double"""
2302  return _IMP_npctransport.SimulationData_get_bounding_box_size(self)
2303 
2304  def set_bounding_box_size(self, box_size):
2305  r"""set_bounding_box_size(SimulationData self, double box_size)"""
2306  return _IMP_npctransport.SimulationData_set_bounding_box_size(self, box_size)
2307 
2308  def get_bounding_sphere_radius(self):
2309  r"""get_bounding_sphere_radius(SimulationData self) -> double"""
2310  return _IMP_npctransport.SimulationData_get_bounding_sphere_radius(self)
2311 
2312  def set_bounding_sphere_radius(self, sphere_radius):
2313  r"""set_bounding_sphere_radius(SimulationData self, double sphere_radius)"""
2314  return _IMP_npctransport.SimulationData_set_bounding_sphere_radius(self, sphere_radius)
2315 
2316  def get_bounding_volume(self):
2317  r"""get_bounding_volume(SimulationData self) -> double"""
2318  return _IMP_npctransport.SimulationData_get_bounding_volume(self)
2319 
2320  def set_bounding_volume(self, volume_A3):
2321  r"""set_bounding_volume(SimulationData self, double volume_A3)"""
2322  return _IMP_npctransport.SimulationData_set_bounding_volume(self, volume_A3)
2323 
2324  def get_has_slab(self):
2325  r"""get_has_slab(SimulationData self) -> bool"""
2326  return _IMP_npctransport.SimulationData_get_has_slab(self)
2327 
2328  def get_is_slab_with_cylindrical_pore(self):
2329  r"""get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2330  return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2331 
2332  def get_is_slab_with_toroidal_pore(self):
2333  r"""get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2334  return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2335 
2336  def get_slab_particle(self):
2337  r"""get_slab_particle(SimulationData self) -> Particle"""
2338  return _IMP_npctransport.SimulationData_get_slab_particle(self)
2339 
2340  def get_cylinder(self):
2341  r"""get_cylinder(SimulationData self) -> Cylinder3D"""
2342  return _IMP_npctransport.SimulationData_get_cylinder(self)
2343 
2344  def get_has_bounding_box(self):
2345  r"""get_has_bounding_box(SimulationData self) -> bool"""
2346  return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2347 
2348  def get_has_bounding_sphere(self):
2349  r"""get_has_bounding_sphere(SimulationData self) -> bool"""
2350  return _IMP_npctransport.SimulationData_get_has_bounding_sphere(self)
2351 
2352  def get_has_bounding_volume(self):
2353  r"""get_has_bounding_volume(SimulationData self) -> bool"""
2354  return _IMP_npctransport.SimulationData_get_has_bounding_volume(self)
2355 
2356  def initialize_positions_from_rmf(self, fh, frame_number=-1):
2357  r"""initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)"""
2358  return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2359 
2360  def link_rmf_file_handle(self, fh, is_restraints=True):
2361  r"""link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)"""
2362  return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2363 
2364  def get_rmf_sos_writer(self):
2365  r"""get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2366  return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2367 
2368  def reset_rmf(self):
2369  r"""reset_rmf(SimulationData self)"""
2370  return _IMP_npctransport.SimulationData_reset_rmf(self)
2371 
2372  def switch_suspend_rmf(self, suspend):
2373  r"""switch_suspend_rmf(SimulationData self, bool suspend)"""
2374  return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2375 
2376  def write_geometry(self, out):
2377  r"""write_geometry(SimulationData self, std::string out)"""
2378  return _IMP_npctransport.SimulationData_write_geometry(self, out)
2379 
2380  def dump_geometry(self):
2381  r"""dump_geometry(SimulationData self)"""
2382  return _IMP_npctransport.SimulationData_dump_geometry(self)
2383 
2384  def get_root_of_type(self, type):
2385  r"""get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2386  return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2387 
2388  def get_number_of_frames(self):
2389  r"""get_number_of_frames(SimulationData self) -> unsigned int"""
2390  return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2391 
2392  def get_number_of_trials(self):
2393  r"""get_number_of_trials(SimulationData self) -> unsigned int"""
2394  return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2395 
2396  def get_root(self):
2397  r"""get_root(SimulationData self) -> Hierarchy"""
2398  return _IMP_npctransport.SimulationData_get_root(self)
2399 
2400  def get_slab_thickness(self):
2401  r"""get_slab_thickness(SimulationData self) -> double"""
2402  return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2403 
2404  def get_tunnel_radius(self):
2405  r"""get_tunnel_radius(SimulationData self) -> double"""
2406  return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2407 
2408  def get_pore_radius(self):
2409  r"""get_pore_radius(SimulationData self) -> double"""
2410  return _IMP_npctransport.SimulationData_get_pore_radius(self)
2411 
2412  def get_tunnel_radius_k(self):
2413  r"""get_tunnel_radius_k(SimulationData self) -> double"""
2414  return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2415 
2416  def get_pore_radius_k(self):
2417  r"""get_pore_radius_k(SimulationData self) -> double"""
2418  return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2419 
2420  def get_is_pore_radius_dynamic(self):
2421  r"""get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2422  return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2423 
2424  def get_pore_anchored_beads_k(self):
2425  r"""get_pore_anchored_beads_k(SimulationData self) -> double"""
2426  return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2427 
2428  def get_static_geometry(self):
2429  r"""get_static_geometry(SimulationData self) -> Geometry"""
2430  return _IMP_npctransport.SimulationData_get_static_geometry(self)
2431 
2432  def get_rmf_dump_interval_frames(self):
2433  r"""get_rmf_dump_interval_frames(SimulationData self) -> int"""
2434  return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2435 
2436  def get_rmf_file_name(self):
2437  r"""get_rmf_file_name(SimulationData self) -> std::string"""
2438  return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2439 
2440  def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2441  r"""set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)"""
2442  return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2443 
2444  def get_version_info(self):
2445  r"""get_version_info(SimulationData self) -> VersionInfo"""
2446  return _IMP_npctransport.SimulationData_get_version_info(self)
2447  __swig_destroy__ = _IMP_npctransport.delete_SimulationData
2448 
2449  def __str__(self):
2450  r"""__str__(SimulationData self) -> std::string"""
2451  return _IMP_npctransport.SimulationData___str__(self)
2452 
2453  def __repr__(self):
2454  r"""__repr__(SimulationData self) -> std::string"""
2455  return _IMP_npctransport.SimulationData___repr__(self)
2456 
2457  @staticmethod
2458  def get_from(o):
2459  return _object_cast_to_SimulationData(o)
2460 
2461 
2462 # Register SimulationData in _IMP_npctransport:
2463 _IMP_npctransport.SimulationData_swigregister(SimulationData)
2464 
2465 def get_simulation_data_key():
2466  r"""get_simulation_data_key() -> IMP::WeakObjectKey"""
2467  return _IMP_npctransport.get_simulation_data_key()
2468 
2469 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2470  r"""write_geometry(IMP::ParticlesTemp const & kaps, IMP::algebra::Sphere3Ds const & kap_sites, IMP::ParticlesTemp const & chains, IMP::algebra::Sphere3Ds const & chain_sites, IMP::RestraintsTemp const & rs, Writer out)"""
2471  return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2472 class ParticleFactory(IMP.Object):
2473  r"""Proxy of C++ IMP::npctransport::ParticleFactory class."""
2474 
2475  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2476  sd_ = property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set, doc=r"""sd_ : IMP::WeakPointer<(IMP::npctransport::SimulationData)>""")
2477  radius_ = property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set, doc=r"""radius_ : double""")
2478  D_factor_ = property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set, doc=r"""D_factor_ : double""")
2479  angular_D_factor_ = property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set, doc=r"""angular_D_factor_ : double""")
2480  color_ = property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set, doc=r"""color_ : IMP::display::Color""")
2481  type_ = property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set, doc=r"""type_ : IMP::core::ParticleType""")
2482 
2483  def __init__(self, *args):
2484  r"""__init__(ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name="Particle factory %1%") -> ParticleFactory"""
2485  _IMP_npctransport.ParticleFactory_swiginit(self, _IMP_npctransport.new_ParticleFactory(*args))
2486 
2487  def create(self, *args):
2488  r"""create(ParticleFactory self, std::string name="") -> Particle"""
2489  return _IMP_npctransport.ParticleFactory_create(self, *args)
2490 
2491  def get_model(self):
2492  r"""get_model(ParticleFactory self) -> Model"""
2493  return _IMP_npctransport.ParticleFactory_get_model(self)
2494 
2495  def get_simulation_data(self):
2496  r"""get_simulation_data(ParticleFactory self) -> SimulationData"""
2497  return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2498 
2499  def get_radius(self):
2500  r"""get_radius(ParticleFactory self) -> double"""
2501  return _IMP_npctransport.ParticleFactory_get_radius(self)
2502 
2503  def get_version_info(self):
2504  r"""get_version_info(ParticleFactory self) -> VersionInfo"""
2505  return _IMP_npctransport.ParticleFactory_get_version_info(self)
2506  __swig_destroy__ = _IMP_npctransport.delete_ParticleFactory
2507 
2508  def __str__(self):
2509  r"""__str__(ParticleFactory self) -> std::string"""
2510  return _IMP_npctransport.ParticleFactory___str__(self)
2511 
2512  def __repr__(self):
2513  r"""__repr__(ParticleFactory self) -> std::string"""
2514  return _IMP_npctransport.ParticleFactory___repr__(self)
2515 
2516  @staticmethod
2517  def get_from(o):
2518  return _object_cast_to_ParticleFactory(o)
2519 
2520 
2521 # Register ParticleFactory in _IMP_npctransport:
2522 _IMP_npctransport.ParticleFactory_swigregister(ParticleFactory)
2523 class HierarchyWithSitesLoadLink(IMP.rmf.HierarchyLoadLink):
2524  r"""Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2525 
2526  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2527 
2528  def __init__(self, fh):
2529  r"""__init__(HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2530  _IMP_npctransport.HierarchyWithSitesLoadLink_swiginit(self, _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh))
2531 
2532  @staticmethod
2533  def get_name():
2534  r"""get_name() -> char const *"""
2535  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2536 
2537  def __str__(self):
2538  r"""__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2539  return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2540 
2541  def __repr__(self):
2542  r"""__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2543  return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2544 
2545  @staticmethod
2546  def get_from(o):
2547  return _object_cast_to_HierarchyWithSitesLoadLink(o)
2548 
2549  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2550 
2551 # Register HierarchyWithSitesLoadLink in _IMP_npctransport:
2552 _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2553 class HierarchyWithSitesSaveLink(IMP.rmf.HierarchySaveLink):
2554  r"""Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2555 
2556  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2557 
2558  def __init__(self, fh):
2559  r"""__init__(HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2560  _IMP_npctransport.HierarchyWithSitesSaveLink_swiginit(self, _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh))
2561 
2562  @staticmethod
2563  def get_name():
2564  r"""get_name() -> char const *"""
2565  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2566 
2567  def __str__(self):
2568  r"""__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2569  return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2570 
2571  def __repr__(self):
2572  r"""__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2573  return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2574 
2575  @staticmethod
2576  def get_from(o):
2577  return _object_cast_to_HierarchyWithSitesSaveLink(o)
2578 
2579  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2580 
2581 # Register HierarchyWithSitesSaveLink in _IMP_npctransport:
2582 _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2583 
2584 def add_test_sites(*args):
2585  r"""
2586  add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2587  add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2588  """
2589  return _IMP_npctransport.add_test_sites(*args)
2590 
2591 def add_hierarchies_with_sites(*args):
2592  r"""
2593  add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2594  add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2595  """
2596  return _IMP_npctransport.add_hierarchies_with_sites(*args)
2597 
2598 def add_hierarchy_with_sites(fh, hs):
2599  r"""add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2600  return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2601 
2603  r"""create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2604  return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2605 
2606 def link_hierarchies_with_sites(fh, hs):
2607  r"""link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2608  return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2609 class Transporting(IMP.Decorator):
2610  r"""Proxy of C++ IMP::npctransport::Transporting class."""
2611 
2612  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2613 
2614  def __init__(self, *args):
2615  r"""
2616  __init__(Transporting self) -> Transporting
2617  __init__(Transporting self, Model m, ParticleIndex id) -> Transporting
2618  __init__(Transporting self, _ParticleAdaptor d) -> Transporting
2619  """
2620  _IMP_npctransport.Transporting_swiginit(self, _IMP_npctransport.new_Transporting(*args))
2621 
2622  def show(self, *args):
2623  r"""show(Transporting self, _ostream out=std::cout)"""
2624  return _IMP_npctransport.Transporting_show(self, *args)
2625 
2626  @staticmethod
2627  def setup_particle(*args):
2628  r"""
2629  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2630  setup_particle(_ParticleAdaptor pa, bool is_last_entry_from_top=False) -> Transporting
2631  """
2632  return _IMP_npctransport.Transporting_setup_particle(*args)
2633 
2634  @staticmethod
2635  def get_is_setup(*args):
2636  r"""
2637  get_is_setup(_ParticleAdaptor p) -> bool
2638  get_is_setup(Model m, ParticleIndex pi) -> bool
2639  """
2640  return _IMP_npctransport.Transporting_get_is_setup(*args)
2641 
2642  def set_is_last_entry_from_top(self, is_last_entry_from_top):
2643  r"""set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2644  return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2645 
2646  def get_is_last_entry_from_top(self):
2647  r"""get_is_last_entry_from_top(Transporting self) -> bool"""
2648  return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2649 
2650  @staticmethod
2651  def get_is_last_entry_from_top_key():
2652  r"""get_is_last_entry_from_top_key() -> IntKey"""
2653  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
2654 
2655  def set_last_tracked_z(self, last_tracked_z):
2656  r"""set_last_tracked_z(Transporting self, double last_tracked_z)"""
2657  return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
2658 
2659  def get_last_tracked_z(self):
2660  r"""get_last_tracked_z(Transporting self) -> double"""
2661  return _IMP_npctransport.Transporting_get_last_tracked_z(self)
2662 
2663  @staticmethod
2664  def get_last_tracked_z_key():
2665  r"""get_last_tracked_z_key() -> FloatKey"""
2666  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
2667 
2668  def set_n_entries_bottom(self, n):
2669  r"""set_n_entries_bottom(Transporting self, int n)"""
2670  return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
2671 
2672  def get_n_entries_bottom(self):
2673  r"""get_n_entries_bottom(Transporting self) -> int"""
2674  return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
2675 
2676  @staticmethod
2677  def get_n_entries_bottom_key():
2678  r"""get_n_entries_bottom_key() -> IntKey"""
2679  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
2680 
2681  def set_n_entries_top(self, n):
2682  r"""set_n_entries_top(Transporting self, int n)"""
2683  return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
2684 
2685  def get_n_entries_top(self):
2686  r"""get_n_entries_top(Transporting self) -> int"""
2687  return _IMP_npctransport.Transporting_get_n_entries_top(self)
2688 
2689  @staticmethod
2690  def get_n_entries_top_key():
2691  r"""get_n_entries_top_key() -> IntKey"""
2692  return _IMP_npctransport.Transporting_get_n_entries_top_key()
2693 
2694  def add_attribute(self, *args):
2695  r"""
2696  add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
2697  add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
2698  add_attribute(Transporting self, IntKey a0, IMP::Int a1)
2699  add_attribute(Transporting self, FloatsKey a0, IMP::Floats a1)
2700  add_attribute(Transporting self, IntsKey a0, IMP::Ints a1)
2701  add_attribute(Transporting self, StringKey a0, IMP::String a1)
2702  add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
2703  add_attribute(Transporting self, ObjectKey a0, Object a1)
2704  add_attribute(Transporting self, SparseFloatKey a0, IMP::Float a1)
2705  add_attribute(Transporting self, SparseIntKey a0, IMP::Int a1)
2706  add_attribute(Transporting self, SparseStringKey a0, IMP::String a1)
2707  add_attribute(Transporting self, SparseParticleIndexKey a0, ParticleIndex a1)
2708  """
2709  return _IMP_npctransport.Transporting_add_attribute(self, *args)
2710 
2711  def get_value(self, *args):
2712  r"""
2713  get_value(Transporting self, FloatKey a0) -> IMP::Float
2714  get_value(Transporting self, IntKey a0) -> IMP::Int
2715  get_value(Transporting self, FloatsKey a0) -> IMP::Floats
2716  get_value(Transporting self, IntsKey a0) -> IMP::Ints
2717  get_value(Transporting self, StringKey a0) -> IMP::String
2718  get_value(Transporting self, ParticleIndexKey a0) -> Particle
2719  get_value(Transporting self, ObjectKey a0) -> Object
2720  get_value(Transporting self, SparseFloatKey a0) -> IMP::Float
2721  get_value(Transporting self, SparseIntKey a0) -> IMP::Int
2722  get_value(Transporting self, SparseStringKey a0) -> IMP::String
2723  get_value(Transporting self, SparseParticleIndexKey a0) -> ParticleIndex
2724  """
2725  return _IMP_npctransport.Transporting_get_value(self, *args)
2726 
2727  def set_value(self, *args):
2728  r"""
2729  set_value(Transporting self, FloatKey a0, IMP::Float a1)
2730  set_value(Transporting self, IntKey a0, IMP::Int a1)
2731  set_value(Transporting self, FloatsKey a0, IMP::Floats a1)
2732  set_value(Transporting self, IntsKey a0, IMP::Ints a1)
2733  set_value(Transporting self, StringKey a0, IMP::String a1)
2734  set_value(Transporting self, ParticleIndexKey a0, Particle a1)
2735  set_value(Transporting self, ObjectKey a0, Object a1)
2736  set_value(Transporting self, SparseFloatKey a0, IMP::Float a1)
2737  set_value(Transporting self, SparseIntKey a0, IMP::Int a1)
2738  set_value(Transporting self, SparseStringKey a0, IMP::String a1)
2739  set_value(Transporting self, SparseParticleIndexKey a0, ParticleIndex a1)
2740  """
2741  return _IMP_npctransport.Transporting_set_value(self, *args)
2742 
2743  def remove_attribute(self, *args):
2744  r"""
2745  remove_attribute(Transporting self, FloatKey a0)
2746  remove_attribute(Transporting self, IntKey a0)
2747  remove_attribute(Transporting self, FloatsKey a0)
2748  remove_attribute(Transporting self, IntsKey a0)
2749  remove_attribute(Transporting self, StringKey a0)
2750  remove_attribute(Transporting self, ParticleIndexKey a0)
2751  remove_attribute(Transporting self, ObjectKey a0)
2752  remove_attribute(Transporting self, SparseFloatKey a0)
2753  remove_attribute(Transporting self, SparseIntKey a0)
2754  remove_attribute(Transporting self, SparseStringKey a0)
2755  remove_attribute(Transporting self, SparseParticleIndexKey a0)
2756  """
2757  return _IMP_npctransport.Transporting_remove_attribute(self, *args)
2758 
2759  def has_attribute(self, *args):
2760  r"""
2761  has_attribute(Transporting self, FloatKey a0) -> bool
2762  has_attribute(Transporting self, IntKey a0) -> bool
2763  has_attribute(Transporting self, FloatsKey a0) -> bool
2764  has_attribute(Transporting self, IntsKey a0) -> bool
2765  has_attribute(Transporting self, StringKey a0) -> bool
2766  has_attribute(Transporting self, ParticleIndexKey a0) -> bool
2767  has_attribute(Transporting self, ObjectKey a0) -> bool
2768  has_attribute(Transporting self, SparseFloatKey a0) -> bool
2769  has_attribute(Transporting self, SparseIntKey a0) -> bool
2770  has_attribute(Transporting self, SparseStringKey a0) -> bool
2771  has_attribute(Transporting self, SparseParticleIndexKey a0) -> bool
2772  """
2773  return _IMP_npctransport.Transporting_has_attribute(self, *args)
2774 
2775  def get_derivative(self, a0):
2776  r"""get_derivative(Transporting self, FloatKey a0) -> double"""
2777  return _IMP_npctransport.Transporting_get_derivative(self, a0)
2778 
2779  def get_name(self):
2780  r"""get_name(Transporting self) -> std::string"""
2781  return _IMP_npctransport.Transporting_get_name(self)
2782 
2783  def clear_caches(self):
2784  r"""clear_caches(Transporting self)"""
2785  return _IMP_npctransport.Transporting_clear_caches(self)
2786 
2787  def set_name(self, a0):
2788  r"""set_name(Transporting self, std::string a0)"""
2789  return _IMP_npctransport.Transporting_set_name(self, a0)
2790 
2791  def set_check_level(self, a0):
2792  r"""set_check_level(Transporting self, IMP::CheckLevel a0)"""
2793  return _IMP_npctransport.Transporting_set_check_level(self, a0)
2794 
2795  def add_to_derivative(self, a0, a1, a2):
2796  r"""add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2797  return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
2798 
2799  def set_is_optimized(self, a0, a1):
2800  r"""set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
2801  return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
2802 
2803  def get_is_optimized(self, a0):
2804  r"""get_is_optimized(Transporting self, FloatKey a0) -> bool"""
2805  return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
2806 
2807  def get_check_level(self):
2808  r"""get_check_level(Transporting self) -> IMP::CheckLevel"""
2809  return _IMP_npctransport.Transporting_get_check_level(self)
2810 
2811  def __eq__(self, *args):
2812  r"""
2813  __eq__(Transporting self, Transporting o) -> bool
2814  __eq__(Transporting self, Particle d) -> bool
2815  """
2816  return _IMP_npctransport.Transporting___eq__(self, *args)
2817 
2818  def __ne__(self, *args):
2819  r"""
2820  __ne__(Transporting self, Transporting o) -> bool
2821  __ne__(Transporting self, Particle d) -> bool
2822  """
2823  return _IMP_npctransport.Transporting___ne__(self, *args)
2824 
2825  def __le__(self, *args):
2826  r"""
2827  __le__(Transporting self, Transporting o) -> bool
2828  __le__(Transporting self, Particle d) -> bool
2829  """
2830  return _IMP_npctransport.Transporting___le__(self, *args)
2831 
2832  def __lt__(self, *args):
2833  r"""
2834  __lt__(Transporting self, Transporting o) -> bool
2835  __lt__(Transporting self, Particle d) -> bool
2836  """
2837  return _IMP_npctransport.Transporting___lt__(self, *args)
2838 
2839  def __ge__(self, *args):
2840  r"""
2841  __ge__(Transporting self, Transporting o) -> bool
2842  __ge__(Transporting self, Particle d) -> bool
2843  """
2844  return _IMP_npctransport.Transporting___ge__(self, *args)
2845 
2846  def __gt__(self, *args):
2847  r"""
2848  __gt__(Transporting self, Transporting o) -> bool
2849  __gt__(Transporting self, Particle d) -> bool
2850  """
2851  return _IMP_npctransport.Transporting___gt__(self, *args)
2852 
2853  def __hash__(self):
2854  r"""__hash__(Transporting self) -> std::size_t"""
2855  return _IMP_npctransport.Transporting___hash__(self)
2856 
2857  def __str__(self):
2858  r"""__str__(Transporting self) -> std::string"""
2859  return _IMP_npctransport.Transporting___str__(self)
2860 
2861  def __repr__(self):
2862  r"""__repr__(Transporting self) -> std::string"""
2863  return _IMP_npctransport.Transporting___repr__(self)
2864 
2865  def _get_as_binary(self):
2866  r"""_get_as_binary(Transporting self) -> PyObject *"""
2867  return _IMP_npctransport.Transporting__get_as_binary(self)
2868 
2869  def _set_from_binary(self, p):
2870  r"""_set_from_binary(Transporting self, PyObject * p)"""
2871  return _IMP_npctransport.Transporting__set_from_binary(self, p)
2872 
2873  def __getstate__(self):
2874  p = self._get_as_binary()
2875  if len(self.__dict__) > 1:
2876  d = self.__dict__.copy()
2877  del d['this']
2878  p = (d, p)
2879  return p
2880 
2881  def __setstate__(self, p):
2882  if not hasattr(self, 'this'):
2883  self.__init__()
2884  if isinstance(p, tuple):
2885  d, p = p
2886  self.__dict__.update(d)
2887  return self._set_from_binary(p)
2888 
2889  __swig_destroy__ = _IMP_npctransport.delete_Transporting
2890 
2891 # Register Transporting in _IMP_npctransport:
2892 _IMP_npctransport.Transporting_swigregister(Transporting)
2893 
2894 def show_ranges(fname):
2895  r"""show_ranges(std::string fname)"""
2896  return _IMP_npctransport.show_ranges(fname)
2897 
2898 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
2899  r"""assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed) -> int"""
2900  return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
2901 
2902 def get_number_of_work_units(configuration_file):
2903  r"""get_number_of_work_units(std::string configuration_file) -> int"""
2904  return _IMP_npctransport.get_number_of_work_units(configuration_file)
2905 class SlabWithPore(IMP.Decorator):
2906  r"""Proxy of C++ IMP::npctransport::SlabWithPore class."""
2907 
2908  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2909 
2910  def __init__(self, *args):
2911  r"""
2912  __init__(SlabWithPore self) -> SlabWithPore
2913  __init__(SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
2914  __init__(SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
2915  """
2916  _IMP_npctransport.SlabWithPore_swiginit(self, _IMP_npctransport.new_SlabWithPore(*args))
2917 
2918  def show(self, *args):
2919  r"""show(SlabWithPore self, _ostream out=std::cout)"""
2920  return _IMP_npctransport.SlabWithPore_show(self, *args)
2921 
2922  @staticmethod
2923  def setup_particle(*args):
2924  r"""
2925  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
2926  setup_particle(_ParticleAdaptor pa, double thickness, double pore_radius) -> SlabWithPore
2927  """
2928  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
2929 
2930  @staticmethod
2931  def get_is_setup(*args):
2932  r"""
2933  get_is_setup(_ParticleAdaptor p) -> bool
2934  get_is_setup(Model m, ParticleIndex pi) -> bool
2935  """
2936  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
2937 
2938  def set_thickness(self, thickness):
2939  r"""set_thickness(SlabWithPore self, double thickness)"""
2940  return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
2941 
2942  def get_thickness(self):
2943  r"""get_thickness(SlabWithPore self) -> IMP::Float"""
2944  return _IMP_npctransport.SlabWithPore_get_thickness(self)
2945 
2946  def get_pore_radius(self):
2947  r"""get_pore_radius(SlabWithPore self) -> IMP::Float"""
2948  return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
2949 
2950  def set_pore_radius(self, r):
2951  r"""set_pore_radius(SlabWithPore self, double r)"""
2952  return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
2953 
2954  def add_to_pore_radius_derivative(self, v, d):
2955  r"""add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
2956  return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
2957 
2958  def get_pore_radius_is_optimized(self):
2959  r"""get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
2960  return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
2961 
2962  def set_pore_radius_is_optimized(self, tf):
2963  r"""set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
2964  return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
2965 
2966  @staticmethod
2967  def get_thickness_key():
2968  r"""get_thickness_key() -> FloatKey"""
2969  return _IMP_npctransport.SlabWithPore_get_thickness_key()
2970 
2971  @staticmethod
2972  def get_pore_radius_key():
2973  r"""get_pore_radius_key() -> FloatKey"""
2974  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
2975 
2976  def add_attribute(self, *args):
2977  r"""
2978  add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
2979  add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
2980  add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
2981  add_attribute(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
2982  add_attribute(SlabWithPore self, IntsKey a0, IMP::Ints a1)
2983  add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
2984  add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
2985  add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
2986  add_attribute(SlabWithPore self, SparseFloatKey a0, IMP::Float a1)
2987  add_attribute(SlabWithPore self, SparseIntKey a0, IMP::Int a1)
2988  add_attribute(SlabWithPore self, SparseStringKey a0, IMP::String a1)
2989  add_attribute(SlabWithPore self, SparseParticleIndexKey a0, ParticleIndex a1)
2990  """
2991  return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
2992 
2993  def get_value(self, *args):
2994  r"""
2995  get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
2996  get_value(SlabWithPore self, IntKey a0) -> IMP::Int
2997  get_value(SlabWithPore self, FloatsKey a0) -> IMP::Floats
2998  get_value(SlabWithPore self, IntsKey a0) -> IMP::Ints
2999  get_value(SlabWithPore self, StringKey a0) -> IMP::String
3000  get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3001  get_value(SlabWithPore self, ObjectKey a0) -> Object
3002  get_value(SlabWithPore self, SparseFloatKey a0) -> IMP::Float
3003  get_value(SlabWithPore self, SparseIntKey a0) -> IMP::Int
3004  get_value(SlabWithPore self, SparseStringKey a0) -> IMP::String
3005  get_value(SlabWithPore self, SparseParticleIndexKey a0) -> ParticleIndex
3006  """
3007  return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3008 
3009  def set_value(self, *args):
3010  r"""
3011  set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3012  set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3013  set_value(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3014  set_value(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3015  set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3016  set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3017  set_value(SlabWithPore self, ObjectKey a0, Object a1)
3018  set_value(SlabWithPore self, SparseFloatKey a0, IMP::Float a1)
3019  set_value(SlabWithPore self, SparseIntKey a0, IMP::Int a1)
3020  set_value(SlabWithPore self, SparseStringKey a0, IMP::String a1)
3021  set_value(SlabWithPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3022  """
3023  return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3024 
3025  def remove_attribute(self, *args):
3026  r"""
3027  remove_attribute(SlabWithPore self, FloatKey a0)
3028  remove_attribute(SlabWithPore self, IntKey a0)
3029  remove_attribute(SlabWithPore self, FloatsKey a0)
3030  remove_attribute(SlabWithPore self, IntsKey a0)
3031  remove_attribute(SlabWithPore self, StringKey a0)
3032  remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3033  remove_attribute(SlabWithPore self, ObjectKey a0)
3034  remove_attribute(SlabWithPore self, SparseFloatKey a0)
3035  remove_attribute(SlabWithPore self, SparseIntKey a0)
3036  remove_attribute(SlabWithPore self, SparseStringKey a0)
3037  remove_attribute(SlabWithPore self, SparseParticleIndexKey a0)
3038  """
3039  return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3040 
3041  def has_attribute(self, *args):
3042  r"""
3043  has_attribute(SlabWithPore self, FloatKey a0) -> bool
3044  has_attribute(SlabWithPore self, IntKey a0) -> bool
3045  has_attribute(SlabWithPore self, FloatsKey a0) -> bool
3046  has_attribute(SlabWithPore self, IntsKey a0) -> bool
3047  has_attribute(SlabWithPore self, StringKey a0) -> bool
3048  has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3049  has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3050  has_attribute(SlabWithPore self, SparseFloatKey a0) -> bool
3051  has_attribute(SlabWithPore self, SparseIntKey a0) -> bool
3052  has_attribute(SlabWithPore self, SparseStringKey a0) -> bool
3053  has_attribute(SlabWithPore self, SparseParticleIndexKey a0) -> bool
3054  """
3055  return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3056 
3057  def get_derivative(self, a0):
3058  r"""get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3059  return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3060 
3061  def get_name(self):
3062  r"""get_name(SlabWithPore self) -> std::string"""
3063  return _IMP_npctransport.SlabWithPore_get_name(self)
3064 
3065  def clear_caches(self):
3066  r"""clear_caches(SlabWithPore self)"""
3067  return _IMP_npctransport.SlabWithPore_clear_caches(self)
3068 
3069  def set_name(self, a0):
3070  r"""set_name(SlabWithPore self, std::string a0)"""
3071  return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3072 
3073  def set_check_level(self, a0):
3074  r"""set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3075  return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3076 
3077  def add_to_derivative(self, a0, a1, a2):
3078  r"""add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3079  return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3080 
3081  def set_is_optimized(self, a0, a1):
3082  r"""set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3083  return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3084 
3085  def get_is_optimized(self, a0):
3086  r"""get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3087  return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3088 
3089  def get_check_level(self):
3090  r"""get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3091  return _IMP_npctransport.SlabWithPore_get_check_level(self)
3092 
3093  def __eq__(self, *args):
3094  r"""
3095  __eq__(SlabWithPore self, SlabWithPore o) -> bool
3096  __eq__(SlabWithPore self, Particle d) -> bool
3097  """
3098  return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3099 
3100  def __ne__(self, *args):
3101  r"""
3102  __ne__(SlabWithPore self, SlabWithPore o) -> bool
3103  __ne__(SlabWithPore self, Particle d) -> bool
3104  """
3105  return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3106 
3107  def __le__(self, *args):
3108  r"""
3109  __le__(SlabWithPore self, SlabWithPore o) -> bool
3110  __le__(SlabWithPore self, Particle d) -> bool
3111  """
3112  return _IMP_npctransport.SlabWithPore___le__(self, *args)
3113 
3114  def __lt__(self, *args):
3115  r"""
3116  __lt__(SlabWithPore self, SlabWithPore o) -> bool
3117  __lt__(SlabWithPore self, Particle d) -> bool
3118  """
3119  return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3120 
3121  def __ge__(self, *args):
3122  r"""
3123  __ge__(SlabWithPore self, SlabWithPore o) -> bool
3124  __ge__(SlabWithPore self, Particle d) -> bool
3125  """
3126  return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3127 
3128  def __gt__(self, *args):
3129  r"""
3130  __gt__(SlabWithPore self, SlabWithPore o) -> bool
3131  __gt__(SlabWithPore self, Particle d) -> bool
3132  """
3133  return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3134 
3135  def __hash__(self):
3136  r"""__hash__(SlabWithPore self) -> std::size_t"""
3137  return _IMP_npctransport.SlabWithPore___hash__(self)
3138 
3139  def __str__(self):
3140  r"""__str__(SlabWithPore self) -> std::string"""
3141  return _IMP_npctransport.SlabWithPore___str__(self)
3142 
3143  def __repr__(self):
3144  r"""__repr__(SlabWithPore self) -> std::string"""
3145  return _IMP_npctransport.SlabWithPore___repr__(self)
3146 
3147  def _get_as_binary(self):
3148  r"""_get_as_binary(SlabWithPore self) -> PyObject *"""
3149  return _IMP_npctransport.SlabWithPore__get_as_binary(self)
3150 
3151  def _set_from_binary(self, p):
3152  r"""_set_from_binary(SlabWithPore self, PyObject * p)"""
3153  return _IMP_npctransport.SlabWithPore__set_from_binary(self, p)
3154 
3155  def __getstate__(self):
3156  p = self._get_as_binary()
3157  if len(self.__dict__) > 1:
3158  d = self.__dict__.copy()
3159  del d['this']
3160  p = (d, p)
3161  return p
3162 
3163  def __setstate__(self, p):
3164  if not hasattr(self, 'this'):
3165  self.__init__()
3166  if isinstance(p, tuple):
3167  d, p = p
3168  self.__dict__.update(d)
3169  return self._set_from_binary(p)
3170 
3171  __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3172 
3173 # Register SlabWithPore in _IMP_npctransport:
3174 _IMP_npctransport.SlabWithPore_swigregister(SlabWithPore)
3175 class SlabWithCylindricalPore(SlabWithPore):
3176  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3177 
3178  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3179 
3180  def __init__(self, *args):
3181  r"""
3182  __init__(SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3183  __init__(SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3184  __init__(SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3185  """
3186  _IMP_npctransport.SlabWithCylindricalPore_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPore(*args))
3187 
3188  def show(self, *args):
3189  r"""show(SlabWithCylindricalPore self, _ostream out=std::cout)"""
3190  return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3191 
3192  @staticmethod
3193  def setup_particle(*args):
3194  r"""
3195  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3196  setup_particle(_ParticleAdaptor pa, double thickness, double radius) -> SlabWithCylindricalPore
3197  """
3198  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3199 
3200  @staticmethod
3201  def get_is_setup(*args):
3202  r"""
3203  get_is_setup(_ParticleAdaptor p) -> bool
3204  get_is_setup(Model m, ParticleIndex pi) -> bool
3205  """
3206  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3207 
3208  @staticmethod
3209  def get_cylindrical_pore_key():
3210  r"""get_cylindrical_pore_key() -> IntKey"""
3211  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3212 
3213  def add_attribute(self, *args):
3214  r"""
3215  add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3216  add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3217  add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3218  add_attribute(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3219  add_attribute(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3220  add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3221  add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3222  add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3223  add_attribute(SlabWithCylindricalPore self, SparseFloatKey a0, IMP::Float a1)
3224  add_attribute(SlabWithCylindricalPore self, SparseIntKey a0, IMP::Int a1)
3225  add_attribute(SlabWithCylindricalPore self, SparseStringKey a0, IMP::String a1)
3226  add_attribute(SlabWithCylindricalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3227  """
3228  return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3229 
3230  def get_value(self, *args):
3231  r"""
3232  get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3233  get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3234  get_value(SlabWithCylindricalPore self, FloatsKey a0) -> IMP::Floats
3235  get_value(SlabWithCylindricalPore self, IntsKey a0) -> IMP::Ints
3236  get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3237  get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3238  get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3239  get_value(SlabWithCylindricalPore self, SparseFloatKey a0) -> IMP::Float
3240  get_value(SlabWithCylindricalPore self, SparseIntKey a0) -> IMP::Int
3241  get_value(SlabWithCylindricalPore self, SparseStringKey a0) -> IMP::String
3242  get_value(SlabWithCylindricalPore self, SparseParticleIndexKey a0) -> ParticleIndex
3243  """
3244  return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3245 
3246  def set_value(self, *args):
3247  r"""
3248  set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3249  set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3250  set_value(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3251  set_value(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3252  set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3253  set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3254  set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3255  set_value(SlabWithCylindricalPore self, SparseFloatKey a0, IMP::Float a1)
3256  set_value(SlabWithCylindricalPore self, SparseIntKey a0, IMP::Int a1)
3257  set_value(SlabWithCylindricalPore self, SparseStringKey a0, IMP::String a1)
3258  set_value(SlabWithCylindricalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3259  """
3260  return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3261 
3262  def remove_attribute(self, *args):
3263  r"""
3264  remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3265  remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3266  remove_attribute(SlabWithCylindricalPore self, FloatsKey a0)
3267  remove_attribute(SlabWithCylindricalPore self, IntsKey a0)
3268  remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3269  remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3270  remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3271  remove_attribute(SlabWithCylindricalPore self, SparseFloatKey a0)
3272  remove_attribute(SlabWithCylindricalPore self, SparseIntKey a0)
3273  remove_attribute(SlabWithCylindricalPore self, SparseStringKey a0)
3274  remove_attribute(SlabWithCylindricalPore self, SparseParticleIndexKey a0)
3275  """
3276  return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3277 
3278  def has_attribute(self, *args):
3279  r"""
3280  has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3281  has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3282  has_attribute(SlabWithCylindricalPore self, FloatsKey a0) -> bool
3283  has_attribute(SlabWithCylindricalPore self, IntsKey a0) -> bool
3284  has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3285  has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3286  has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3287  has_attribute(SlabWithCylindricalPore self, SparseFloatKey a0) -> bool
3288  has_attribute(SlabWithCylindricalPore self, SparseIntKey a0) -> bool
3289  has_attribute(SlabWithCylindricalPore self, SparseStringKey a0) -> bool
3290  has_attribute(SlabWithCylindricalPore self, SparseParticleIndexKey a0) -> bool
3291  """
3292  return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3293 
3294  def get_derivative(self, a0):
3295  r"""get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3296  return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3297 
3298  def get_name(self):
3299  r"""get_name(SlabWithCylindricalPore self) -> std::string"""
3300  return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3301 
3302  def clear_caches(self):
3303  r"""clear_caches(SlabWithCylindricalPore self)"""
3304  return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3305 
3306  def set_name(self, a0):
3307  r"""set_name(SlabWithCylindricalPore self, std::string a0)"""
3308  return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3309 
3310  def set_check_level(self, a0):
3311  r"""set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3312  return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3313 
3314  def add_to_derivative(self, a0, a1, a2):
3315  r"""add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3316  return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3317 
3318  def set_is_optimized(self, a0, a1):
3319  r"""set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3320  return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3321 
3322  def get_is_optimized(self, a0):
3323  r"""get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3324  return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3325 
3326  def get_check_level(self):
3327  r"""get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3328  return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3329 
3330  def __eq__(self, *args):
3331  r"""
3332  __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3333  __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3334  """
3335  return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3336 
3337  def __ne__(self, *args):
3338  r"""
3339  __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3340  __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3341  """
3342  return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3343 
3344  def __le__(self, *args):
3345  r"""
3346  __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3347  __le__(SlabWithCylindricalPore self, Particle d) -> bool
3348  """
3349  return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3350 
3351  def __lt__(self, *args):
3352  r"""
3353  __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3354  __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3355  """
3356  return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3357 
3358  def __ge__(self, *args):
3359  r"""
3360  __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3361  __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3362  """
3363  return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3364 
3365  def __gt__(self, *args):
3366  r"""
3367  __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3368  __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3369  """
3370  return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3371 
3372  def __hash__(self):
3373  r"""__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3374  return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3375 
3376  def __str__(self):
3377  r"""__str__(SlabWithCylindricalPore self) -> std::string"""
3378  return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3379 
3380  def __repr__(self):
3381  r"""__repr__(SlabWithCylindricalPore self) -> std::string"""
3382  return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3383 
3384  def _get_as_binary(self):
3385  r"""_get_as_binary(SlabWithCylindricalPore self) -> PyObject *"""
3386  return _IMP_npctransport.SlabWithCylindricalPore__get_as_binary(self)
3387 
3388  def _set_from_binary(self, p):
3389  r"""_set_from_binary(SlabWithCylindricalPore self, PyObject * p)"""
3390  return _IMP_npctransport.SlabWithCylindricalPore__set_from_binary(self, p)
3391 
3392  def __getstate__(self):
3393  p = self._get_as_binary()
3394  if len(self.__dict__) > 1:
3395  d = self.__dict__.copy()
3396  del d['this']
3397  p = (d, p)
3398  return p
3399 
3400  def __setstate__(self, p):
3401  if not hasattr(self, 'this'):
3402  self.__init__()
3403  if isinstance(p, tuple):
3404  d, p = p
3405  self.__dict__.update(d)
3406  return self._set_from_binary(p)
3407 
3408  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3409 
3410 # Register SlabWithCylindricalPore in _IMP_npctransport:
3411 _IMP_npctransport.SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3412 class SlabWithToroidalPore(SlabWithPore):
3413  r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3414 
3415  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3416 
3417  def __init__(self, *args):
3418  r"""
3419  __init__(SlabWithToroidalPore self) -> SlabWithToroidalPore
3420  __init__(SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3421  __init__(SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3422  """
3423  _IMP_npctransport.SlabWithToroidalPore_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPore(*args))
3424 
3425  def show(self, *args):
3426  r"""show(SlabWithToroidalPore self, _ostream out=std::cout)"""
3427  return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3428 
3429  @staticmethod
3430  def setup_particle(*args):
3431  r"""
3432  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3433  setup_particle(_ParticleAdaptor pa, double thickness, double major_radius) -> SlabWithToroidalPore
3434  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3435  setup_particle(_ParticleAdaptor pa, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3436  """
3437  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3438 
3439  @staticmethod
3440  def get_is_setup(*args):
3441  r"""
3442  get_is_setup(_ParticleAdaptor p) -> bool
3443  get_is_setup(Model m, ParticleIndex pi) -> bool
3444  """
3445  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3446 
3447  def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3448  r"""set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3449  return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3450 
3451  def get_minor_radius_h2v_aspect_ratio(self):
3452  r"""get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3453  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3454 
3455  def get_vertical_minor_radius(self):
3456  r"""get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3457  return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3458 
3459  def set_vertical_minor_radius(self, rv):
3460  r"""set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3461  return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3462 
3463  def get_horizontal_minor_radius(self):
3464  r"""get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3465  return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3466 
3467  def set_horizontal_minor_radius(self, rh):
3468  r"""set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3469  return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3470 
3471  @staticmethod
3472  def get_minor_radius_h2v_aspect_ratio_key():
3473  r"""get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3474  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3475 
3476  @staticmethod
3477  def get_toroidal_pore_key():
3478  r"""get_toroidal_pore_key() -> IntKey"""
3479  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3480 
3481  def add_attribute(self, *args):
3482  r"""
3483  add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3484  add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3485  add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3486  add_attribute(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3487  add_attribute(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3488  add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3489  add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3490  add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3491  add_attribute(SlabWithToroidalPore self, SparseFloatKey a0, IMP::Float a1)
3492  add_attribute(SlabWithToroidalPore self, SparseIntKey a0, IMP::Int a1)
3493  add_attribute(SlabWithToroidalPore self, SparseStringKey a0, IMP::String a1)
3494  add_attribute(SlabWithToroidalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3495  """
3496  return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3497 
3498  def get_value(self, *args):
3499  r"""
3500  get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3501  get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3502  get_value(SlabWithToroidalPore self, FloatsKey a0) -> IMP::Floats
3503  get_value(SlabWithToroidalPore self, IntsKey a0) -> IMP::Ints
3504  get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3505  get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3506  get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3507  get_value(SlabWithToroidalPore self, SparseFloatKey a0) -> IMP::Float
3508  get_value(SlabWithToroidalPore self, SparseIntKey a0) -> IMP::Int
3509  get_value(SlabWithToroidalPore self, SparseStringKey a0) -> IMP::String
3510  get_value(SlabWithToroidalPore self, SparseParticleIndexKey a0) -> ParticleIndex
3511  """
3512  return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3513 
3514  def set_value(self, *args):
3515  r"""
3516  set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3517  set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3518  set_value(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3519  set_value(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3520  set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3521  set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3522  set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3523  set_value(SlabWithToroidalPore self, SparseFloatKey a0, IMP::Float a1)
3524  set_value(SlabWithToroidalPore self, SparseIntKey a0, IMP::Int a1)
3525  set_value(SlabWithToroidalPore self, SparseStringKey a0, IMP::String a1)
3526  set_value(SlabWithToroidalPore self, SparseParticleIndexKey a0, ParticleIndex a1)
3527  """
3528  return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3529 
3530  def remove_attribute(self, *args):
3531  r"""
3532  remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3533  remove_attribute(SlabWithToroidalPore self, IntKey a0)
3534  remove_attribute(SlabWithToroidalPore self, FloatsKey a0)
3535  remove_attribute(SlabWithToroidalPore self, IntsKey a0)
3536  remove_attribute(SlabWithToroidalPore self, StringKey a0)
3537  remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3538  remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3539  remove_attribute(SlabWithToroidalPore self, SparseFloatKey a0)
3540  remove_attribute(SlabWithToroidalPore self, SparseIntKey a0)
3541  remove_attribute(SlabWithToroidalPore self, SparseStringKey a0)
3542  remove_attribute(SlabWithToroidalPore self, SparseParticleIndexKey a0)
3543  """
3544  return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3545 
3546  def has_attribute(self, *args):
3547  r"""
3548  has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3549  has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3550  has_attribute(SlabWithToroidalPore self, FloatsKey a0) -> bool
3551  has_attribute(SlabWithToroidalPore self, IntsKey a0) -> bool
3552  has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3553  has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3554  has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3555  has_attribute(SlabWithToroidalPore self, SparseFloatKey a0) -> bool
3556  has_attribute(SlabWithToroidalPore self, SparseIntKey a0) -> bool
3557  has_attribute(SlabWithToroidalPore self, SparseStringKey a0) -> bool
3558  has_attribute(SlabWithToroidalPore self, SparseParticleIndexKey a0) -> bool
3559  """
3560  return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3561 
3562  def get_derivative(self, a0):
3563  r"""get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3564  return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3565 
3566  def get_name(self):
3567  r"""get_name(SlabWithToroidalPore self) -> std::string"""
3568  return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3569 
3570  def clear_caches(self):
3571  r"""clear_caches(SlabWithToroidalPore self)"""
3572  return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3573 
3574  def set_name(self, a0):
3575  r"""set_name(SlabWithToroidalPore self, std::string a0)"""
3576  return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3577 
3578  def set_check_level(self, a0):
3579  r"""set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3580  return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3581 
3582  def add_to_derivative(self, a0, a1, a2):
3583  r"""add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3584  return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3585 
3586  def set_is_optimized(self, a0, a1):
3587  r"""set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3588  return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3589 
3590  def get_is_optimized(self, a0):
3591  r"""get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3592  return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
3593 
3594  def get_check_level(self):
3595  r"""get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
3596  return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
3597 
3598  def __eq__(self, *args):
3599  r"""
3600  __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3601  __eq__(SlabWithToroidalPore self, Particle d) -> bool
3602  """
3603  return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
3604 
3605  def __ne__(self, *args):
3606  r"""
3607  __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3608  __ne__(SlabWithToroidalPore self, Particle d) -> bool
3609  """
3610  return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
3611 
3612  def __le__(self, *args):
3613  r"""
3614  __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3615  __le__(SlabWithToroidalPore self, Particle d) -> bool
3616  """
3617  return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
3618 
3619  def __lt__(self, *args):
3620  r"""
3621  __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3622  __lt__(SlabWithToroidalPore self, Particle d) -> bool
3623  """
3624  return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
3625 
3626  def __ge__(self, *args):
3627  r"""
3628  __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3629  __ge__(SlabWithToroidalPore self, Particle d) -> bool
3630  """
3631  return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
3632 
3633  def __gt__(self, *args):
3634  r"""
3635  __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3636  __gt__(SlabWithToroidalPore self, Particle d) -> bool
3637  """
3638  return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
3639 
3640  def __hash__(self):
3641  r"""__hash__(SlabWithToroidalPore self) -> std::size_t"""
3642  return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
3643 
3644  def __str__(self):
3645  r"""__str__(SlabWithToroidalPore self) -> std::string"""
3646  return _IMP_npctransport.SlabWithToroidalPore___str__(self)
3647 
3648  def __repr__(self):
3649  r"""__repr__(SlabWithToroidalPore self) -> std::string"""
3650  return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
3651 
3652  def _get_as_binary(self):
3653  r"""_get_as_binary(SlabWithToroidalPore self) -> PyObject *"""
3654  return _IMP_npctransport.SlabWithToroidalPore__get_as_binary(self)
3655 
3656  def _set_from_binary(self, p):
3657  r"""_set_from_binary(SlabWithToroidalPore self, PyObject * p)"""
3658  return _IMP_npctransport.SlabWithToroidalPore__set_from_binary(self, p)
3659 
3660  def __getstate__(self):
3661  p = self._get_as_binary()
3662  if len(self.__dict__) > 1:
3663  d = self.__dict__.copy()
3664  del d['this']
3665  p = (d, p)
3666  return p
3667 
3668  def __setstate__(self, p):
3669  if not hasattr(self, 'this'):
3670  self.__init__()
3671  if isinstance(p, tuple):
3672  d, p = p
3673  self.__dict__.update(d)
3674  return self._set_from_binary(p)
3675 
3676  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
3677 
3678 # Register SlabWithToroidalPore in _IMP_npctransport:
3679 _IMP_npctransport.SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
3680 
3681 def __lshift__(*args):
3682  r"""
3683  __lshift__(_ostream out, RelaxingSpring n) -> _ostream
3684  __lshift__(_ostream out, Transporting n) -> _ostream
3685  __lshift__(_ostream out, SlabWithPore n) -> _ostream
3686  __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
3687  __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
3688  """
3689  return _IMP_npctransport.__lshift__(*args)
3690 class SlabWithCylindricalPorePairScore(IMP.PairScore):
3691  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
3692 
3693  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3694 
3695  def __init__(self, k):
3696  r"""__init__(SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
3697  _IMP_npctransport.SlabWithCylindricalPorePairScore_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k))
3698 
3699  def get_displacement_direction(self, slab, v):
3700  r"""get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
3701  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
3702 
3703  def get_displacement_magnitude(self, slab, v):
3704  r"""get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
3705  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
3706 
3707  def do_get_inputs(self, m, pis):
3708  r"""do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3709  return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
3710 
3711  def get_version_info(self):
3712  r"""get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
3713  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
3714  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPorePairScore
3715 
3716  def __str__(self):
3717  r"""__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
3718  return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
3719 
3720  def __repr__(self):
3721  r"""__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
3722  return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
3723 
3724  @staticmethod
3725  def get_from(o):
3726  return _object_cast_to_SlabWithCylindricalPorePairScore(o)
3727 
3728 
3729 # Register SlabWithCylindricalPorePairScore in _IMP_npctransport:
3730 _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
3731 class SlabWithToroidalPorePairScore(IMP.PairScore):
3732  r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
3733 
3734  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3735 
3736  def __init__(self, k):
3737  r"""__init__(SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
3738  _IMP_npctransport.SlabWithToroidalPorePairScore_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPorePairScore(k))
3739 
3740  def do_get_inputs(self, m, pis):
3741  r"""do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3742  return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
3743 
3744  def get_version_info(self):
3745  r"""get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
3746  return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
3747  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPorePairScore
3748 
3749  def __str__(self):
3750  r"""__str__(SlabWithToroidalPorePairScore self) -> std::string"""
3751  return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
3752 
3753  def __repr__(self):
3754  r"""__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
3755  return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
3756 
3757  @staticmethod
3758  def get_from(o):
3759  return _object_cast_to_SlabWithToroidalPorePairScore(o)
3760 
3761 
3762 # Register SlabWithToroidalPorePairScore in _IMP_npctransport:
3763 _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
3764 class SlabWithCylindricalPoreWireGeometry(IMP.display.Geometry):
3765  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
3766 
3767  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3768 
3769  def __init__(self, height, radius, length):
3770  r"""__init__(SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
3771  _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length))
3772 
3773  def get_version_info(self):
3774  r"""get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
3775  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
3776  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreWireGeometry
3777 
3778  def __str__(self):
3779  r"""__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
3780  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
3781 
3782  def __repr__(self):
3783  r"""__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
3784  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
3785 
3786  @staticmethod
3787  def get_from(o):
3788  return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
3789 
3790 
3791 # Register SlabWithCylindricalPoreWireGeometry in _IMP_npctransport:
3792 _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
3793 class SlabWithCylindricalPoreSurfaceGeometry(IMP.display.SurfaceMeshGeometry):
3794  r"""Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
3795 
3796  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3797 
3798  def __init__(self, height, radius, length):
3799  r"""__init__(SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
3800  _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swiginit(self, _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length))
3801 
3802  def __str__(self):
3803  r"""__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
3804  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
3805 
3806  def __repr__(self):
3807  r"""__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
3808  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
3809 
3810  @staticmethod
3811  def get_from(o):
3812  return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
3813 
3814  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
3815 
3816 # Register SlabWithCylindricalPoreSurfaceGeometry in _IMP_npctransport:
3817 _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
3818 class SlabWithToroidalPoreWireGeometry(IMP.display.Geometry):
3819  r"""Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
3820 
3821  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3822 
3823  def __init__(self, *args):
3824  r"""
3825  __init__(SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
3826  __init__(SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
3827  """
3828  _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swiginit(self, _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args))
3829 
3830  def get_version_info(self):
3831  r"""get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
3832  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
3833  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPoreWireGeometry
3834 
3835  def __str__(self):
3836  r"""__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
3837  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
3838 
3839  def __repr__(self):
3840  r"""__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
3841  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
3842 
3843  @staticmethod
3844  def get_from(o):
3845  return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
3846 
3847 
3848 # Register SlabWithToroidalPoreWireGeometry in _IMP_npctransport:
3849 _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
3850 class _GenericAttributeSingletonScoreForPoreRadus(IMP.SingletonScore):
3851  r"""Proxy of C++ IMP::core::GenericAttributeSingletonScore< IMP::core::Harmonic > class."""
3852 
3853  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3854  __repr__ = _swig_repr
3855 
3856  def __init__(self, f, k):
3857  r"""__init__(_GenericAttributeSingletonScoreForPoreRadus self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
3858  _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swiginit(self, _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k))
3859 
3860  def do_get_inputs(self, m, pis):
3861  r"""do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3862  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
3863 
3864  def get_unary_function(self):
3865  r"""get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
3866  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
3867 
3868  def get_version_info(self):
3869  r"""get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
3870  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
3871  __swig_destroy__ = _IMP_npctransport.delete__GenericAttributeSingletonScoreForPoreRadus
3872 
3873 # Register _GenericAttributeSingletonScoreForPoreRadus in _IMP_npctransport:
3874 _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
3875 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
3876  r"""Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
3877 
3878  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3879 
3880  def __init__(self, mean, k):
3881  r"""__init__(PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
3882  _IMP_npctransport.PoreRadiusSingletonScore_swiginit(self, _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k))
3883 
3884  def set_k(self, k):
3885  r"""set_k(PoreRadiusSingletonScore self, double k)"""
3886  return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
3887  __swig_destroy__ = _IMP_npctransport.delete_PoreRadiusSingletonScore
3888 
3889  def __str__(self):
3890  r"""__str__(PoreRadiusSingletonScore self) -> std::string"""
3891  return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
3892 
3893  def __repr__(self):
3894  r"""__repr__(PoreRadiusSingletonScore self) -> std::string"""
3895  return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
3896 
3897  @staticmethod
3898  def get_from(o):
3899  return _object_cast_to_PoreRadiusSingletonScore(o)
3900 
3901 
3902 # Register PoreRadiusSingletonScore in _IMP_npctransport:
3903 _IMP_npctransport.PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
3904 class ExcludeZRangeSingletonScore(IMP.SingletonScore):
3905  r"""Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
3906 
3907  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3908 
3909  def __init__(self, bottom, top, k):
3910  r"""__init__(ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
3911  _IMP_npctransport.ExcludeZRangeSingletonScore_swiginit(self, _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k))
3912 
3913  def get_bottom_z(self):
3914  r"""get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
3915  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
3916 
3917  def get_top_z(self):
3918  r"""get_top_z(ExcludeZRangeSingletonScore self) -> double"""
3919  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
3920 
3921  def get_k(self):
3922  r"""get_k(ExcludeZRangeSingletonScore self) -> double"""
3923  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
3924 
3925  def do_get_inputs(self, m, pis):
3926  r"""do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3927  return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
3928 
3929  def get_version_info(self):
3930  r"""get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
3931  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
3932  __swig_destroy__ = _IMP_npctransport.delete_ExcludeZRangeSingletonScore
3933 
3934  def __str__(self):
3935  r"""__str__(ExcludeZRangeSingletonScore self) -> std::string"""
3936  return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
3937 
3938  def __repr__(self):
3939  r"""__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
3940  return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
3941 
3942  @staticmethod
3943  def get_from(o):
3944  return _object_cast_to_ExcludeZRangeSingletonScore(o)
3945 
3946 
3947 # Register ExcludeZRangeSingletonScore in _IMP_npctransport:
3948 _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
3949 class ZBiasSingletonScore(IMP.SingletonScore):
3950  r"""Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
3951 
3952  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3953 
3954  def __init__(self, *args):
3955  r"""__init__(ZBiasSingletonScore self, double k, double max_r=HALF_SQRT_MAX_DOUBLE) -> ZBiasSingletonScore"""
3956  _IMP_npctransport.ZBiasSingletonScore_swiginit(self, _IMP_npctransport.new_ZBiasSingletonScore(*args))
3957 
3958  def get_k(self):
3959  r"""get_k(ZBiasSingletonScore self) -> double"""
3960  return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
3961 
3962  def set_k(self, k):
3963  r"""set_k(ZBiasSingletonScore self, double k)"""
3964  return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
3965 
3966  def do_get_inputs(self, m, pis):
3967  r"""do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3968  return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
3969 
3970  def get_version_info(self):
3971  r"""get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
3972  return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
3973  __swig_destroy__ = _IMP_npctransport.delete_ZBiasSingletonScore
3974 
3975  def __str__(self):
3976  r"""__str__(ZBiasSingletonScore self) -> std::string"""
3977  return _IMP_npctransport.ZBiasSingletonScore___str__(self)
3978 
3979  def __repr__(self):
3980  r"""__repr__(ZBiasSingletonScore self) -> std::string"""
3981  return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
3982 
3983  @staticmethod
3984  def get_from(o):
3985  return _object_cast_to_ZBiasSingletonScore(o)
3986 
3987 
3988 # Register ZBiasSingletonScore in _IMP_npctransport:
3989 _IMP_npctransport.ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
3990 class BodyStatisticsOptimizerState(IMP.OptimizerState):
3991  r"""Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
3992 
3993  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3994 
3995  def __init__(self, p, statistics_manager=None, periodicity=1):
3996  r"""__init__(BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState"""
3997  _IMP_npctransport.BodyStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity))
3998 
3999  def get_correlation_time(self):
4000  r"""get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4001  return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4002 
4003  def get_diffusion_coefficient(self):
4004  r"""get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4005  return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4006 
4007  def update_particle_type_zr_distribution_map(self):
4008  r"""update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4009  return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4010 
4011  def do_update(self, call_num):
4012  r"""do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4013  return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4014 
4015  def get_version_info(self):
4016  r"""get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4017  return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4018  __swig_destroy__ = _IMP_npctransport.delete_BodyStatisticsOptimizerState
4019 
4020  def __str__(self):
4021  r"""__str__(BodyStatisticsOptimizerState self) -> std::string"""
4022  return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4023 
4024  def __repr__(self):
4025  r"""__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4026  return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4027 
4028  @staticmethod
4029  def get_from(o):
4030  return _object_cast_to_BodyStatisticsOptimizerState(o)
4031 
4032 
4033 # Register BodyStatisticsOptimizerState in _IMP_npctransport:
4034 _IMP_npctransport.BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4035 class ParticleTransportStatisticsOptimizerState(IMP.OptimizerState):
4036  r"""Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
4037 
4038  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4039 
4040  def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4041  r"""__init__(ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0, WeakPointer< IMP::atom::Simulator > owner=0) -> ParticleTransportStatisticsOptimizerState"""
4042  _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner))
4043 
4044  def set_owner(self, owner):
4045  r"""set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4046  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4047 
4048  def get_owner(self):
4049  r"""get_owner(ParticleTransportStatisticsOptimizerState self) -> Simulator"""
4050  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4051 
4052  def get_n_transports_up(self):
4053  r"""get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4054  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4055 
4056  def get_n_transports_down(self):
4057  r"""get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4058  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4059 
4060  def get_total_n_transports(self):
4061  r"""get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4062  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4063 
4064  def get_transport_time_points_in_ns(self):
4065  r"""get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4066  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4067 
4068  def do_update(self, call_num):
4069  r"""do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4070  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4071 
4072  def get_version_info(self):
4073  r"""get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4074  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4075  __swig_destroy__ = _IMP_npctransport.delete_ParticleTransportStatisticsOptimizerState
4076 
4077  def __str__(self):
4078  r"""__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4079  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4080 
4081  def __repr__(self):
4082  r"""__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4083  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4084 
4085  @staticmethod
4086  def get_from(o):
4087  return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4088 
4089 
4090 # Register ParticleTransportStatisticsOptimizerState in _IMP_npctransport:
4091 _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4092 class ChainStatisticsOptimizerState(IMP.OptimizerState):
4093  r"""Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
4094 
4095  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4096 
4097  def __init__(self, ps, periodicity=1):
4098  r"""__init__(ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState"""
4099  _IMP_npctransport.ChainStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity))
4100 
4101  def get_correlation_time(self):
4102  r"""get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4103  return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4104 
4105  def get_local_diffusion_coefficients(self):
4106  r"""get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4107  return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4108 
4109  def get_diffusion_coefficient(self):
4110  r"""get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
4111  return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
4112 
4113  def get_mean_radius_of_gyration(self):
4114  r"""get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4115  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
4116 
4117  def get_mean_square_radius_of_gyration(self):
4118  r"""get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4119  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4120 
4121  def get_mean_end_to_end_distance(self):
4122  r"""get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4123  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4124 
4125  def get_mean_square_end_to_end_distance(self):
4126  r"""get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4127  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4128 
4129  def get_mean_bond_distance(self):
4130  r"""get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4131  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4132 
4133  def get_mean_square_bond_distance(self):
4134  r"""get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4135  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4136 
4137  def do_update(self, call_num):
4138  r"""do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4139  return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4140 
4141  def get_version_info(self):
4142  r"""get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4143  return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4144  __swig_destroy__ = _IMP_npctransport.delete_ChainStatisticsOptimizerState
4145 
4146  def __str__(self):
4147  r"""__str__(ChainStatisticsOptimizerState self) -> std::string"""
4148  return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4149 
4150  def __repr__(self):
4151  r"""__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4152  return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4153 
4154  @staticmethod
4155  def get_from(o):
4156  return _object_cast_to_ChainStatisticsOptimizerState(o)
4157 
4158 
4159 # Register ChainStatisticsOptimizerState in _IMP_npctransport:
4160 _IMP_npctransport.ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4161 class BipartitePairsStatisticsOptimizerState(IMP.OptimizerState):
4162  r"""Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4163 
4164  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4165 
4166  def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4167  r"""__init__(BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0, double slack=1.0) -> BipartitePairsStatisticsOptimizerState"""
4168  _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swiginit(self, _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack))
4169 
4170  def get_interaction_type(self):
4171  r"""get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4172  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4173 
4174  def get_average_number_of_contacts(self):
4175  r"""get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4176  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4177 
4178  def get_average_off_per_contact_per_ns(self):
4179  r"""get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4180  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4181 
4182  def get_average_off_per_bound_I_per_ns(self):
4183  r"""get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4184  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4185 
4186  def get_average_off_per_bound_II_per_ns(self):
4187  r"""get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4188  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4189 
4190  def get_average_on_per_missing_contact_per_ns(self):
4191  r"""get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4192  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4193 
4194  def get_average_on_per_unbound_I_per_ns(self):
4195  r"""get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4196  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4197 
4198  def get_average_on_per_unbound_II_per_ns(self):
4199  r"""get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4200  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4201 
4202  def get_average_fraction_bound_particles_I(self):
4203  r"""get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4204  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4205 
4206  def get_average_fraction_bound_particles_II(self):
4207  r"""get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4208  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4209 
4210  def get_average_fraction_bound_particle_sites_I(self):
4211  r"""get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4212  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4213 
4214  def get_average_fraction_bound_particle_sites_II(self):
4215  r"""get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4216  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4217 
4218  def get_average_fraction_nonspecific_interactions_I(self):
4219  r"""get_average_fraction_nonspecific_interactions_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4220  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_I(self)
4221 
4222  def get_average_fraction_nonspecific_interactions_II(self):
4223  r"""get_average_fraction_nonspecific_interactions_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4224  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_II(self)
4225 
4226  def get_number_of_particles_1(self):
4227  r"""get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4228  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4229 
4230  def get_number_of_particles_2(self):
4231  r"""get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4232  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4233 
4234  def get_misc_stats_period_ns(self):
4235  r"""get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4236  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4237 
4238  def get_off_stats_period_ns(self):
4239  r"""get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4240  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4241 
4242  def get_off_I_stats_period_ns(self):
4243  r"""get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4244  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4245 
4246  def get_off_II_stats_period_ns(self):
4247  r"""get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4248  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4249 
4250  def get_on_stats_period_ns(self):
4251  r"""get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4252  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4253 
4254  def get_on_I_stats_period_ns(self):
4255  r"""get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4256  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4257 
4258  def get_on_II_stats_period_ns(self):
4259  r"""get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4260  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4261 
4262  def get_version_info(self):
4263  r"""get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4264  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4265  __swig_destroy__ = _IMP_npctransport.delete_BipartitePairsStatisticsOptimizerState
4266 
4267  def __str__(self):
4268  r"""__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4269  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4270 
4271  def __repr__(self):
4272  r"""__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4273  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4274 
4275  @staticmethod
4276  def get_from(o):
4277  return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4278 
4279 
4280 # Register BipartitePairsStatisticsOptimizerState in _IMP_npctransport:
4281 _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4282 
4283 def get_close_pairs_range(*args):
4284  r"""
4285  get_close_pairs_range(double max_range, double max_range_factor) -> double
4286  get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4287  """
4288  return _IMP_npctransport.get_close_pairs_range(*args)
4289 
4290 def get_time_step(*args):
4291  r"""
4292  get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0) -> double
4293  get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4294  """
4295  return _IMP_npctransport.get_time_step(*args)
4296 
4297 def get_frames_from_ns(ns, time_step):
4298  r"""get_frames_from_ns(double ns, double time_step) -> int"""
4299  return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4300 
4301 def get_number_of_frames(config, time_step):
4302  r"""get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4303  return _IMP_npctransport.get_number_of_frames(config, time_step)
4304 
4305 def get_dump_interval_in_frames(config, time_step):
4306  r"""get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4307  return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4308 
4309 def get_statistics_interval_in_frames(assign, time_step, default_value_ns=0.1):
4310  r"""get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int"""
4311  return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4312 
4313 def get_output_statistics_interval_in_frames(assign, time_step, default_value_ns=1.0):
4314  r"""get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int"""
4315  return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4316 
4317 def initialize_positions(*args):
4318  r"""initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints=IMP::RestraintsTemp(), bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False, bool are_fgs_pre_initialized=False)"""
4319  return _IMP_npctransport.initialize_positions(*args)
4320 
4321 def get_optimizable_particles(particles):
4322  r"""get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4323  return _IMP_npctransport.get_optimizable_particles(particles)
4324 
4325 def get_non_optimizable_particles(particles):
4326  r"""get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4327  return _IMP_npctransport.get_non_optimizable_particles(particles)
4328 
4329 def get_particle_indexes(particles):
4330  r"""get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4331  return _IMP_npctransport.get_particle_indexes(particles)
4332 
4333 def get_protobuf_configuration_from_text(config_txt, config_pb):
4334  r"""get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4335  return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4336 
4337 def get_spheres_from_vectors(vs, radius):
4338  r"""get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4339  return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4340 
4341 def get_spheres_centers(spheres):
4342  r"""get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4343  return _IMP_npctransport.get_spheres_centers(spheres)
4344 
4346  r"""copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4347  return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4348 
4350  r"""copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4351  return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4352 
4353 def copy_FGs_coordinates(src_sd, trg_sd):
4354  r"""copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4355  return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4356 class Avro2PBReader(object):
4357  r"""Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4358 
4359  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
4360 
4361  def __init__(self, *args):
4362  r"""
4363  __init__(Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4364  __init__(Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4365  """
4366  _IMP_npctransport.Avro2PBReader_swiginit(self, _IMP_npctransport.new_Avro2PBReader(*args))
4367  __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4368 
4369  def read_next(self):
4370  r"""read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4371  return _IMP_npctransport.Avro2PBReader_read_next(self)
4372 
4373  def get_is_valid(self):
4374  r"""get_is_valid(Avro2PBReader self) -> bool"""
4375  return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4376 
4377  def get_cur_file_name(self):
4378  r"""get_cur_file_name(Avro2PBReader self) -> std::string"""
4379  return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4380 
4381  def show(self, *args):
4382  r"""show(Avro2PBReader self, _ostream out=std::cout)"""
4383  return _IMP_npctransport.Avro2PBReader_show(self, *args)
4384 
4385  def __str__(self):
4386  r"""__str__(Avro2PBReader self) -> std::string"""
4387  return _IMP_npctransport.Avro2PBReader___str__(self)
4388 
4389  def __repr__(self):
4390  r"""__repr__(Avro2PBReader self) -> std::string"""
4391  return _IMP_npctransport.Avro2PBReader___repr__(self)
4392 
4393 # Register Avro2PBReader in _IMP_npctransport:
4394 _IMP_npctransport.Avro2PBReader_swigregister(Avro2PBReader)
4395 
4396 def startup(argc):
4397  r"""startup(int argc) -> SimulationData"""
4398  return _IMP_npctransport.startup(argc)
4399 
4400 def remove_Nup42(sd):
4401  r"""remove_Nup42(SimulationData sd)"""
4402  return _IMP_npctransport.remove_Nup42(sd)
4403 
4404 def inflate_floater(sd, floater_name, new_radius):
4405  r"""inflate_floater(SimulationData sd, std::string const floater_name, float const new_radius)"""
4406  return _IMP_npctransport.inflate_floater(sd, floater_name, new_radius)
4407 
4408 def reset_box_size(sd, box_size):
4409  r"""reset_box_size(SimulationData sd, double box_size)"""
4410  return _IMP_npctransport.reset_box_size(sd, box_size)
4411 
4412 def do_main_loop(sd, init_restraints):
4413  r"""do_main_loop(SimulationData sd, IMP::RestraintsTemp const & init_restraints)"""
4414  return _IMP_npctransport.do_main_loop(sd, init_restraints)
4415 
4416 try:
4417  from .npctransport_pb2 import *
4418  import google.protobuf
4419 except ImportError:
4420  print("no protobuf support in python")
4421 from ._configuration import *
4422 
4423 timer = SimpleTimer
4424 
4425 
4426 def get_module_version():
4427  r"""get_module_version() -> std::string const"""
4428  return _IMP_npctransport.get_module_version()
4429 
4430 def get_example_path(fname):
4431  r"""get_example_path(std::string fname) -> std::string"""
4432  return _IMP_npctransport.get_example_path(fname)
4433 
4434 def get_data_path(fname):
4435  r"""get_data_path(std::string fname) -> std::string"""
4436  return _IMP_npctransport.get_data_path(fname)
4437 
4438 from . import _version_check
4439 _version_check.check_version(get_module_version())
4440 __version__ = get_module_version()
4441 
4442 
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)
void remove_Nup42(SimulationData *sd)
remove nup42 and its anchors (also from obstacles)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
Various classes to hold sets of particles.
int assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed)
The base class for geometry.
int get_output_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
Definition: typedefs.h:45
IMP::npctransport::SimulationData * startup(int argc, char *argv[])
A base class for geometry from a set of particles.
double get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0)
Make CGAL functionality available to IMP.
void copy_FGs_coordinates(SimulationData const *src_sd, SimulationData *trg_sd)
copy coordinates of src_sd to trg_sd for FG repeats only
std::string get_module_version()
Return the version of this module, as a string.
void do_main_loop(SimulationData *sd, const RestraintsTemp &init_restraints)
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
int get_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)
void get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
Simple Brownian dynamics simulator.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
Common base class for heavy weight IMP objects.
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 inflate_floater(SimulationData *sd, const std::string floater_name, const float new_radius)
inflate floater of specified type to new_radius
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
Interface to specialized Particle types (e.g. atoms)
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
void reset_box_size(SimulationData *sd, double box_size)
change box size sd to specified box size and update output file
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
FGChain * get_fg_chain(atom::Hierarchy root)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for developing and analyzing benchmarks of IMP code.
InteractionType make_ordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
convenience method for creating and interaction type in swig
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