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IMP Reference Guide  2.18.0
The Integrative Modeling Platform
version 2.18.0
npctransport/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.7
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 2007-2022 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 
16 
17 from sys import version_info
18 if version_info >= (2, 6, 0):
19  def swig_import_helper():
20  from os.path import dirname
21  import imp
22  fp = None
23  try:
24  fp, pathname, description = imp.find_module('_IMP_npctransport', [dirname(__file__)])
25  except ImportError:
26  import _IMP_npctransport
27  return _IMP_npctransport
28  if fp is not None:
29  try:
30  _mod = imp.load_module('_IMP_npctransport', fp, pathname, description)
31  finally:
32  fp.close()
33  return _mod
34  _IMP_npctransport = swig_import_helper()
35  del swig_import_helper
36 else:
37  import _IMP_npctransport
38 del version_info
39 try:
40  _swig_property = property
41 except NameError:
42  pass # Python < 2.2 doesn't have 'property'.
43 
44 
45 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
46  if (name == "thisown"):
47  return self.this.own(value)
48  if (name == "this"):
49  if type(value).__name__ == 'SwigPyObject':
50  self.__dict__[name] = value
51  return
52  method = class_type.__swig_setmethods__.get(name, None)
53  if method:
54  return method(self, value)
55  if (not static):
56  object.__setattr__(self, name, value)
57  else:
58  raise AttributeError("You cannot add attributes to %s" % self)
59 
60 
61 def _swig_setattr(self, class_type, name, value):
62  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
63 
64 
65 def _swig_getattr_nondynamic(self, class_type, name, static=1):
66  if (name == "thisown"):
67  return self.this.own()
68  method = class_type.__swig_getmethods__.get(name, None)
69  if method:
70  return method(self)
71  if (not static):
72  return object.__getattr__(self, name)
73  else:
74  raise AttributeError(name)
75 
76 def _swig_getattr(self, class_type, name):
77  return _swig_getattr_nondynamic(self, class_type, name, 0)
78 
79 
80 def _swig_repr(self):
81  try:
82  strthis = "proxy of " + self.this.__repr__()
83  except:
84  strthis = ""
85  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
86 
87 try:
88  _object = object
89  _newclass = 1
90 except AttributeError:
91  class _object:
92  pass
93  _newclass = 0
94 
95 
96 
97 def _swig_setattr_nondynamic_method(set):
98  def set_attr(self, name, value):
99  if (name == "thisown"):
100  return self.this.own(value)
101  if hasattr(self, name) or (name == "this"):
102  set(self, name, value)
103  else:
104  raise AttributeError("You cannot add attributes to %s" % self)
105  return set_attr
106 
107 
108 try:
109  import weakref
110  weakref_proxy = weakref.proxy
111 except:
112  weakref_proxy = lambda x: x
113 
114 
115 class IMP_NPCTRANSPORT_SwigPyIterator(object):
116  """Proxy of C++ swig::IMP_NPCTRANSPORT_SwigPyIterator class"""
117  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
118 
119  def __init__(self, *args, **kwargs):
120  raise AttributeError("No constructor defined - class is abstract")
121  __repr__ = _swig_repr
122  __swig_destroy__ = _IMP_npctransport.delete_IMP_NPCTRANSPORT_SwigPyIterator
123  __del__ = lambda self: None
124 
125  def value(self):
126  """value(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
127  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_value(self)
128 
129 
130  def incr(self, n=1):
131  """
132  incr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
133  incr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
134  """
135  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_incr(self, n)
136 
137 
138  def decr(self, n=1):
139  """
140  decr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
141  decr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
142  """
143  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_decr(self, n)
144 
145 
146  def distance(self, x):
147  """distance(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t"""
148  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_distance(self, x)
149 
150 
151  def equal(self, x):
152  """equal(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
153  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_equal(self, x)
154 
155 
156  def copy(self):
157  """copy(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator"""
158  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_copy(self)
159 
160 
161  def next(self):
162  """next(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
163  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_next(self)
164 
165 
166  def __next__(self):
167  """__next__(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
168  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___next__(self)
169 
170 
171  def previous(self):
172  """previous(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
173  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_previous(self)
174 
175 
176  def advance(self, n):
177  """advance(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
178  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_advance(self, n)
179 
180 
181  def __eq__(self, x):
182  """__eq__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
183  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___eq__(self, x)
184 
185 
186  def __ne__(self, x):
187  """__ne__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
188  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___ne__(self, x)
189 
190 
191  def __iadd__(self, n):
192  """__iadd__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
193  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___iadd__(self, n)
194 
195 
196  def __isub__(self, n):
197  """__isub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
198  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___isub__(self, n)
199 
200 
201  def __add__(self, n):
202  """__add__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
203  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___add__(self, n)
204 
205 
206  def __sub__(self, *args):
207  """
208  __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator
209  __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t
210  """
211  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___sub__(self, *args)
212 
213  def __iter__(self):
214  return self
215 IMP_NPCTRANSPORT_SwigPyIterator_swigregister = _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_swigregister
216 IMP_NPCTRANSPORT_SwigPyIterator_swigregister(IMP_NPCTRANSPORT_SwigPyIterator)
217 
218 
219 _value_types=[]
220 _object_types=[]
221 _raii_types=[]
222 _plural_types=[]
223 
224 
225 _IMP_npctransport.IMP_DEBUG_swigconstant(_IMP_npctransport)
226 IMP_DEBUG = _IMP_npctransport.IMP_DEBUG
227 
228 _IMP_npctransport.IMP_RELEASE_swigconstant(_IMP_npctransport)
229 IMP_RELEASE = _IMP_npctransport.IMP_RELEASE
230 
231 _IMP_npctransport.IMP_SILENT_swigconstant(_IMP_npctransport)
232 IMP_SILENT = _IMP_npctransport.IMP_SILENT
233 
234 _IMP_npctransport.IMP_PROGRESS_swigconstant(_IMP_npctransport)
235 IMP_PROGRESS = _IMP_npctransport.IMP_PROGRESS
236 
237 _IMP_npctransport.IMP_TERSE_swigconstant(_IMP_npctransport)
238 IMP_TERSE = _IMP_npctransport.IMP_TERSE
239 
240 _IMP_npctransport.IMP_VERBOSE_swigconstant(_IMP_npctransport)
241 IMP_VERBOSE = _IMP_npctransport.IMP_VERBOSE
242 
243 _IMP_npctransport.IMP_MEMORY_swigconstant(_IMP_npctransport)
244 IMP_MEMORY = _IMP_npctransport.IMP_MEMORY
245 
246 _IMP_npctransport.IMP_NONE_swigconstant(_IMP_npctransport)
247 IMP_NONE = _IMP_npctransport.IMP_NONE
248 
249 _IMP_npctransport.IMP_USAGE_swigconstant(_IMP_npctransport)
250 IMP_USAGE = _IMP_npctransport.IMP_USAGE
251 
252 _IMP_npctransport.IMP_INTERNAL_swigconstant(_IMP_npctransport)
253 IMP_INTERNAL = _IMP_npctransport.IMP_INTERNAL
254 
255 _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_npctransport)
256 IMP_KERNEL_HAS_LOG4CXX = _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX
257 
258 _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_npctransport)
259 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR
260 
261 _IMP_npctransport.IMP_COMPILER_HAS_RANDOM_SHUFFLE_swigconstant(_IMP_npctransport)
262 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_npctransport.IMP_COMPILER_HAS_RANDOM_SHUFFLE
263 
264 _IMP_npctransport.IMP_COMPILER_HAS_THREE_WAY_swigconstant(_IMP_npctransport)
265 IMP_COMPILER_HAS_THREE_WAY = _IMP_npctransport.IMP_COMPILER_HAS_THREE_WAY
266 
267 _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
268 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM
269 
270 _IMP_npctransport.IMP_KERNEL_HAS_NUMPY_swigconstant(_IMP_npctransport)
271 IMP_KERNEL_HAS_NUMPY = _IMP_npctransport.IMP_KERNEL_HAS_NUMPY
272 
273 _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_npctransport)
274 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
275 
276 _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_npctransport)
277 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
278 
279 _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_npctransport)
280 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
281 
282 _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
283 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
284 
285 import sys
286 class _DirectorObjects(object):
287  """@internal Simple class to keep references to director objects
288  to prevent premature deletion."""
289  def __init__(self):
290  self._objects = []
291  def register(self, obj):
292  """Take a reference to a director object; will only work for
293  refcounted C++ classes"""
294  if hasattr(obj, 'get_ref_count'):
295  self._objects.append(obj)
296  def cleanup(self):
297  """Only drop our reference and allow cleanup by Python if no other
298  Python references exist (we hold 3 references: one in self._objects,
299  one in x, and one in the argument list for getrefcount) *and* no
300  other C++ references exist (the Python object always holds one)"""
301  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
302  or x.get_ref_count() > 1]
303 # Do in two steps so the references are kept until the end of the
304 # function (deleting references may trigger a fresh call to this method)
305  self._objects = objs
306  def get_object_count(self):
307  """Get number of director objects (useful for testing only)"""
308  return len(self._objects)
309 _director_objects = _DirectorObjects()
310 
311 class _ostream(object):
312  """Proxy of C++ std::ostream class"""
313  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
314 
315  def __init__(self, *args, **kwargs):
316  raise AttributeError("No constructor defined")
317  __repr__ = _swig_repr
318 
319  def write(self, osa_buf):
320  """write(_ostream self, char const * osa_buf)"""
321  return _IMP_npctransport._ostream_write(self, osa_buf)
322 
323 _ostream_swigregister = _IMP_npctransport._ostream_swigregister
324 _ostream_swigregister(_ostream)
325 
326 
327 _IMP_npctransport.IMP_HAS_NOEXCEPT_swigconstant(_IMP_npctransport)
328 IMP_HAS_NOEXCEPT = _IMP_npctransport.IMP_HAS_NOEXCEPT
329 
330 _IMP_npctransport.IMP_C_OPEN_BINARY_swigconstant(_IMP_npctransport)
331 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
332 import IMP
333 
334 _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
335 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
336 
337 _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
338 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
339 
340 _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
341 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
342 
343 _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
344 IMP_BENCHMARK_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SERIALIZATION
345 
346 _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
347 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
348 
349 _IMP_npctransport.IMP_BENCHMARK_HAS_NUMPY_swigconstant(_IMP_npctransport)
350 IMP_BENCHMARK_HAS_NUMPY = _IMP_npctransport.IMP_BENCHMARK_HAS_NUMPY
351 
352 _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
353 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
354 import IMP.benchmark
355 
356 _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
357 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
358 
359 _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
360 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
361 
362 _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
363 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
364 
365 _IMP_npctransport.IMP_CGAL_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
366 IMP_CGAL_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SERIALIZATION
367 
368 _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
369 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
370 
371 _IMP_npctransport.IMP_CGAL_HAS_NUMPY_swigconstant(_IMP_npctransport)
372 IMP_CGAL_HAS_NUMPY = _IMP_npctransport.IMP_CGAL_HAS_NUMPY
373 
374 _IMP_npctransport.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
375 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
376 import IMP.cgal
377 
378 _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
379 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
380 
381 _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
382 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
383 
384 _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
385 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
386 
387 _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
388 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
389 
390 _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
391 IMP_ALGEBRA_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SERIALIZATION
392 
393 _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
394 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
395 
396 _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_npctransport)
397 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
398 
399 _IMP_npctransport.IMP_ALGEBRA_HAS_NUMPY_swigconstant(_IMP_npctransport)
400 IMP_ALGEBRA_HAS_NUMPY = _IMP_npctransport.IMP_ALGEBRA_HAS_NUMPY
401 
402 _IMP_npctransport.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_npctransport)
403 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
404 
405 _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
406 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
407 import IMP.algebra
408 
409 _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
410 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
411 
412 _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
413 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
414 
415 _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
416 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
417 
418 _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
419 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
420 
421 _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
422 IMP_DISPLAY_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SERIALIZATION
423 
424 _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
425 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
426 
427 _IMP_npctransport.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_npctransport)
428 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
429 
430 _IMP_npctransport.IMP_DISPLAY_HAS_NUMPY_swigconstant(_IMP_npctransport)
431 IMP_DISPLAY_HAS_NUMPY = _IMP_npctransport.IMP_DISPLAY_HAS_NUMPY
432 
433 _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
434 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
435 import IMP.display
436 
437 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
438 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
439 
440 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
441 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
442 
443 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
444 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
445 
446 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
447 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
448 
449 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
450 IMP_SCORE_FUNCTOR_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SERIALIZATION
451 
452 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
453 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
454 
455 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_npctransport)
456 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
457 
458 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_npctransport)
459 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
460 
461 _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_NUMPY_swigconstant(_IMP_npctransport)
462 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_NUMPY
463 
464 _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
465 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
466 import IMP.score_functor
467 
468 _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
469 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
470 
471 _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
472 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
473 
474 _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
475 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
476 
477 _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
478 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
479 
480 _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
481 IMP_STATISTICS_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SERIALIZATION
482 
483 _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
484 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
485 
486 _IMP_npctransport.IMP_STATISTICS_HAS_CGAL_swigconstant(_IMP_npctransport)
487 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
488 
489 _IMP_npctransport.IMP_STATISTICS_HAS_NUMPY_swigconstant(_IMP_npctransport)
490 IMP_STATISTICS_HAS_NUMPY = _IMP_npctransport.IMP_STATISTICS_HAS_NUMPY
491 
492 _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
493 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
494 import IMP.statistics
495 
496 _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
497 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
498 
499 _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_npctransport)
500 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
501 
502 _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
503 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
504 
505 _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
506 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
507 
508 _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
509 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
510 
511 _IMP_npctransport.IMP_CORE_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
512 IMP_CORE_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_CORE_HAS_BOOST_SERIALIZATION
513 
514 _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
515 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
516 
517 _IMP_npctransport.IMP_CORE_HAS_CGAL_swigconstant(_IMP_npctransport)
518 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
519 
520 _IMP_npctransport.IMP_CORE_HAS_HDF5_swigconstant(_IMP_npctransport)
521 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
522 
523 _IMP_npctransport.IMP_CORE_HAS_NUMPY_swigconstant(_IMP_npctransport)
524 IMP_CORE_HAS_NUMPY = _IMP_npctransport.IMP_CORE_HAS_NUMPY
525 
526 _IMP_npctransport.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
527 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
528 import IMP.core
529 
530 _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_npctransport)
531 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
532 
533 _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
534 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
535 
536 _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_npctransport)
537 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
538 
539 _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_npctransport)
540 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
541 
542 _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_npctransport)
543 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
544 
545 _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
546 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
547 
548 _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
549 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
550 
551 _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
552 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
553 
554 _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
555 IMP_CONTAINER_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SERIALIZATION
556 
557 _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
558 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
559 
560 _IMP_npctransport.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_npctransport)
561 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
562 
563 _IMP_npctransport.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_npctransport)
564 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
565 
566 _IMP_npctransport.IMP_CONTAINER_HAS_NUMPY_swigconstant(_IMP_npctransport)
567 IMP_CONTAINER_HAS_NUMPY = _IMP_npctransport.IMP_CONTAINER_HAS_NUMPY
568 
569 _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
570 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
571 
572 _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP_swigconstant(_IMP_npctransport)
573 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
574 
575 _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP_swigconstant(_IMP_npctransport)
576 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
577 
578 _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
579 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
580 import IMP.container
581 
582 _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
583 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
584 
585 _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_npctransport)
586 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
587 
588 _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_npctransport)
589 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
590 
591 _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
592 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
593 
594 _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
595 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
596 
597 _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_npctransport)
598 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
599 
600 _IMP_npctransport.IMP_ATOM_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
601 IMP_ATOM_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SERIALIZATION
602 
603 _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
604 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
605 
606 _IMP_npctransport.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_npctransport)
607 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
608 
609 _IMP_npctransport.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_npctransport)
610 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
611 
612 _IMP_npctransport.IMP_ATOM_HAS_NUMPY_swigconstant(_IMP_npctransport)
613 IMP_ATOM_HAS_NUMPY = _IMP_npctransport.IMP_ATOM_HAS_NUMPY
614 
615 _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
616 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
617 
618 _IMP_npctransport.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
619 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
620 
621 _IMP_npctransport.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_npctransport)
622 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
623 
624 _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_npctransport)
625 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
626 
627 _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_npctransport)
628 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
629 
630 _IMP_npctransport.IMP_CHAIN_TYPE_INDEX_swigconstant(_IMP_npctransport)
631 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
632 import IMP.atom
633 
634 _IMP_npctransport.IMP_EM_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
635 IMP_EM_HAS_IMP_CGAL = _IMP_npctransport.IMP_EM_HAS_IMP_CGAL
636 
637 _IMP_npctransport.IMP_EM_HAS_IMP_CONTAINER_swigconstant(_IMP_npctransport)
638 IMP_EM_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_EM_HAS_IMP_CONTAINER
639 
640 _IMP_npctransport.IMP_EM_HAS_IMP_DISPLAY_swigconstant(_IMP_npctransport)
641 IMP_EM_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_EM_HAS_IMP_DISPLAY
642 
643 _IMP_npctransport.IMP_EM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_npctransport)
644 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_EM_HAS_IMP_SCORE_FUNCTOR
645 
646 _IMP_npctransport.IMP_EM_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
647 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_FILESYSTEM
648 
649 _IMP_npctransport.IMP_EM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
650 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
651 
652 _IMP_npctransport.IMP_EM_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
653 IMP_EM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_EM_HAS_BOOST_RANDOM
654 
655 _IMP_npctransport.IMP_EM_HAS_BOOST_REGEX_swigconstant(_IMP_npctransport)
656 IMP_EM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_EM_HAS_BOOST_REGEX
657 
658 _IMP_npctransport.IMP_EM_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
659 IMP_EM_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_EM_HAS_BOOST_SERIALIZATION
660 
661 _IMP_npctransport.IMP_EM_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
662 IMP_EM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_SYSTEM
663 
664 _IMP_npctransport.IMP_EM_HAS_CGAL_swigconstant(_IMP_npctransport)
665 IMP_EM_HAS_CGAL = _IMP_npctransport.IMP_EM_HAS_CGAL
666 
667 _IMP_npctransport.IMP_EM_HAS_HDF5_swigconstant(_IMP_npctransport)
668 IMP_EM_HAS_HDF5 = _IMP_npctransport.IMP_EM_HAS_HDF5
669 
670 _IMP_npctransport.IMP_EM_HAS_NUMPY_swigconstant(_IMP_npctransport)
671 IMP_EM_HAS_NUMPY = _IMP_npctransport.IMP_EM_HAS_NUMPY
672 
673 _IMP_npctransport.IMP_EM_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
674 IMP_EM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_EM_HAS_PYTHON_IHM
675 
676 _IMP_npctransport.IMPEM_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
677 IMPEM_SHOW_WARNINGS = _IMP_npctransport.IMPEM_SHOW_WARNINGS
678 import IMP.em
679 
680 _IMP_npctransport.IMP_SAXS_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
681 IMP_SAXS_HAS_IMP_CGAL = _IMP_npctransport.IMP_SAXS_HAS_IMP_CGAL
682 
683 _IMP_npctransport.IMP_SAXS_HAS_IMP_CONTAINER_swigconstant(_IMP_npctransport)
684 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_SAXS_HAS_IMP_CONTAINER
685 
686 _IMP_npctransport.IMP_SAXS_HAS_IMP_DISPLAY_swigconstant(_IMP_npctransport)
687 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_SAXS_HAS_IMP_DISPLAY
688 
689 _IMP_npctransport.IMP_SAXS_HAS_IMP_KERNEL_swigconstant(_IMP_npctransport)
690 IMP_SAXS_HAS_IMP_KERNEL = _IMP_npctransport.IMP_SAXS_HAS_IMP_KERNEL
691 
692 _IMP_npctransport.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_npctransport)
693 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
694 
695 _IMP_npctransport.IMP_SAXS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
696 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_FILESYSTEM
697 
698 _IMP_npctransport.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
699 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
700 
701 _IMP_npctransport.IMP_SAXS_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
702 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_RANDOM
703 
704 _IMP_npctransport.IMP_SAXS_HAS_BOOST_REGEX_swigconstant(_IMP_npctransport)
705 IMP_SAXS_HAS_BOOST_REGEX = _IMP_npctransport.IMP_SAXS_HAS_BOOST_REGEX
706 
707 _IMP_npctransport.IMP_SAXS_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
708 IMP_SAXS_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_SAXS_HAS_BOOST_SERIALIZATION
709 
710 _IMP_npctransport.IMP_SAXS_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
711 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_SYSTEM
712 
713 _IMP_npctransport.IMP_SAXS_HAS_CGAL_swigconstant(_IMP_npctransport)
714 IMP_SAXS_HAS_CGAL = _IMP_npctransport.IMP_SAXS_HAS_CGAL
715 
716 _IMP_npctransport.IMP_SAXS_HAS_HDF5_swigconstant(_IMP_npctransport)
717 IMP_SAXS_HAS_HDF5 = _IMP_npctransport.IMP_SAXS_HAS_HDF5
718 
719 _IMP_npctransport.IMP_SAXS_HAS_NUMPY_swigconstant(_IMP_npctransport)
720 IMP_SAXS_HAS_NUMPY = _IMP_npctransport.IMP_SAXS_HAS_NUMPY
721 
722 _IMP_npctransport.IMP_SAXS_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
723 IMP_SAXS_HAS_PYTHON_IHM = _IMP_npctransport.IMP_SAXS_HAS_PYTHON_IHM
724 
725 _IMP_npctransport.IMPSAXS_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
726 IMPSAXS_SHOW_WARNINGS = _IMP_npctransport.IMPSAXS_SHOW_WARNINGS
727 import IMP.saxs
728 
729 _IMP_npctransport.IMP_ISD_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
730 IMP_ISD_HAS_IMP_CGAL = _IMP_npctransport.IMP_ISD_HAS_IMP_CGAL
731 
732 _IMP_npctransport.IMP_ISD_HAS_IMP_DISPLAY_swigconstant(_IMP_npctransport)
733 IMP_ISD_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_ISD_HAS_IMP_DISPLAY
734 
735 _IMP_npctransport.IMP_ISD_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_npctransport)
736 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
737 
738 _IMP_npctransport.IMP_ISD_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
739 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_FILESYSTEM
740 
741 _IMP_npctransport.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
742 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
743 
744 _IMP_npctransport.IMP_ISD_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
745 IMP_ISD_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ISD_HAS_BOOST_RANDOM
746 
747 _IMP_npctransport.IMP_ISD_HAS_BOOST_REGEX_swigconstant(_IMP_npctransport)
748 IMP_ISD_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ISD_HAS_BOOST_REGEX
749 
750 _IMP_npctransport.IMP_ISD_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
751 IMP_ISD_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_ISD_HAS_BOOST_SERIALIZATION
752 
753 _IMP_npctransport.IMP_ISD_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
754 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_SYSTEM
755 
756 _IMP_npctransport.IMP_ISD_HAS_CGAL_swigconstant(_IMP_npctransport)
757 IMP_ISD_HAS_CGAL = _IMP_npctransport.IMP_ISD_HAS_CGAL
758 
759 _IMP_npctransport.IMP_ISD_HAS_HDF5_swigconstant(_IMP_npctransport)
760 IMP_ISD_HAS_HDF5 = _IMP_npctransport.IMP_ISD_HAS_HDF5
761 
762 _IMP_npctransport.IMP_ISD_HAS_NUMPY_swigconstant(_IMP_npctransport)
763 IMP_ISD_HAS_NUMPY = _IMP_npctransport.IMP_ISD_HAS_NUMPY
764 
765 _IMP_npctransport.IMP_ISD_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
766 IMP_ISD_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ISD_HAS_PYTHON_IHM
767 
768 _IMP_npctransport.IMPISD_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
769 IMPISD_SHOW_WARNINGS = _IMP_npctransport.IMPISD_SHOW_WARNINGS
770 import IMP.isd
771 
772 _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
773 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
774 
775 _IMP_npctransport.IMP_RMF_HAS_IMP_EM_swigconstant(_IMP_npctransport)
776 IMP_RMF_HAS_IMP_EM = _IMP_npctransport.IMP_RMF_HAS_IMP_EM
777 
778 _IMP_npctransport.IMP_RMF_HAS_IMP_SAXS_swigconstant(_IMP_npctransport)
779 IMP_RMF_HAS_IMP_SAXS = _IMP_npctransport.IMP_RMF_HAS_IMP_SAXS
780 
781 _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_npctransport)
782 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
783 
784 _IMP_npctransport.IMP_RMF_HAS_IMP_STATISTICS_swigconstant(_IMP_npctransport)
785 IMP_RMF_HAS_IMP_STATISTICS = _IMP_npctransport.IMP_RMF_HAS_IMP_STATISTICS
786 
787 _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
788 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
789 
790 _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
791 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
792 
793 _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
794 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
795 
796 _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX_swigconstant(_IMP_npctransport)
797 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
798 
799 _IMP_npctransport.IMP_RMF_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
800 IMP_RMF_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_RMF_HAS_BOOST_SERIALIZATION
801 
802 _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
803 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
804 
805 _IMP_npctransport.IMP_RMF_HAS_CGAL_swigconstant(_IMP_npctransport)
806 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
807 
808 _IMP_npctransport.IMP_RMF_HAS_HDF5_swigconstant(_IMP_npctransport)
809 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
810 
811 _IMP_npctransport.IMP_RMF_HAS_NUMPY_swigconstant(_IMP_npctransport)
812 IMP_RMF_HAS_NUMPY = _IMP_npctransport.IMP_RMF_HAS_NUMPY
813 
814 _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
815 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
816 
817 _IMP_npctransport.IMPRMF_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
818 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
819 import IMP.rmf
820 import RMF
821 
822 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL_swigconstant(_IMP_npctransport)
823 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
824 
825 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_EM_swigconstant(_IMP_npctransport)
826 IMP_NPCTRANSPORT_HAS_IMP_EM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_EM
827 
828 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_ISD_swigconstant(_IMP_npctransport)
829 IMP_NPCTRANSPORT_HAS_IMP_ISD = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_ISD
830 
831 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_SAXS_swigconstant(_IMP_npctransport)
832 IMP_NPCTRANSPORT_HAS_IMP_SAXS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_SAXS
833 
834 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_npctransport)
835 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
836 
837 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_npctransport)
838 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
839 
840 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM_swigconstant(_IMP_npctransport)
841 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
842 
843 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX_swigconstant(_IMP_npctransport)
844 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
845 
846 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_npctransport)
847 IMP_NPCTRANSPORT_HAS_BOOST_SERIALIZATION = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SERIALIZATION
848 
849 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM_swigconstant(_IMP_npctransport)
850 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
851 
852 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL_swigconstant(_IMP_npctransport)
853 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
854 
855 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5_swigconstant(_IMP_npctransport)
856 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
857 
858 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_NUMPY_swigconstant(_IMP_npctransport)
859 IMP_NPCTRANSPORT_HAS_NUMPY = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_NUMPY
860 
861 _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM_swigconstant(_IMP_npctransport)
862 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
863 
864 _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS_swigconstant(_IMP_npctransport)
865 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
866 
867 _object_types.append("SitesPairScore")
868 
869 
870 def _object_cast_to_SitesPairScore(o):
871  """_object_cast_to_SitesPairScore(Object o) -> SitesPairScore"""
872  return _IMP_npctransport._object_cast_to_SitesPairScore(o)
873 
874 _object_types.append("Scoring")
875 
876 
877 def _object_cast_to_Scoring(o):
878  """_object_cast_to_Scoring(Object o) -> Scoring"""
879  return _IMP_npctransport._object_cast_to_Scoring(o)
880 
881 _object_types.append("BrownianDynamicsTAMDWithSlabSupport")
882 
883 
884 def _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o):
885  """_object_cast_to_BrownianDynamicsTAMDWithSlabSupport(Object o) -> BrownianDynamicsTAMDWithSlabSupport"""
886  return _IMP_npctransport._object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
887 
888 _object_types.append("Statistics")
889 
890 
891 def _object_cast_to_Statistics(o):
892  """_object_cast_to_Statistics(Object o) -> Statistics"""
893  return _IMP_npctransport._object_cast_to_Statistics(o)
894 
895 _object_types.append("SimulationData")
896 
897 
898 def _object_cast_to_SimulationData(o):
899  """_object_cast_to_SimulationData(Object o) -> SimulationData"""
900  return _IMP_npctransport._object_cast_to_SimulationData(o)
901 
902 _object_types.append("SitesGeometry")
903 
904 
905 def _object_cast_to_SitesGeometry(o):
906  """_object_cast_to_SitesGeometry(Object o) -> SitesGeometry"""
907  return _IMP_npctransport._object_cast_to_SitesGeometry(o)
908 
909 _object_types.append("TypedSitesGeometry")
910 
911 
912 def _object_cast_to_TypedSitesGeometry(o):
913  """_object_cast_to_TypedSitesGeometry(Object o) -> TypedSitesGeometry"""
914  return _IMP_npctransport._object_cast_to_TypedSitesGeometry(o)
915 
916 _object_types.append("SlabWithCylindricalPorePairScore")
917 
918 
919 def _object_cast_to_SlabWithCylindricalPorePairScore(o):
920  """_object_cast_to_SlabWithCylindricalPorePairScore(Object o) -> SlabWithCylindricalPorePairScore"""
921  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPorePairScore(o)
922 
923 _object_types.append("SlabWithToroidalPorePairScore")
924 
925 
926 def _object_cast_to_SlabWithToroidalPorePairScore(o):
927  """_object_cast_to_SlabWithToroidalPorePairScore(Object o) -> SlabWithToroidalPorePairScore"""
928  return _IMP_npctransport._object_cast_to_SlabWithToroidalPorePairScore(o)
929 
930 _object_types.append("PoreRadiusSingletonScore")
931 
932 
933 def _object_cast_to_PoreRadiusSingletonScore(o):
934  """_object_cast_to_PoreRadiusSingletonScore(Object o) -> PoreRadiusSingletonScore"""
935  return _IMP_npctransport._object_cast_to_PoreRadiusSingletonScore(o)
936 
937 _object_types.append("ExcludeZRangeSingletonScore")
938 
939 
940 def _object_cast_to_ExcludeZRangeSingletonScore(o):
941  """_object_cast_to_ExcludeZRangeSingletonScore(Object o) -> ExcludeZRangeSingletonScore"""
942  return _IMP_npctransport._object_cast_to_ExcludeZRangeSingletonScore(o)
943 
944 _object_types.append("ZBiasSingletonScore")
945 
946 
947 def _object_cast_to_ZBiasSingletonScore(o):
948  """_object_cast_to_ZBiasSingletonScore(Object o) -> ZBiasSingletonScore"""
949  return _IMP_npctransport._object_cast_to_ZBiasSingletonScore(o)
950 
951 _object_types.append("SlabWithCylindricalPoreWireGeometry")
952 
953 
954 def _object_cast_to_SlabWithCylindricalPoreWireGeometry(o):
955  """_object_cast_to_SlabWithCylindricalPoreWireGeometry(Object o) -> SlabWithCylindricalPoreWireGeometry"""
956  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
957 
958 _object_types.append("SlabWithCylindricalPoreSurfaceGeometry")
959 
960 
961 def _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o):
962  """_object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(Object o) -> SlabWithCylindricalPoreSurfaceGeometry"""
963  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
964 
965 _object_types.append("SlabWithToroidalPoreWireGeometry")
966 
967 
968 def _object_cast_to_SlabWithToroidalPoreWireGeometry(o):
969  """_object_cast_to_SlabWithToroidalPoreWireGeometry(Object o) -> SlabWithToroidalPoreWireGeometry"""
970  return _IMP_npctransport._object_cast_to_SlabWithToroidalPoreWireGeometry(o)
971 
972 _object_types.append("LinearSoftSpherePairScore")
973 
974 
975 def _object_cast_to_LinearSoftSpherePairScore(o):
976  """_object_cast_to_LinearSoftSpherePairScore(Object o) -> LinearSoftSpherePairScore"""
977  return _IMP_npctransport._object_cast_to_LinearSoftSpherePairScore(o)
978 
979 _object_types.append("FunctorLinearSoftSpherePairScore")
980 
981 
982 def _object_cast_to_FunctorLinearSoftSpherePairScore(o):
983  """_object_cast_to_FunctorLinearSoftSpherePairScore(Object o) -> FunctorLinearSoftSpherePairScore"""
984  return _IMP_npctransport._object_cast_to_FunctorLinearSoftSpherePairScore(o)
985 
986 _object_types.append("LinearInteractionPairScore")
987 
988 
989 def _object_cast_to_LinearInteractionPairScore(o):
990  """_object_cast_to_LinearInteractionPairScore(Object o) -> LinearInteractionPairScore"""
991  return _IMP_npctransport._object_cast_to_LinearInteractionPairScore(o)
992 
993 _object_types.append("FunctorLinearInteractionPairScore")
994 
995 
996 def _object_cast_to_FunctorLinearInteractionPairScore(o):
997  """_object_cast_to_FunctorLinearInteractionPairScore(Object o) -> FunctorLinearInteractionPairScore"""
998  return _IMP_npctransport._object_cast_to_FunctorLinearInteractionPairScore(o)
999 
1000 _object_types.append("LinearWellPairScore")
1001 
1002 
1003 def _object_cast_to_LinearWellPairScore(o):
1004  """_object_cast_to_LinearWellPairScore(Object o) -> LinearWellPairScore"""
1005  return _IMP_npctransport._object_cast_to_LinearWellPairScore(o)
1006 
1007 _object_types.append("HarmonicSpringSingletonScore")
1008 
1009 
1010 def _object_cast_to_HarmonicSpringSingletonScore(o):
1011  """_object_cast_to_HarmonicSpringSingletonScore(Object o) -> HarmonicSpringSingletonScore"""
1012  return _IMP_npctransport._object_cast_to_HarmonicSpringSingletonScore(o)
1013 
1014 _object_types.append("HierarchyWithSitesSaveLink")
1015 
1016 
1017 def _object_cast_to_HierarchyWithSitesSaveLink(o):
1018  """_object_cast_to_HierarchyWithSitesSaveLink(Object o) -> HierarchyWithSitesSaveLink"""
1019  return _IMP_npctransport._object_cast_to_HierarchyWithSitesSaveLink(o)
1020 
1021 _object_types.append("HierarchyWithSitesLoadLink")
1022 
1023 
1024 def _object_cast_to_HierarchyWithSitesLoadLink(o):
1025  """_object_cast_to_HierarchyWithSitesLoadLink(Object o) -> HierarchyWithSitesLoadLink"""
1026  return _IMP_npctransport._object_cast_to_HierarchyWithSitesLoadLink(o)
1027 
1028 _object_types.append("ChainStatisticsOptimizerState")
1029 
1030 
1031 def _object_cast_to_ChainStatisticsOptimizerState(o):
1032  """_object_cast_to_ChainStatisticsOptimizerState(Object o) -> ChainStatisticsOptimizerState"""
1033  return _IMP_npctransport._object_cast_to_ChainStatisticsOptimizerState(o)
1034 
1035 _object_types.append("BodyStatisticsOptimizerState")
1036 
1037 
1038 def _object_cast_to_BodyStatisticsOptimizerState(o):
1039  """_object_cast_to_BodyStatisticsOptimizerState(Object o) -> BodyStatisticsOptimizerState"""
1040  return _IMP_npctransport._object_cast_to_BodyStatisticsOptimizerState(o)
1041 
1042 _object_types.append("BipartitePairsStatisticsOptimizerState")
1043 
1044 
1045 def _object_cast_to_BipartitePairsStatisticsOptimizerState(o):
1046  """_object_cast_to_BipartitePairsStatisticsOptimizerState(Object o) -> BipartitePairsStatisticsOptimizerState"""
1047  return _IMP_npctransport._object_cast_to_BipartitePairsStatisticsOptimizerState(o)
1048 
1049 _object_types.append("ParticleTransportStatisticsOptimizerState")
1050 
1051 
1052 def _object_cast_to_ParticleTransportStatisticsOptimizerState(o):
1053  """_object_cast_to_ParticleTransportStatisticsOptimizerState(Object o) -> ParticleTransportStatisticsOptimizerState"""
1054  return _IMP_npctransport._object_cast_to_ParticleTransportStatisticsOptimizerState(o)
1055 
1056 _object_types.append("FGChain")
1057 
1058 
1059 def _object_cast_to_FGChain(o):
1060  """_object_cast_to_FGChain(Object o) -> FGChain"""
1061  return _IMP_npctransport._object_cast_to_FGChain(o)
1062 
1063 _object_types.append("ParticleFactory")
1064 
1065 
1066 def _object_cast_to_ParticleFactory(o):
1067  """_object_cast_to_ParticleFactory(Object o) -> ParticleFactory"""
1068  return _IMP_npctransport._object_cast_to_ParticleFactory(o)
1069 
1070 Avro2PBReaders=list
1071 _plural_types.append("Avro2PBReaders")
1072 _value_types.append("Avro2PBReader")
1073 
1074 
1075 SitesPairScoreParametersList=list
1076 _plural_types.append("SitesPairScoreParametersList")
1077 _value_types.append("SitesPairScoreParameters")
1078 
1079 
1080 def Transportings(l=[]):
1081  return [Transporting(x) for x in l]
1082 _plural_types.append("Transportings")
1083 
1084 
1085 _value_types.append("Transporting")
1086 
1087 
1088 def SlabWithPores(l=[]):
1089  return [SlabWithPore(x) for x in l]
1090 _plural_types.append("SlabWithPores")
1091 
1092 
1093 _value_types.append("SlabWithPore")
1094 
1095 
1096 def SlabWithCylindricalPores(l=[]):
1097  return [SlabWithCylindricalPore(x) for x in l]
1098 _plural_types.append("SlabWithCylindricalPores")
1099 
1100 
1101 _value_types.append("SlabWithCylindricalPore")
1102 
1103 
1104 def RelaxingSprings(l=[]):
1105  return [RelaxingSpring(x) for x in l]
1106 _plural_types.append("RelaxingSprings")
1107 
1108 
1109 _value_types.append("RelaxingSpring")
1110 
1111 
1112 def SlabWithToroidalPores(l=[]):
1113  return [SlabWithToroidalPore(x) for x in l]
1114 _plural_types.append("SlabWithToroidalPores")
1115 
1116 
1117 _value_types.append("SlabWithToroidalPore")
1118 
1119 class _DoubleParameter(object):
1120  """Proxy of C++ IMP::npctransport::Parameter<(double)> class"""
1121  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1122  __repr__ = _swig_repr
1123 
1124  def __init__(self, *args):
1125  """
1126  __init__(IMP::npctransport::Parameter<(double)> self) -> _DoubleParameter
1127  __init__(IMP::npctransport::Parameter<(double)> self, double t) -> _DoubleParameter
1128  """
1129  this = _IMP_npctransport.new__DoubleParameter(*args)
1130  try:
1131  self.this.append(this)
1132  except:
1133  self.this = this
1134 
1135  def get_value(self):
1136  """get_value(_DoubleParameter self) -> double"""
1137  return _IMP_npctransport._DoubleParameter_get_value(self)
1138 
1139 
1140  def is_init(self):
1141  """is_init(_DoubleParameter self) -> bool"""
1142  return _IMP_npctransport._DoubleParameter_is_init(self)
1143 
1144  __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
1145  __del__ = lambda self: None
1146 _DoubleParameter_swigregister = _IMP_npctransport._DoubleParameter_swigregister
1147 _DoubleParameter_swigregister(_DoubleParameter)
1148 
1149 class _IntParameter(object):
1150  """Proxy of C++ IMP::npctransport::Parameter<(int)> class"""
1151  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1152  __repr__ = _swig_repr
1153 
1154  def __init__(self, *args):
1155  """
1156  __init__(IMP::npctransport::Parameter<(int)> self) -> _IntParameter
1157  __init__(IMP::npctransport::Parameter<(int)> self, int t) -> _IntParameter
1158  """
1159  this = _IMP_npctransport.new__IntParameter(*args)
1160  try:
1161  self.this.append(this)
1162  except:
1163  self.this = this
1164 
1165  def get_value(self):
1166  """get_value(_IntParameter self) -> int"""
1167  return _IMP_npctransport._IntParameter_get_value(self)
1168 
1169 
1170  def is_init(self):
1171  """is_init(_IntParameter self) -> bool"""
1172  return _IMP_npctransport._IntParameter_is_init(self)
1173 
1174  __swig_destroy__ = _IMP_npctransport.delete__IntParameter
1175  __del__ = lambda self: None
1176 _IntParameter_swigregister = _IMP_npctransport._IntParameter_swigregister
1177 _IntParameter_swigregister(_IntParameter)
1178 
1179 class _BoolParameter(object):
1180  """Proxy of C++ IMP::npctransport::Parameter<(bool)> class"""
1181  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1182  __repr__ = _swig_repr
1183 
1184  def __init__(self, *args):
1185  """
1186  __init__(IMP::npctransport::Parameter<(bool)> self) -> _BoolParameter
1187  __init__(IMP::npctransport::Parameter<(bool)> self, bool t) -> _BoolParameter
1188  """
1189  this = _IMP_npctransport.new__BoolParameter(*args)
1190  try:
1191  self.this.append(this)
1192  except:
1193  self.this = this
1194 
1195  def get_value(self):
1196  """get_value(_BoolParameter self) -> bool"""
1197  return _IMP_npctransport._BoolParameter_get_value(self)
1198 
1199 
1200  def is_init(self):
1201  """is_init(_BoolParameter self) -> bool"""
1202  return _IMP_npctransport._BoolParameter_is_init(self)
1203 
1204  __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
1205  __del__ = lambda self: None
1206 _BoolParameter_swigregister = _IMP_npctransport._BoolParameter_swigregister
1207 _BoolParameter_swigregister(_BoolParameter)
1208 
1209 
1210 def make_ordered_interaction_type(t0, t1):
1211  """make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
1212  return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
1213 
1214 def make_unordered_interaction_type(t0, t1):
1215  """make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
1216  return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
1217 
1218 def make_unordered_particle_index_pair(*args):
1219  """
1220  make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
1221  make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
1222  """
1223  return _IMP_npctransport.make_unordered_particle_index_pair(*args)
1224 class LinearSoftSpherePairScore(IMP.PairScore):
1225  """Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class"""
1226  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1227 
1228  def __init__(self, *args):
1229  """
1230  __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k, std::string name) -> LinearSoftSpherePairScore
1231  __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k) -> LinearSoftSpherePairScore
1232  """
1233  this = _IMP_npctransport.new_LinearSoftSpherePairScore(*args)
1234  try:
1235  self.this.append(this)
1236  except:
1237  self.this = this
1238 
1239  def do_get_inputs(self, m, pis):
1240  """do_get_inputs(LinearSoftSpherePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1241  return _IMP_npctransport.LinearSoftSpherePairScore_do_get_inputs(self, m, pis)
1242 
1243 
1244  def get_k(self):
1245  """get_k(LinearSoftSpherePairScore self) -> double"""
1246  return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
1247 
1248 
1249  def get_version_info(self):
1250  """get_version_info(LinearSoftSpherePairScore self) -> VersionInfo"""
1251  return _IMP_npctransport.LinearSoftSpherePairScore_get_version_info(self)
1252 
1253 
1254  def __str__(self):
1255  """__str__(LinearSoftSpherePairScore self) -> std::string"""
1256  return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
1257 
1258 
1259  def __repr__(self):
1260  """__repr__(LinearSoftSpherePairScore self) -> std::string"""
1261  return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
1262 
1263 
1264  @staticmethod
1265  def get_from(o):
1266  return _object_cast_to_LinearSoftSpherePairScore(o)
1267 
1268 LinearSoftSpherePairScore_swigregister = _IMP_npctransport.LinearSoftSpherePairScore_swigregister
1269 LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
1270 
1271 class LinearInteractionPairScore(IMP.PairScore):
1272  """Proxy of C++ IMP::npctransport::LinearInteractionPairScore class"""
1273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1274 
1275  def __init__(self, *args):
1276  """
1277  __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr, std::string name) -> LinearInteractionPairScore
1278  __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr) -> LinearInteractionPairScore
1279  """
1280  this = _IMP_npctransport.new_LinearInteractionPairScore(*args)
1281  try:
1282  self.this.append(this)
1283  except:
1284  self.this = this
1285 
1286  def evaluate_if_good_index(self, *args):
1287  """
1288  evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPair const & p, DerivativeAccumulator da, double max) -> double
1289  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
1290  """
1291  return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
1292 
1293 
1294  def do_get_inputs(self, m, pis):
1295  """do_get_inputs(LinearInteractionPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1296  return _IMP_npctransport.LinearInteractionPairScore_do_get_inputs(self, m, pis)
1297 
1298 
1299  def get_range_attraction(self):
1300  """get_range_attraction(LinearInteractionPairScore self) -> double"""
1301  return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
1302 
1303 
1304  def get_k_attraction(self):
1305  """get_k_attraction(LinearInteractionPairScore self) -> double"""
1306  return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
1307 
1308 
1309  def set_k_attraction(self, k_attr):
1310  """set_k_attraction(LinearInteractionPairScore self, double k_attr)"""
1311  return _IMP_npctransport.LinearInteractionPairScore_set_k_attraction(self, k_attr)
1312 
1313 
1314  def get_k_repulsion(self):
1315  """get_k_repulsion(LinearInteractionPairScore self) -> double"""
1316  return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
1317 
1318 
1319  def set_k_repulsion(self, k_rep):
1320  """set_k_repulsion(LinearInteractionPairScore self, double k_rep)"""
1321  return _IMP_npctransport.LinearInteractionPairScore_set_k_repulsion(self, k_rep)
1322 
1323 
1324  def get_version_info(self):
1325  """get_version_info(LinearInteractionPairScore self) -> VersionInfo"""
1326  return _IMP_npctransport.LinearInteractionPairScore_get_version_info(self)
1327 
1328 
1329  def __str__(self):
1330  """__str__(LinearInteractionPairScore self) -> std::string"""
1331  return _IMP_npctransport.LinearInteractionPairScore___str__(self)
1332 
1333 
1334  def __repr__(self):
1335  """__repr__(LinearInteractionPairScore self) -> std::string"""
1336  return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
1337 
1338 
1339  @staticmethod
1340  def get_from(o):
1341  return _object_cast_to_LinearInteractionPairScore(o)
1342 
1343 LinearInteractionPairScore_swigregister = _IMP_npctransport.LinearInteractionPairScore_swigregister
1344 LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
1345 
1346 class LinearWellPairScore(IMP.PairScore):
1347  """Proxy of C++ IMP::npctransport::LinearWellPairScore class"""
1348  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1349 
1350  def __init__(self, *args):
1351  """
1352  __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k, std::string name) -> LinearWellPairScore
1353  __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k) -> LinearWellPairScore
1354  """
1355  this = _IMP_npctransport.new_LinearWellPairScore(*args)
1356  try:
1357  self.this.append(this)
1358  except:
1359  self.this = this
1360 
1361  def set_rest_length_factor(self, rest_length_factor):
1362  """set_rest_length_factor(LinearWellPairScore self, double rest_length_factor)"""
1363  return _IMP_npctransport.LinearWellPairScore_set_rest_length_factor(self, rest_length_factor)
1364 
1365 
1366  def get_rest_length_factor(self):
1367  """get_rest_length_factor(LinearWellPairScore self) -> double"""
1368  return _IMP_npctransport.LinearWellPairScore_get_rest_length_factor(self)
1369 
1370 
1371  def set_k(self, k):
1372  """set_k(LinearWellPairScore self, double k)"""
1373  return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
1374 
1375 
1376  def get_k(self):
1377  """get_k(LinearWellPairScore self) -> double"""
1378  return _IMP_npctransport.LinearWellPairScore_get_k(self)
1379 
1380 
1381  def do_get_inputs(self, m, pis):
1382  """do_get_inputs(LinearWellPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1383  return _IMP_npctransport.LinearWellPairScore_do_get_inputs(self, m, pis)
1384 
1385 
1386  def get_version_info(self):
1387  """get_version_info(LinearWellPairScore self) -> VersionInfo"""
1388  return _IMP_npctransport.LinearWellPairScore_get_version_info(self)
1389 
1390 
1391  def __str__(self):
1392  """__str__(LinearWellPairScore self) -> std::string"""
1393  return _IMP_npctransport.LinearWellPairScore___str__(self)
1394 
1395 
1396  def __repr__(self):
1397  """__repr__(LinearWellPairScore self) -> std::string"""
1398  return _IMP_npctransport.LinearWellPairScore___repr__(self)
1399 
1400 
1401  @staticmethod
1402  def get_from(o):
1403  return _object_cast_to_LinearWellPairScore(o)
1404 
1405 LinearWellPairScore_swigregister = _IMP_npctransport.LinearWellPairScore_swigregister
1406 LinearWellPairScore_swigregister(LinearWellPairScore)
1407 
1408 class RelaxingSpring(IMP.Decorator):
1409  """Proxy of C++ IMP::npctransport::RelaxingSpring class"""
1410  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1411 
1412  def __init__(self, *args):
1413  """
1414  __init__(IMP::npctransport::RelaxingSpring self) -> RelaxingSpring
1415  __init__(IMP::npctransport::RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
1416  __init__(IMP::npctransport::RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
1417  """
1418  this = _IMP_npctransport.new_RelaxingSpring(*args)
1419  try:
1420  self.this.append(this)
1421  except:
1422  self.this = this
1423 
1424  def show(self, *args):
1425  """
1426  show(RelaxingSpring self, _ostream out)
1427  show(RelaxingSpring self)
1428  """
1429  return _IMP_npctransport.RelaxingSpring_show(self, *args)
1430 
1431 
1432  def setup_particle(*args):
1433  """
1434  setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1435  setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1436  """
1437  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1438 
1439  setup_particle = staticmethod(setup_particle)
1440 
1441  def get_is_setup(*args):
1442  """
1443  get_is_setup(_ParticleAdaptor p) -> bool
1444  get_is_setup(Model m, ParticleIndex pi) -> bool
1445  """
1446  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1447 
1448  get_is_setup = staticmethod(get_is_setup)
1449 
1450  def get_bonded_particle_0_key():
1451  """get_bonded_particle_0_key() -> ParticleIndexKey"""
1452  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1453 
1454  get_bonded_particle_0_key = staticmethod(get_bonded_particle_0_key)
1455 
1456  def get_bonded_particle_1_key():
1457  """get_bonded_particle_1_key() -> ParticleIndexKey"""
1458  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1459 
1460  get_bonded_particle_1_key = staticmethod(get_bonded_particle_1_key)
1461 
1462  def get_equilibrium_rest_length_factor_key():
1463  """get_equilibrium_rest_length_factor_key() -> FloatKey"""
1464  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1465 
1466  get_equilibrium_rest_length_factor_key = staticmethod(get_equilibrium_rest_length_factor_key)
1467 
1468  def get_rest_length_key():
1469  """get_rest_length_key() -> FloatKey"""
1470  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1471 
1472  get_rest_length_key = staticmethod(get_rest_length_key)
1473 
1474  def get_rest_length_diffusion_coefficient_key():
1475  """get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1476  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1477 
1478  get_rest_length_diffusion_coefficient_key = staticmethod(get_rest_length_diffusion_coefficient_key)
1479 
1480  def get_bonded_particle_0(self):
1481  """get_bonded_particle_0(RelaxingSpring self) -> Particle"""
1482  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0(self)
1483 
1484 
1485  def get_bonded_particle_1(self):
1486  """get_bonded_particle_1(RelaxingSpring self) -> Particle"""
1487  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1(self)
1488 
1489 
1490  def get_bonded_particle_index_0(self):
1491  """get_bonded_particle_index_0(RelaxingSpring self) -> ParticleIndex"""
1492  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_0(self)
1493 
1494 
1495  def get_bonded_particle_index_1(self):
1496  """get_bonded_particle_index_1(RelaxingSpring self) -> ParticleIndex"""
1497  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_1(self)
1498 
1499 
1500  def get_equilibrium_rest_length_factor(self):
1501  """get_equilibrium_rest_length_factor(RelaxingSpring self) -> IMP::Float"""
1502  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor(self)
1503 
1504 
1505  def set_equilibrium_rest_length_factor(self, t):
1506  """set_equilibrium_rest_length_factor(RelaxingSpring self, IMP::Float t)"""
1507  return _IMP_npctransport.RelaxingSpring_set_equilibrium_rest_length_factor(self, t)
1508 
1509 
1510  def get_rest_length(self):
1511  """get_rest_length(RelaxingSpring self) -> IMP::Float"""
1512  return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1513 
1514 
1515  def set_rest_length(self, t):
1516  """set_rest_length(RelaxingSpring self, IMP::Float t)"""
1517  return _IMP_npctransport.RelaxingSpring_set_rest_length(self, t)
1518 
1519 
1520  def get_rest_length_diffusion_coefficient(self):
1521  """get_rest_length_diffusion_coefficient(RelaxingSpring self) -> IMP::Float"""
1522  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient(self)
1523 
1524 
1525  def set_rest_length_diffusion_coefficient(self, t):
1526  """set_rest_length_diffusion_coefficient(RelaxingSpring self, IMP::Float t)"""
1527  return _IMP_npctransport.RelaxingSpring_set_rest_length_diffusion_coefficient(self, t)
1528 
1529 
1530  def add_to_rest_length_derivative(self, d, da):
1531  """add_to_rest_length_derivative(RelaxingSpring self, double d, DerivativeAccumulator da)"""
1532  return _IMP_npctransport.RelaxingSpring_add_to_rest_length_derivative(self, d, da)
1533 
1534 
1535  def get_rest_length_derivative(self):
1536  """get_rest_length_derivative(RelaxingSpring self) -> double"""
1537  return _IMP_npctransport.RelaxingSpring_get_rest_length_derivative(self)
1538 
1539 
1540  def add_attribute(self, *args):
1541  """
1542  add_attribute(RelaxingSpring self, FloatKey k, IMP::Float v, bool opt)
1543  add_attribute(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1544  add_attribute(RelaxingSpring self, IntKey a0, IMP::Int a1)
1545  add_attribute(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1546  add_attribute(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1547  add_attribute(RelaxingSpring self, StringKey a0, IMP::String a1)
1548  add_attribute(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1549  add_attribute(RelaxingSpring self, ObjectKey a0, Object a1)
1550  """
1551  return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1552 
1553 
1554  def get_value(self, *args):
1555  """
1556  get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1557  get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1558  get_value(RelaxingSpring self, FloatsKey a0) -> IMP::Floats
1559  get_value(RelaxingSpring self, IntsKey a0) -> IMP::Ints
1560  get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1561  get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1562  get_value(RelaxingSpring self, ObjectKey a0) -> Object
1563  """
1564  return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1565 
1566 
1567  def set_value(self, *args):
1568  """
1569  set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1570  set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1571  set_value(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1572  set_value(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1573  set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1574  set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1575  set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1576  """
1577  return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1578 
1579 
1580  def remove_attribute(self, *args):
1581  """
1582  remove_attribute(RelaxingSpring self, FloatKey a0)
1583  remove_attribute(RelaxingSpring self, IntKey a0)
1584  remove_attribute(RelaxingSpring self, FloatsKey a0)
1585  remove_attribute(RelaxingSpring self, IntsKey a0)
1586  remove_attribute(RelaxingSpring self, StringKey a0)
1587  remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1588  remove_attribute(RelaxingSpring self, ObjectKey a0)
1589  """
1590  return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1591 
1592 
1593  def has_attribute(self, *args):
1594  """
1595  has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1596  has_attribute(RelaxingSpring self, IntKey a0) -> bool
1597  has_attribute(RelaxingSpring self, FloatsKey a0) -> bool
1598  has_attribute(RelaxingSpring self, IntsKey a0) -> bool
1599  has_attribute(RelaxingSpring self, StringKey a0) -> bool
1600  has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1601  has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1602  """
1603  return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1604 
1605 
1606  def get_derivative(self, a0):
1607  """get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1608  return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1609 
1610 
1611  def get_name(self):
1612  """get_name(RelaxingSpring self) -> std::string"""
1613  return _IMP_npctransport.RelaxingSpring_get_name(self)
1614 
1615 
1616  def clear_caches(self):
1617  """clear_caches(RelaxingSpring self)"""
1618  return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1619 
1620 
1621  def set_name(self, a0):
1622  """set_name(RelaxingSpring self, std::string a0)"""
1623  return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1624 
1625 
1626  def set_check_level(self, a0):
1627  """set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1628  return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1629 
1630 
1631  def add_to_derivative(self, a0, a1, a2):
1632  """add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1633  return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1634 
1635 
1636  def set_is_optimized(self, a0, a1):
1637  """set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1638  return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1639 
1640 
1641  def get_is_optimized(self, a0):
1642  """get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1643  return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1644 
1645 
1646  def get_check_level(self):
1647  """get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1648  return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1649 
1650 
1651  def __eq__(self, *args):
1652  """
1653  __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1654  __eq__(RelaxingSpring self, Particle d) -> bool
1655  """
1656  return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1657 
1658 
1659  def __ne__(self, *args):
1660  """
1661  __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1662  __ne__(RelaxingSpring self, Particle d) -> bool
1663  """
1664  return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1665 
1666 
1667  def __le__(self, *args):
1668  """
1669  __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1670  __le__(RelaxingSpring self, Particle d) -> bool
1671  """
1672  return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1673 
1674 
1675  def __lt__(self, *args):
1676  """
1677  __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1678  __lt__(RelaxingSpring self, Particle d) -> bool
1679  """
1680  return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1681 
1682 
1683  def __ge__(self, *args):
1684  """
1685  __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1686  __ge__(RelaxingSpring self, Particle d) -> bool
1687  """
1688  return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1689 
1690 
1691  def __gt__(self, *args):
1692  """
1693  __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1694  __gt__(RelaxingSpring self, Particle d) -> bool
1695  """
1696  return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1697 
1698 
1699  def __hash__(self):
1700  """__hash__(RelaxingSpring self) -> std::size_t"""
1701  return _IMP_npctransport.RelaxingSpring___hash__(self)
1702 
1703 
1704  def __str__(self):
1705  """__str__(RelaxingSpring self) -> std::string"""
1706  return _IMP_npctransport.RelaxingSpring___str__(self)
1707 
1708 
1709  def __repr__(self):
1710  """__repr__(RelaxingSpring self) -> std::string"""
1711  return _IMP_npctransport.RelaxingSpring___repr__(self)
1712 
1713  __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1714  __del__ = lambda self: None
1715 RelaxingSpring_swigregister = _IMP_npctransport.RelaxingSpring_swigregister
1716 RelaxingSpring_swigregister(RelaxingSpring)
1717 
1718 def RelaxingSpring_setup_particle(*args):
1719  """
1720  setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1721  RelaxingSpring_setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1722  """
1723  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1724 
1725 def RelaxingSpring_get_is_setup(*args):
1726  """
1727  get_is_setup(_ParticleAdaptor p) -> bool
1728  RelaxingSpring_get_is_setup(Model m, ParticleIndex pi) -> bool
1729  """
1730  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1731 
1732 def RelaxingSpring_get_bonded_particle_0_key():
1733  """RelaxingSpring_get_bonded_particle_0_key() -> ParticleIndexKey"""
1734  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1735 
1736 def RelaxingSpring_get_bonded_particle_1_key():
1737  """RelaxingSpring_get_bonded_particle_1_key() -> ParticleIndexKey"""
1738  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1739 
1740 def RelaxingSpring_get_equilibrium_rest_length_factor_key():
1741  """RelaxingSpring_get_equilibrium_rest_length_factor_key() -> FloatKey"""
1742  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1743 
1744 def RelaxingSpring_get_rest_length_key():
1745  """RelaxingSpring_get_rest_length_key() -> FloatKey"""
1746  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1747 
1748 def RelaxingSpring_get_rest_length_diffusion_coefficient_key():
1749  """RelaxingSpring_get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1750  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1751 
1752 class HarmonicSpringSingletonScore(IMP.SingletonScore):
1753  """Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class"""
1754  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1755 
1756  def __init__(self, *args):
1757  """
1758  __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2, std::string name) -> HarmonicSpringSingletonScore
1759  __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2) -> HarmonicSpringSingletonScore
1760  """
1761  this = _IMP_npctransport.new_HarmonicSpringSingletonScore(*args)
1762  try:
1763  self.this.append(this)
1764  except:
1765  self.this = this
1766 
1767  def set_k1(self, k1):
1768  """set_k1(HarmonicSpringSingletonScore self, double k1)"""
1769  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1770 
1771 
1772  def get_k1(self):
1773  """get_k1(HarmonicSpringSingletonScore self) -> double"""
1774  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1775 
1776 
1777  def set_k2(self, k2):
1778  """set_k2(HarmonicSpringSingletonScore self, double k2)"""
1779  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1780 
1781 
1782  def get_k2(self):
1783  """get_k2(HarmonicSpringSingletonScore self) -> double"""
1784  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1785 
1786 
1787  def do_get_inputs(self, m, pis):
1788  """do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1789  return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1790 
1791 
1792  def get_version_info(self):
1793  """get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1794  return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1795 
1796 
1797  def __str__(self):
1798  """__str__(HarmonicSpringSingletonScore self) -> std::string"""
1799  return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1800 
1801 
1802  def __repr__(self):
1803  """__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1804  return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1805 
1806 
1807  @staticmethod
1808  def get_from(o):
1809  return _object_cast_to_HarmonicSpringSingletonScore(o)
1810 
1811 HarmonicSpringSingletonScore_swigregister = _IMP_npctransport.HarmonicSpringSingletonScore_swigregister
1812 HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1813 
1814 class LinearInteraction(object):
1815  """Proxy of C++ IMP::npctransport::LinearInteraction class"""
1816  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1817  __repr__ = _swig_repr
1818 
1819  def __init__(self, krep, attr_range, kattr):
1820  """__init__(IMP::npctransport::LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction"""
1821  this = _IMP_npctransport.new_LinearInteraction(krep, attr_range, kattr)
1822  try:
1823  self.this.append(this)
1824  except:
1825  self.this = this
1826 
1827  def show(self, *args):
1828  """
1829  show(LinearInteraction self, _ostream out)
1830  show(LinearInteraction self)
1831  """
1832  return _IMP_npctransport.LinearInteraction_show(self, *args)
1833 
1834  __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1835  __del__ = lambda self: None
1836 LinearInteraction_swigregister = _IMP_npctransport.LinearInteraction_swigregister
1837 LinearInteraction_swigregister(LinearInteraction)
1838 
1839 class _DistancePairScoreForLinearSoftSphere(IMP.PairScore):
1840  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> class"""
1841  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1842  __repr__ = _swig_repr
1843 
1844  def __init__(self, *args):
1845  """
1846  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearSoftSphere
1847  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0) -> _DistancePairScoreForLinearSoftSphere
1848  """
1849  this = _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args)
1850  try:
1851  self.this.append(this)
1852  except:
1853  self.this = this
1854 
1855  def do_get_inputs(self, m, pis):
1856  """do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1857  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1858 
1859 
1860  def get_score_functor(self):
1861  """get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1862  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1863 
1864 
1865  def get_version_info(self):
1866  """get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1867  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1868 
1869 _DistancePairScoreForLinearSoftSphere_swigregister = _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister
1870 _DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1871 
1872 class _DistancePairScoreForLinearInteraction(IMP.PairScore):
1873  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> class"""
1874  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1875  __repr__ = _swig_repr
1876 
1877  def __init__(self, *args):
1878  """
1879  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearInteraction
1880  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0) -> _DistancePairScoreForLinearInteraction
1881  """
1882  this = _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args)
1883  try:
1884  self.this.append(this)
1885  except:
1886  self.this = this
1887 
1888  def do_get_inputs(self, m, pis):
1889  """do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1890  return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1891 
1892 
1893  def get_score_functor(self):
1894  """get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1895  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1896 
1897 
1898  def get_version_info(self):
1899  """get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1900  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1901 
1902 _DistancePairScoreForLinearInteraction_swigregister = _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister
1903 _DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1904 
1905 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1906  """Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class"""
1907  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1908 
1909  def __init__(self, *args):
1910  """
1911  __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k, std::string name) -> FunctorLinearSoftSpherePairScore
1912  __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k) -> FunctorLinearSoftSpherePairScore
1913  """
1914  this = _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args)
1915  try:
1916  self.this.append(this)
1917  except:
1918  self.this = this
1919 
1920  def __str__(self):
1921  """__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1922  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1923 
1924 
1925  def __repr__(self):
1926  """__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1927  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1928 
1929 
1930  @staticmethod
1931  def get_from(o):
1932  return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1933 
1934 FunctorLinearSoftSpherePairScore_swigregister = _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister
1935 FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1936 
1937 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1938  """Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class"""
1939  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1940 
1941  def __init__(self, *args):
1942  """
1943  __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name) -> FunctorLinearInteractionPairScore
1944  __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr) -> FunctorLinearInteractionPairScore
1945  """
1946  this = _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args)
1947  try:
1948  self.this.append(this)
1949  except:
1950  self.this = this
1951 
1952  def __str__(self):
1953  """__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1954  return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1955 
1956 
1957  def __repr__(self):
1958  """__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1959  return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1960 
1961 
1962  @staticmethod
1963  def get_from(o):
1964  return _object_cast_to_FunctorLinearInteractionPairScore(o)
1965 
1966 FunctorLinearInteractionPairScore_swigregister = _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister
1967 FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1968 
1969 class BrownianDynamicsTAMDWithSlabSupport(IMP.atom.BrownianDynamicsTAMD):
1970  """Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class"""
1971  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1972 
1973  def __init__(self, *args):
1974  """
1975  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport
1976  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name) -> BrownianDynamicsTAMDWithSlabSupport
1977  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m) -> BrownianDynamicsTAMDWithSlabSupport
1978  """
1979  this = _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args)
1980  try:
1981  self.this.append(this)
1982  except:
1983  self.this = this
1984 
1985  def __str__(self):
1986  """__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1987  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1988 
1989 
1990  def __repr__(self):
1991  """__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1992  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1993 
1994 
1995  @staticmethod
1996  def get_from(o):
1997  return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1998 
1999  __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
2000  __del__ = lambda self: None
2001 BrownianDynamicsTAMDWithSlabSupport_swigregister = _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister
2002 BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
2003 
2004 class SitesPairScoreParameters(object):
2005  """Proxy of C++ IMP::npctransport::SitesPairScoreParameters class"""
2006  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2007  r = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set)
2008  k = _swig_property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set)
2009  r2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set)
2010  kr = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set)
2011  kr2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set)
2012  cosSigma1_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set)
2013  cosSigma2_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set)
2014  is_orientational = _swig_property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set)
2015 
2016  def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
2017  """
2018  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters
2019  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0) -> SitesPairScoreParameters
2020  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient) -> SitesPairScoreParameters
2021  """
2022  this = _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg)
2023  try:
2024  self.this.append(this)
2025  except:
2026  self.this = this
2027 
2028  def set_range(self, r):
2029  """set_range(SitesPairScoreParameters self, double r)"""
2030  return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
2031 
2032 
2033  def set_force_coefficient(self, k):
2034  """set_force_coefficient(SitesPairScoreParameters self, double k)"""
2035  return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
2036 
2037 
2038  def set_sigma1_max(self, sigma1_max_deg):
2039  """set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
2040  return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
2041 
2042 
2043  def set_sigma2_max(self, sigma2_max_deg):
2044  """set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
2045  return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
2046 
2047 
2048  def update_is_orientational(self):
2049  """update_is_orientational(SitesPairScoreParameters self)"""
2050  return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
2051 
2052 
2053  def show(self, *args):
2054  """
2055  show(SitesPairScoreParameters self, _ostream out)
2056  show(SitesPairScoreParameters self)
2057  """
2058  return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
2059 
2060 
2061  def __str__(self):
2062  """__str__(SitesPairScoreParameters self) -> std::string"""
2063  return _IMP_npctransport.SitesPairScoreParameters___str__(self)
2064 
2065 
2066  def __repr__(self):
2067  """__repr__(SitesPairScoreParameters self) -> std::string"""
2068  return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
2069 
2070  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
2071  __del__ = lambda self: None
2072 SitesPairScoreParameters_swigregister = _IMP_npctransport.SitesPairScoreParameters_swigregister
2073 SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
2074 
2075 class SitesGeometry(IMP.core.XYZRGeometry):
2076  """Proxy of C++ IMP::npctransport::SitesGeometry class"""
2077  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2078 
2079  def __init__(self, p, sites):
2080  """__init__(IMP::npctransport::SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
2081  this = _IMP_npctransport.new_SitesGeometry(p, sites)
2082  try:
2083  self.this.append(this)
2084  except:
2085  self.this = this
2086 
2087  def __str__(self):
2088  """__str__(SitesGeometry self) -> std::string"""
2089  return _IMP_npctransport.SitesGeometry___str__(self)
2090 
2091 
2092  def __repr__(self):
2093  """__repr__(SitesGeometry self) -> std::string"""
2094  return _IMP_npctransport.SitesGeometry___repr__(self)
2095 
2096 
2097  @staticmethod
2098  def get_from(o):
2099  return _object_cast_to_SitesGeometry(o)
2100 
2101 SitesGeometry_swigregister = _IMP_npctransport.SitesGeometry_swigregister
2102 SitesGeometry_swigregister(SitesGeometry)
2103 
2104 class TypedSitesGeometry(IMP.display.SingletonsGeometry):
2105  """Proxy of C++ IMP::npctransport::TypedSitesGeometry class"""
2106  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2107 
2108  def __init__(self, sc):
2109  """__init__(IMP::npctransport::TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
2110  this = _IMP_npctransport.new_TypedSitesGeometry(sc)
2111  try:
2112  self.this.append(this)
2113  except:
2114  self.this = this
2115 
2116  def set_sites(self, t, s):
2117  """set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
2118  return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
2119 
2120 
2121  def get_version_info(self):
2122  """get_version_info(TypedSitesGeometry self) -> VersionInfo"""
2123  return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
2124 
2125 
2126  def __str__(self):
2127  """__str__(TypedSitesGeometry self) -> std::string"""
2128  return _IMP_npctransport.TypedSitesGeometry___str__(self)
2129 
2130 
2131  def __repr__(self):
2132  """__repr__(TypedSitesGeometry self) -> std::string"""
2133  return _IMP_npctransport.TypedSitesGeometry___repr__(self)
2134 
2135 
2136  @staticmethod
2137  def get_from(o):
2138  return _object_cast_to_TypedSitesGeometry(o)
2139 
2140 TypedSitesGeometry_swigregister = _IMP_npctransport.TypedSitesGeometry_swigregister
2141 TypedSitesGeometry_swigregister(TypedSitesGeometry)
2142 
2143 class SitesPairScore(LinearInteractionPairScore):
2144  """Proxy of C++ IMP::npctransport::SitesPairScore class"""
2145  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2146 
2147  def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
2148  """__init__(IMP::npctransport::SitesPairScore self, double range, double k, double sigma0_deg, double sigma1_deg, double range_nonspec_attraction, double k_nonspec_attraction, double k_nonspec_repulsion, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1) -> SitesPairScore"""
2149  this = _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1)
2150  try:
2151  self.this.append(this)
2152  except:
2153  self.this = this
2154 
2155  def get_sites_range(self):
2156  """get_sites_range(SitesPairScore self) -> double"""
2157  return _IMP_npctransport.SitesPairScore_get_sites_range(self)
2158 
2159 
2160  def get_sites_k(self):
2161  """get_sites_k(SitesPairScore self) -> double"""
2162  return _IMP_npctransport.SitesPairScore_get_sites_k(self)
2163 
2164 
2165  def get_parameters(self):
2166  """get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
2167  return _IMP_npctransport.SitesPairScore_get_parameters(self)
2168 
2169 
2170  def set_sites(self, sites0, sites1):
2171  """set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
2172  return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
2173 
2174 
2175  def set_sites0(self, sites0):
2176  """set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
2177  return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
2178 
2179 
2180  def set_sites1(self, sites1):
2181  """set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
2182  return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
2183 
2184 
2185  def __str__(self):
2186  """__str__(SitesPairScore self) -> std::string"""
2187  return _IMP_npctransport.SitesPairScore___str__(self)
2188 
2189 
2190  def __repr__(self):
2191  """__repr__(SitesPairScore self) -> std::string"""
2192  return _IMP_npctransport.SitesPairScore___repr__(self)
2193 
2194 
2195  @staticmethod
2196  def get_from(o):
2197  return _object_cast_to_SitesPairScore(o)
2198 
2199 SitesPairScore_swigregister = _IMP_npctransport.SitesPairScore_swigregister
2200 SitesPairScore_swigregister(SitesPairScore)
2201 
2202 class FGChain(IMP.Object):
2203  """Proxy of C++ IMP::npctransport::FGChain class"""
2204  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2205 
2206  def __init__(self, *args):
2207  """
2208  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name) -> FGChain
2209  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0) -> FGChain
2210  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0) -> FGChain
2211  __init__(IMP::npctransport::FGChain self, Particle root) -> FGChain
2212  """
2213  this = _IMP_npctransport.new_FGChain(*args)
2214  try:
2215  self.this.append(this)
2216  except:
2217  self.this = this
2218 
2219  def get_root(self):
2220  """get_root(FGChain self) -> Hierarchy"""
2221  return _IMP_npctransport.FGChain_get_root(self)
2222 
2223 
2224  def get_beads(self):
2225  """get_beads(FGChain self) -> IMP::ParticlesTemp"""
2226  return _IMP_npctransport.FGChain_get_beads(self)
2227 
2228 
2229  def get_bead(self, i):
2230  """get_bead(FGChain self, unsigned int i) -> Particle"""
2231  return _IMP_npctransport.FGChain_get_bead(self, i)
2232 
2233 
2234  def get_bead_index(self, i):
2235  """get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
2236  return _IMP_npctransport.FGChain_get_bead_index(self, i)
2237 
2238 
2239  def get_number_of_beads(self):
2240  """get_number_of_beads(FGChain self) -> unsigned int"""
2241  return _IMP_npctransport.FGChain_get_number_of_beads(self)
2242 
2243 
2244  def get_chain_restraints(self, scoring_manager):
2245  """get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
2246  return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
2247 
2248 
2249  def set_rest_length_factor(self, rlf):
2250  """set_rest_length_factor(FGChain self, double rlf)"""
2251  return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
2252 
2253 
2254  def set_backbone_k(self, k):
2255  """set_backbone_k(FGChain self, double k)"""
2256  return _IMP_npctransport.FGChain_set_backbone_k(self, k)
2257 
2258 
2259  def get_rest_length_factor(self):
2260  """get_rest_length_factor(FGChain self) -> double"""
2261  return _IMP_npctransport.FGChain_get_rest_length_factor(self)
2262 
2263 
2264  def get_backbone_k(self):
2265  """get_backbone_k(FGChain self) -> double"""
2266  return _IMP_npctransport.FGChain_get_backbone_k(self)
2267 
2268 
2269  def get_version_info(self):
2270  """get_version_info(FGChain self) -> VersionInfo"""
2271  return _IMP_npctransport.FGChain_get_version_info(self)
2272 
2273 
2274  def __str__(self):
2275  """__str__(FGChain self) -> std::string"""
2276  return _IMP_npctransport.FGChain___str__(self)
2277 
2278 
2279  def __repr__(self):
2280  """__repr__(FGChain self) -> std::string"""
2281  return _IMP_npctransport.FGChain___repr__(self)
2282 
2283 
2284  @staticmethod
2285  def get_from(o):
2286  return _object_cast_to_FGChain(o)
2287 
2288 FGChain_swigregister = _IMP_npctransport.FGChain_swigregister
2289 FGChain_swigregister(FGChain)
2290 
2291 
2292 def create_fg_chain(sd, parent, fg_data, c):
2293  """create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
2294  return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
2295 
2296 def get_fg_chain(*args):
2297  """
2298  get_fg_chain(Hierarchy root) -> FGChain
2299  get_fg_chain(Particle p_root) -> FGChain
2300  """
2301  return _IMP_npctransport.get_fg_chain(*args)
2302 class Scoring(IMP.Object):
2303  """Proxy of C++ IMP::npctransport::Scoring class"""
2304  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2305 
2306  def __init__(self, owner_sd, data):
2307  """__init__(IMP::npctransport::Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
2308  this = _IMP_npctransport.new_Scoring(owner_sd, data)
2309  try:
2310  self.this.append(this)
2311  except:
2312  self.this = this
2313 
2314  def get_scoring_function(self, force_update=False):
2315  """
2316  get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction
2317  get_scoring_function(Scoring self) -> ScoringFunction
2318  """
2319  return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
2320 
2321 
2322  def get_scoring_function_restraints(self, force_update=False):
2323  """
2324  get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints
2325  get_scoring_function_restraints(Scoring self) -> IMP::Restraints
2326  """
2327  return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
2328 
2329 
2330  def get_custom_scoring_function(self, *args):
2331  """
2332  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
2333  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
2334  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
2335  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
2336  """
2337  return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
2338 
2339 
2340  def get_close_beads_container(self, update=False):
2341  """
2342  get_close_beads_container(Scoring self, bool update=False) -> PairContainer
2343  get_close_beads_container(Scoring self) -> PairContainer
2344  """
2345  return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
2346 
2347 
2348  def get_predicates_pair_restraint(self, update=False):
2349  """
2350  get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint
2351  get_predicates_pair_restraint(Scoring self) -> PredicatePairsRestraint
2352  """
2353  return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
2354 
2355 
2356  def get_bounding_volume_restraint(self, update=False):
2357  """
2358  get_bounding_volume_restraint(Scoring self, bool update=False) -> Restraint
2359  get_bounding_volume_restraint(Scoring self) -> Restraint
2360  """
2361  return _IMP_npctransport.Scoring_get_bounding_volume_restraint(self, update)
2362 
2363 
2364  def get_slab_restraint(self, update=False):
2365  """
2366  get_slab_restraint(Scoring self, bool update=False) -> Restraint
2367  get_slab_restraint(Scoring self) -> Restraint
2368  """
2369  return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
2370 
2371 
2372  def add_interaction(self, idata):
2373  """add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
2374  return _IMP_npctransport.Scoring_add_interaction(self, idata)
2375 
2376 
2377  def create_close_beads_container(self, *args):
2378  """
2379  create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
2380  create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
2381  """
2382  return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
2383 
2384 
2385  def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
2386  """
2387  create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint
2388  create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs) -> PredicatePairsRestraint
2389  """
2390  return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
2391 
2392 
2393  def create_bounding_volume_restraint(self, beads):
2394  """create_bounding_volume_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
2395  return _IMP_npctransport.Scoring_create_bounding_volume_restraint(self, beads)
2396 
2397 
2398  def create_slab_restraint(self, beads):
2399  """create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
2400  return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
2401 
2402 
2403  def get_model(self):
2404  """get_model(Scoring self) -> Model"""
2405  return _IMP_npctransport.Scoring_get_model(self)
2406 
2407 
2408  def get_sd(self):
2409  """get_sd(Scoring self) -> SimulationData"""
2410  return _IMP_npctransport.Scoring_get_sd(self)
2411 
2412 
2413  def get_has_bounding_box(self):
2414  """get_has_bounding_box(Scoring self) -> bool"""
2415  return _IMP_npctransport.Scoring_get_has_bounding_box(self)
2416 
2417 
2418  def get_has_bounding_sphere(self):
2419  """get_has_bounding_sphere(Scoring self) -> bool"""
2420  return _IMP_npctransport.Scoring_get_has_bounding_sphere(self)
2421 
2422 
2423  def get_has_bounding_volume(self):
2424  """get_has_bounding_volume(Scoring self) -> bool"""
2425  return _IMP_npctransport.Scoring_get_has_bounding_volume(self)
2426 
2427 
2428  def get_default_backbone_k(self):
2429  """get_default_backbone_k(Scoring self) -> double"""
2430  return _IMP_npctransport.Scoring_get_default_backbone_k(self)
2431 
2432 
2433  def get_is_backbone_harmonic(self):
2434  """get_is_backbone_harmonic(Scoring self) -> bool"""
2435  return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
2436 
2437 
2438  def get_excluded_volume_k(self):
2439  """get_excluded_volume_k(Scoring self) -> double"""
2440  return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
2441 
2442 
2443  def get_interaction_k(self):
2444  """get_interaction_k(Scoring self) -> double"""
2445  return _IMP_npctransport.Scoring_get_interaction_k(self)
2446 
2447 
2448  def get_predicate_pair_score(self, *args):
2449  """
2450  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
2451  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
2452  """
2453  return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
2454 
2455 
2456  def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
2457  """
2458  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double
2459  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True) -> double
2460  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2) -> double
2461  """
2462  return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
2463 
2464 
2465  def get_ordered_type_pair_predicate(self):
2466  """get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
2467  return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
2468 
2469 
2470  def add_chain_restraints(self, chain):
2471  """add_chain_restraints(Scoring self, FGChain chain)"""
2472  return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
2473 
2474 
2475  def get_chain_restraints_on(self, beads):
2476  """get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
2477  return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
2478 
2479 
2480  def get_all_chain_restraints(self):
2481  """get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
2482  return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
2483 
2484 
2485  def remove_particle_type(self, pt):
2486  """remove_particle_type(Scoring self, ParticleType pt)"""
2487  return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
2488 
2489 
2490  def add_z_bias_restraint(self, *args):
2491  """
2492  add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
2493  add_z_bias_restraint(Scoring self, Particle p, double k)
2494  """
2495  return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
2496 
2497 
2498  def get_z_bias_restraints(self):
2499  """get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
2500  return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
2501 
2502 
2503  def create_z_bias_restraint(self, ps, k):
2504  """create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
2505  return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
2506 
2507 
2508  def add_custom_restraint(self, r):
2509  """add_custom_restraint(Scoring self, Restraint r)"""
2510  return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
2511 
2512 
2513  def add_custom_restraints(self, R):
2514  """add_custom_restraints(Scoring self, IMP::Restraints R)"""
2515  return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
2516 
2517 
2518  def clear_custom_restraints(self):
2519  """clear_custom_restraints(Scoring self)"""
2520  return _IMP_npctransport.Scoring_clear_custom_restraints(self)
2521 
2522 
2523  def get_custom_restraints(self):
2524  """get_custom_restraints(Scoring self) -> IMP::Restraints"""
2525  return _IMP_npctransport.Scoring_get_custom_restraints(self)
2526 
2527 
2528  def add_restrained_anchor_bead(self, p):
2529  """add_restrained_anchor_bead(Scoring self, Particle p)"""
2530  return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
2531 
2532 
2533  def get_pore_radius_restraint(self):
2534  """get_pore_radius_restraint(Scoring self) -> Restraint"""
2535  return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
2536 
2537 
2538  def get_range(self):
2539  """get_range(Scoring self) -> double"""
2540  return _IMP_npctransport.Scoring_get_range(self)
2541 
2542 
2543  def set_interaction_range_factor(self, type, value):
2544  """set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
2545  return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
2546 
2547 
2548  def set_interaction_k_factor(self, type, value):
2549  """set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
2550  return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
2551 
2552 
2553  def get_version_info(self):
2554  """get_version_info(Scoring self) -> VersionInfo"""
2555  return _IMP_npctransport.Scoring_get_version_info(self)
2556 
2557 
2558  def __str__(self):
2559  """__str__(Scoring self) -> std::string"""
2560  return _IMP_npctransport.Scoring___str__(self)
2561 
2562 
2563  def __repr__(self):
2564  """__repr__(Scoring self) -> std::string"""
2565  return _IMP_npctransport.Scoring___repr__(self)
2566 
2567 
2568  @staticmethod
2569  def get_from(o):
2570  return _object_cast_to_Scoring(o)
2571 
2572 Scoring_swigregister = _IMP_npctransport.Scoring_swigregister
2573 Scoring_swigregister(Scoring)
2574 
2575 class timer(object):
2576  """Proxy of C++ boost::timer class"""
2577  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2578  __repr__ = _swig_repr
2579 
2580  def __init__(self):
2581  """__init__(boost::timer self) -> timer"""
2582  this = _IMP_npctransport.new_timer()
2583  try:
2584  self.this.append(this)
2585  except:
2586  self.this = this
2587  __swig_destroy__ = _IMP_npctransport.delete_timer
2588  __del__ = lambda self: None
2589 timer_swigregister = _IMP_npctransport.timer_swigregister
2590 timer_swigregister(timer)
2591 
2592 class Statistics(IMP.Object):
2593  """Proxy of C++ IMP::npctransport::Statistics class"""
2594  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2595 
2596  def remove_particle_type(self, pt):
2597  """remove_particle_type(Statistics self, ParticleType pt)"""
2598  return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2599 
2600 
2601  def __init__(self, sd, statistics_interval_frames, output_file_name):
2602  """__init__(IMP::npctransport::Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2603  this = _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name)
2604  try:
2605  self.this.append(this)
2606  except:
2607  self.this = this
2608 
2609  def add_fg_chain_stats(self, fg_chain):
2610  """add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2611  return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2612 
2613 
2614  def add_floater_stats(self, p):
2615  """add_floater_stats(Statistics self, Particle p)"""
2616  return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2617 
2618 
2619  def add_interaction_stats(self, type0, type1):
2620  """add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2621  return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2622 
2623 
2624  def add_optimizer_states(self, o=None):
2625  """
2626  add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates
2627  add_optimizer_states(Statistics self) -> IMP::OptimizerStates
2628  """
2629  return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2630 
2631 
2632  def update_particle_type_zr_distribution_map(self, p):
2633  """update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2634  return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2635 
2636 
2637  def update_particle_type_xyz_distribution_map(self, p):
2638  """update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2639  return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2640 
2641 
2642  def update(self, timer, nf_new=1):
2643  """
2644  update(Statistics self, timer timer, unsigned int nf_new=1)
2645  update(Statistics self, timer timer)
2646  """
2647  return _IMP_npctransport.Statistics_update(self, timer, nf_new)
2648 
2649 
2650  def reset_statistics_optimizer_states(self):
2651  """reset_statistics_optimizer_states(Statistics self)"""
2652  return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2653 
2654 
2655  def set_interrupted(self, tf):
2656  """set_interrupted(Statistics self, bool tf)"""
2657  return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2658 
2659 
2660  def get_model(self):
2661  """get_model(Statistics self) -> Model"""
2662  return _IMP_npctransport.Statistics_get_model(self)
2663 
2664 
2665  def get_sd(self):
2666  """get_sd(Statistics self) -> SimulationData"""
2667  return _IMP_npctransport.Statistics_get_sd(self)
2668 
2669 
2670  def get_is_activated(self):
2671  """get_is_activated(Statistics self) -> bool"""
2672  return _IMP_npctransport.Statistics_get_is_activated(self)
2673 
2674 
2675  def get_output_file_name(self):
2676  """get_output_file_name(Statistics self) -> std::string"""
2677  return _IMP_npctransport.Statistics_get_output_file_name(self)
2678 
2679 
2680  def get_version_info(self):
2681  """get_version_info(Statistics self) -> VersionInfo"""
2682  return _IMP_npctransport.Statistics_get_version_info(self)
2683 
2684 
2685  def __str__(self):
2686  """__str__(Statistics self) -> std::string"""
2687  return _IMP_npctransport.Statistics___str__(self)
2688 
2689 
2690  def __repr__(self):
2691  """__repr__(Statistics self) -> std::string"""
2692  return _IMP_npctransport.Statistics___repr__(self)
2693 
2694 
2695  @staticmethod
2696  def get_from(o):
2697  return _object_cast_to_Statistics(o)
2698 
2699 Statistics_swigregister = _IMP_npctransport.Statistics_swigregister
2700 Statistics_swigregister(Statistics)
2701 
2702 
2703 def create_boost_timer():
2704  """create_boost_timer() -> timer"""
2705  return _IMP_npctransport.create_boost_timer()
2706 
2707 _IMP_npctransport.IMPNPCTRANSPORT_VERSION_swigconstant(_IMP_npctransport)
2708 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2709 class SimulationData(IMP.Object):
2710  """Proxy of C++ IMP::npctransport::SimulationData class"""
2711  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2712 
2713  def get_output_npctransport_version(self):
2714  """get_output_npctransport_version(SimulationData self) -> double"""
2715  return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2716 
2717 
2718  def get_range(self):
2719  """get_range(SimulationData self) -> double"""
2720  return _IMP_npctransport.SimulationData_get_range(self)
2721 
2722 
2723  def get_output_statistics_interval_frames(self):
2724  """get_output_statistics_interval_frames(SimulationData self) -> int"""
2725  return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2726 
2727 
2728  def get_is_exclude_floaters_from_slab_initially(self):
2729  """get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2730  return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2731 
2732 
2733  def get_are_floaters_on_one_slab_side(self):
2734  """get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2735  return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2736 
2737 
2738  def get_is_xyz_hist_stats(self):
2739  """get_is_xyz_hist_stats(SimulationData self) -> bool"""
2740  return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2741 
2742 
2743  def get_angular_d_factor(self):
2744  """get_angular_d_factor(SimulationData self) -> double"""
2745  return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2746 
2747 
2748  def __init__(self, *args):
2749  """
2750  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name, std::string new_output_file) -> SimulationData
2751  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name) -> SimulationData
2752  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick) -> SimulationData
2753  """
2754  this = _IMP_npctransport.new_SimulationData(*args)
2755  try:
2756  self.this.append(this)
2757  except:
2758  self.this = this
2759 
2760  def get_model(self):
2761  """get_model(SimulationData self) -> Model"""
2762  return _IMP_npctransport.SimulationData_get_model(self)
2763 
2764 
2765  def get_scoring(self):
2766  """get_scoring(SimulationData self) -> Scoring"""
2767  return _IMP_npctransport.SimulationData_get_scoring(self)
2768 
2769 
2770  def get_statistics(self):
2771  """get_statistics(SimulationData self) -> Statistics"""
2772  return _IMP_npctransport.SimulationData_get_statistics(self)
2773 
2774 
2775  def get_bd(self, recreate=False):
2776  """
2777  get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics
2778  get_bd(SimulationData self) -> BrownianDynamics
2779  """
2780  return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2781 
2782 
2783  def activate_statistics(self):
2784  """activate_statistics(SimulationData self)"""
2785  return _IMP_npctransport.SimulationData_activate_statistics(self)
2786 
2787 
2788  def get_statistics_fraction(self):
2789  """get_statistics_fraction(SimulationData self) -> double"""
2790  return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2791 
2792 
2793  def get_is_fg_bead(self, *args):
2794  """
2795  get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2796  get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2797  """
2798  return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2799 
2800 
2801  def get_is_fg_chain(self, *args):
2802  """
2803  get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2804  get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2805  """
2806  return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2807 
2808 
2809  def get_fg_bead_types(self):
2810  """get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2811  return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2812 
2813 
2814  def get_fg_chain_types(self):
2815  """get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2816  return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2817 
2818 
2819  def get_floater_types(self):
2820  """get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2821  return _IMP_npctransport.SimulationData_get_floater_types(self)
2822 
2823 
2824  def get_obstacle_types(self):
2825  """get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2826  return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2827 
2828 
2829  def get_fg_chain_roots(self):
2830  """get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2831  return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2832 
2833 
2834  def get_fg_chains(self):
2835  """get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2836  return _IMP_npctransport.SimulationData_get_fg_chains(self)
2837 
2838 
2839  def get_obstacle_particles(self):
2840  """get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2841  return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2842 
2843 
2844  def get_beads(self):
2845  """get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2846  return _IMP_npctransport.SimulationData_get_beads(self)
2847 
2848 
2849  def get_optimizable_beads(self):
2850  """get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2851  return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2852 
2853 
2854  def get_non_optimizable_beads(self):
2855  """get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2856  return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2857 
2858 
2859  def get_is_backbone_harmonic(self):
2860  """get_is_backbone_harmonic(SimulationData self) -> bool"""
2861  return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2862 
2863 
2864  def get_backbone_tau_ns(self):
2865  """get_backbone_tau_ns(SimulationData self) -> double"""
2866  return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2867 
2868 
2869  def get_temperature_k(self):
2870  """get_temperature_k(SimulationData self) -> double"""
2871  return _IMP_npctransport.SimulationData_get_temperature_k(self)
2872 
2873 
2874  def get_initial_simulation_time_ns(self):
2875  """get_initial_simulation_time_ns(SimulationData self) -> double"""
2876  return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2877 
2878 
2879  def get_site_centers(self, t0):
2880  """get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2881  return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2882 
2883 
2884  def get_sites(self, t0):
2885  """get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2886  return _IMP_npctransport.SimulationData_get_sites(self, t0)
2887 
2888 
2889  def set_sites(self, *args):
2890  """
2891  set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2892  set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2893  """
2894  return _IMP_npctransport.SimulationData_set_sites(self, *args)
2895 
2896 
2897  def get_site_display_radius(self, arg2):
2898  """get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2899  return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2900 
2901 
2902  def get_maximum_number_of_minutes(self):
2903  """get_maximum_number_of_minutes(SimulationData self) -> double"""
2904  return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2905 
2906 
2907  def remove_particle_type(self, pt):
2908  """remove_particle_type(SimulationData self, ParticleType pt)"""
2909  return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2910 
2911 
2912  def remove_fgs_with_prefix(self, s_fg_type):
2913  """remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2914  return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2915 
2916 
2917  def get_bounding_box(self):
2918  """get_bounding_box(SimulationData self) -> BoundingBox3D"""
2919  return _IMP_npctransport.SimulationData_get_bounding_box(self)
2920 
2921 
2922  def get_bounding_sphere(self):
2923  """get_bounding_sphere(SimulationData self) -> Sphere3D"""
2924  return _IMP_npctransport.SimulationData_get_bounding_sphere(self)
2925 
2926 
2927  def get_bounding_box_size(self):
2928  """get_bounding_box_size(SimulationData self) -> double"""
2929  return _IMP_npctransport.SimulationData_get_bounding_box_size(self)
2930 
2931 
2932  def set_bounding_box_size(self, box_size):
2933  """set_bounding_box_size(SimulationData self, double box_size)"""
2934  return _IMP_npctransport.SimulationData_set_bounding_box_size(self, box_size)
2935 
2936 
2937  def get_bounding_sphere_radius(self):
2938  """get_bounding_sphere_radius(SimulationData self) -> double"""
2939  return _IMP_npctransport.SimulationData_get_bounding_sphere_radius(self)
2940 
2941 
2942  def set_bounding_sphere_radius(self, sphere_radius):
2943  """set_bounding_sphere_radius(SimulationData self, double sphere_radius)"""
2944  return _IMP_npctransport.SimulationData_set_bounding_sphere_radius(self, sphere_radius)
2945 
2946 
2947  def get_bounding_volume(self):
2948  """get_bounding_volume(SimulationData self) -> double"""
2949  return _IMP_npctransport.SimulationData_get_bounding_volume(self)
2950 
2951 
2952  def set_bounding_volume(self, volume_A3):
2953  """set_bounding_volume(SimulationData self, double volume_A3)"""
2954  return _IMP_npctransport.SimulationData_set_bounding_volume(self, volume_A3)
2955 
2956 
2957  def get_has_slab(self):
2958  """get_has_slab(SimulationData self) -> bool"""
2959  return _IMP_npctransport.SimulationData_get_has_slab(self)
2960 
2961 
2962  def get_is_slab_with_cylindrical_pore(self):
2963  """get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2964  return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2965 
2966 
2967  def get_is_slab_with_toroidal_pore(self):
2968  """get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2969  return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2970 
2971 
2972  def get_slab_particle(self):
2973  """get_slab_particle(SimulationData self) -> Particle"""
2974  return _IMP_npctransport.SimulationData_get_slab_particle(self)
2975 
2976 
2977  def get_cylinder(self):
2978  """get_cylinder(SimulationData self) -> Cylinder3D"""
2979  return _IMP_npctransport.SimulationData_get_cylinder(self)
2980 
2981 
2982  def get_has_bounding_box(self):
2983  """get_has_bounding_box(SimulationData self) -> bool"""
2984  return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2985 
2986 
2987  def get_has_bounding_sphere(self):
2988  """get_has_bounding_sphere(SimulationData self) -> bool"""
2989  return _IMP_npctransport.SimulationData_get_has_bounding_sphere(self)
2990 
2991 
2992  def get_has_bounding_volume(self):
2993  """get_has_bounding_volume(SimulationData self) -> bool"""
2994  return _IMP_npctransport.SimulationData_get_has_bounding_volume(self)
2995 
2996 
2997  def initialize_positions_from_rmf(self, fh, frame_number=-1):
2998  """
2999  initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)
3000  initialize_positions_from_rmf(SimulationData self, FileConstHandle fh)
3001  """
3002  return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
3003 
3004 
3005  def link_rmf_file_handle(self, fh, is_restraints=True):
3006  """
3007  link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)
3008  link_rmf_file_handle(SimulationData self, FileHandle fh)
3009  """
3010  return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
3011 
3012 
3013  def get_rmf_sos_writer(self):
3014  """get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
3015  return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
3016 
3017 
3018  def reset_rmf(self):
3019  """reset_rmf(SimulationData self)"""
3020  return _IMP_npctransport.SimulationData_reset_rmf(self)
3021 
3022 
3023  def switch_suspend_rmf(self, suspend):
3024  """switch_suspend_rmf(SimulationData self, bool suspend)"""
3025  return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
3026 
3027 
3028  def write_geometry(self, out):
3029  """write_geometry(SimulationData self, std::string out)"""
3030  return _IMP_npctransport.SimulationData_write_geometry(self, out)
3031 
3032 
3033  def dump_geometry(self):
3034  """dump_geometry(SimulationData self)"""
3035  return _IMP_npctransport.SimulationData_dump_geometry(self)
3036 
3037 
3038  def get_root_of_type(self, type):
3039  """get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
3040  return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
3041 
3042 
3043  def get_number_of_frames(self):
3044  """get_number_of_frames(SimulationData self) -> unsigned int"""
3045  return _IMP_npctransport.SimulationData_get_number_of_frames(self)
3046 
3047 
3048  def get_number_of_trials(self):
3049  """get_number_of_trials(SimulationData self) -> unsigned int"""
3050  return _IMP_npctransport.SimulationData_get_number_of_trials(self)
3051 
3052 
3053  def get_root(self):
3054  """get_root(SimulationData self) -> Hierarchy"""
3055  return _IMP_npctransport.SimulationData_get_root(self)
3056 
3057 
3058  def get_slab_thickness(self):
3059  """get_slab_thickness(SimulationData self) -> double"""
3060  return _IMP_npctransport.SimulationData_get_slab_thickness(self)
3061 
3062 
3063  def get_tunnel_radius(self):
3064  """get_tunnel_radius(SimulationData self) -> double"""
3065  return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
3066 
3067 
3068  def get_pore_radius(self):
3069  """get_pore_radius(SimulationData self) -> double"""
3070  return _IMP_npctransport.SimulationData_get_pore_radius(self)
3071 
3072 
3073  def get_tunnel_radius_k(self):
3074  """get_tunnel_radius_k(SimulationData self) -> double"""
3075  return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
3076 
3077 
3078  def get_pore_radius_k(self):
3079  """get_pore_radius_k(SimulationData self) -> double"""
3080  return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
3081 
3082 
3083  def get_is_pore_radius_dynamic(self):
3084  """get_is_pore_radius_dynamic(SimulationData self) -> bool"""
3085  return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
3086 
3087 
3088  def get_pore_anchored_beads_k(self):
3089  """get_pore_anchored_beads_k(SimulationData self) -> double"""
3090  return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
3091 
3092 
3093  def get_static_geometry(self):
3094  """get_static_geometry(SimulationData self) -> Geometry"""
3095  return _IMP_npctransport.SimulationData_get_static_geometry(self)
3096 
3097 
3098  def get_rmf_dump_interval_frames(self):
3099  """get_rmf_dump_interval_frames(SimulationData self) -> int"""
3100  return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
3101 
3102 
3103  def get_rmf_file_name(self):
3104  """get_rmf_file_name(SimulationData self) -> std::string"""
3105  return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
3106 
3107 
3108  def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
3109  """
3110  set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)
3111  set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True)
3112  set_rmf_file(SimulationData self, std::string const & new_name)
3113  """
3114  return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
3115 
3116 
3117  def get_version_info(self):
3118  """get_version_info(SimulationData self) -> VersionInfo"""
3119  return _IMP_npctransport.SimulationData_get_version_info(self)
3120 
3121 
3122  def __str__(self):
3123  """__str__(SimulationData self) -> std::string"""
3124  return _IMP_npctransport.SimulationData___str__(self)
3125 
3126 
3127  def __repr__(self):
3128  """__repr__(SimulationData self) -> std::string"""
3129  return _IMP_npctransport.SimulationData___repr__(self)
3130 
3131 
3132  @staticmethod
3133  def get_from(o):
3134  return _object_cast_to_SimulationData(o)
3135 
3136 SimulationData_swigregister = _IMP_npctransport.SimulationData_swigregister
3137 SimulationData_swigregister(SimulationData)
3138 
3139 
3140 def get_simulation_data_key():
3141  """get_simulation_data_key() -> IMP::WeakObjectKey"""
3142  return _IMP_npctransport.get_simulation_data_key()
3143 
3144 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
3145  """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)"""
3146  return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
3147 class ParticleFactory(IMP.Object):
3148  """Proxy of C++ IMP::npctransport::ParticleFactory class"""
3149  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3150  sd_ = _swig_property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set)
3151  radius_ = _swig_property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set)
3152  D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set)
3153  angular_D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set)
3154  color_ = _swig_property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set)
3155  type_ = _swig_property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set)
3156 
3157  def __init__(self, *args):
3158  """
3159  __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name) -> ParticleFactory
3160  __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type) -> ParticleFactory
3161  """
3162  this = _IMP_npctransport.new_ParticleFactory(*args)
3163  try:
3164  self.this.append(this)
3165  except:
3166  self.this = this
3167 
3168  def create(self, *args):
3169  """
3170  create(ParticleFactory self, std::string name) -> Particle
3171  create(ParticleFactory self) -> Particle
3172  """
3173  return _IMP_npctransport.ParticleFactory_create(self, *args)
3174 
3175 
3176  def get_model(self):
3177  """get_model(ParticleFactory self) -> Model"""
3178  return _IMP_npctransport.ParticleFactory_get_model(self)
3179 
3180 
3181  def get_simulation_data(self):
3182  """get_simulation_data(ParticleFactory self) -> SimulationData"""
3183  return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
3184 
3185 
3186  def get_radius(self):
3187  """get_radius(ParticleFactory self) -> double"""
3188  return _IMP_npctransport.ParticleFactory_get_radius(self)
3189 
3190 
3191  def get_version_info(self):
3192  """get_version_info(ParticleFactory self) -> VersionInfo"""
3193  return _IMP_npctransport.ParticleFactory_get_version_info(self)
3194 
3195 
3196  def __str__(self):
3197  """__str__(ParticleFactory self) -> std::string"""
3198  return _IMP_npctransport.ParticleFactory___str__(self)
3199 
3200 
3201  def __repr__(self):
3202  """__repr__(ParticleFactory self) -> std::string"""
3203  return _IMP_npctransport.ParticleFactory___repr__(self)
3204 
3205 
3206  @staticmethod
3207  def get_from(o):
3208  return _object_cast_to_ParticleFactory(o)
3209 
3210 ParticleFactory_swigregister = _IMP_npctransport.ParticleFactory_swigregister
3211 ParticleFactory_swigregister(ParticleFactory)
3212 
3213 class HierarchyWithSitesLoadLink(IMP.rmf.HierarchyLoadLink):
3214  """Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class"""
3215  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3216 
3217  def __init__(self, fh):
3218  """__init__(IMP::npctransport::HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
3219  this = _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh)
3220  try:
3221  self.this.append(this)
3222  except:
3223  self.this = this
3224 
3225  def get_name():
3226  """get_name() -> char const *"""
3227  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
3228 
3229  get_name = staticmethod(get_name)
3230 
3231  def __str__(self):
3232  """__str__(HierarchyWithSitesLoadLink self) -> std::string"""
3233  return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
3234 
3235 
3236  def __repr__(self):
3237  """__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
3238  return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
3239 
3240 
3241  @staticmethod
3242  def get_from(o):
3243  return _object_cast_to_HierarchyWithSitesLoadLink(o)
3244 
3245  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
3246  __del__ = lambda self: None
3247 HierarchyWithSitesLoadLink_swigregister = _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister
3248 HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
3249 
3250 def HierarchyWithSitesLoadLink_get_name():
3251  """HierarchyWithSitesLoadLink_get_name() -> char const *"""
3252  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
3253 
3254 class HierarchyWithSitesSaveLink(IMP.rmf.HierarchySaveLink):
3255  """Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class"""
3256  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3257 
3258  def __init__(self, fh):
3259  """__init__(IMP::npctransport::HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
3260  this = _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh)
3261  try:
3262  self.this.append(this)
3263  except:
3264  self.this = this
3265 
3266  def get_name():
3267  """get_name() -> char const *"""
3268  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
3269 
3270  get_name = staticmethod(get_name)
3271 
3272  def __str__(self):
3273  """__str__(HierarchyWithSitesSaveLink self) -> std::string"""
3274  return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
3275 
3276 
3277  def __repr__(self):
3278  """__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
3279  return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
3280 
3281 
3282  @staticmethod
3283  def get_from(o):
3284  return _object_cast_to_HierarchyWithSitesSaveLink(o)
3285 
3286  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
3287  __del__ = lambda self: None
3288 HierarchyWithSitesSaveLink_swigregister = _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister
3289 HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
3290 
3291 def HierarchyWithSitesSaveLink_get_name():
3292  """HierarchyWithSitesSaveLink_get_name() -> char const *"""
3293  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
3294 
3295 
3296 def add_test_sites(*args):
3297  """
3298  add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
3299  add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
3300  """
3301  return _IMP_npctransport.add_test_sites(*args)
3302 
3303 def add_hierarchies_with_sites(*args):
3304  """
3305  add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
3306  add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
3307  """
3308  return _IMP_npctransport.add_hierarchies_with_sites(*args)
3309 
3310 def add_hierarchy_with_sites(fh, hs):
3311  """add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
3312  return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
3313 
3314 def create_hierarchies_with_sites(fh, m):
3315  """create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
3316  return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
3317 
3318 def link_hierarchies_with_sites(fh, hs):
3319  """link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
3320  return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
3321 class Transporting(IMP.Decorator):
3322  """Proxy of C++ IMP::npctransport::Transporting class"""
3323  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3324 
3325  def __init__(self, *args):
3326  """
3327  __init__(IMP::npctransport::Transporting self) -> Transporting
3328  __init__(IMP::npctransport::Transporting self, Model m, ParticleIndex id) -> Transporting
3329  __init__(IMP::npctransport::Transporting self, _ParticleAdaptor d) -> Transporting
3330  """
3331  this = _IMP_npctransport.new_Transporting(*args)
3332  try:
3333  self.this.append(this)
3334  except:
3335  self.this = this
3336 
3337  def show(self, *args):
3338  """
3339  show(Transporting self, _ostream out)
3340  show(Transporting self)
3341  """
3342  return _IMP_npctransport.Transporting_show(self, *args)
3343 
3344 
3345  def setup_particle(*args):
3346  """
3347  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
3348  setup_particle(Model m, ParticleIndex pi) -> Transporting
3349  setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
3350  setup_particle(_ParticleAdaptor decorator) -> Transporting
3351  """
3352  return _IMP_npctransport.Transporting_setup_particle(*args)
3353 
3354  setup_particle = staticmethod(setup_particle)
3355 
3356  def get_is_setup(*args):
3357  """
3358  get_is_setup(_ParticleAdaptor p) -> bool
3359  get_is_setup(Model m, ParticleIndex pi) -> bool
3360  """
3361  return _IMP_npctransport.Transporting_get_is_setup(*args)
3362 
3363  get_is_setup = staticmethod(get_is_setup)
3364 
3365  def set_is_last_entry_from_top(self, is_last_entry_from_top):
3366  """set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
3367  return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
3368 
3369 
3370  def get_is_last_entry_from_top(self):
3371  """get_is_last_entry_from_top(Transporting self) -> bool"""
3372  return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
3373 
3374 
3375  def get_is_last_entry_from_top_key():
3376  """get_is_last_entry_from_top_key() -> IntKey"""
3377  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3378 
3379  get_is_last_entry_from_top_key = staticmethod(get_is_last_entry_from_top_key)
3380 
3381  def set_last_tracked_z(self, last_tracked_z):
3382  """set_last_tracked_z(Transporting self, double last_tracked_z)"""
3383  return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
3384 
3385 
3386  def get_last_tracked_z(self):
3387  """get_last_tracked_z(Transporting self) -> double"""
3388  return _IMP_npctransport.Transporting_get_last_tracked_z(self)
3389 
3390 
3391  def get_last_tracked_z_key():
3392  """get_last_tracked_z_key() -> FloatKey"""
3393  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3394 
3395  get_last_tracked_z_key = staticmethod(get_last_tracked_z_key)
3396 
3397  def set_n_entries_bottom(self, n):
3398  """set_n_entries_bottom(Transporting self, int n)"""
3399  return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
3400 
3401 
3402  def get_n_entries_bottom(self):
3403  """get_n_entries_bottom(Transporting self) -> int"""
3404  return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
3405 
3406 
3407  def get_n_entries_bottom_key():
3408  """get_n_entries_bottom_key() -> IntKey"""
3409  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3410 
3411  get_n_entries_bottom_key = staticmethod(get_n_entries_bottom_key)
3412 
3413  def set_n_entries_top(self, n):
3414  """set_n_entries_top(Transporting self, int n)"""
3415  return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
3416 
3417 
3418  def get_n_entries_top(self):
3419  """get_n_entries_top(Transporting self) -> int"""
3420  return _IMP_npctransport.Transporting_get_n_entries_top(self)
3421 
3422 
3423  def get_n_entries_top_key():
3424  """get_n_entries_top_key() -> IntKey"""
3425  return _IMP_npctransport.Transporting_get_n_entries_top_key()
3426 
3427  get_n_entries_top_key = staticmethod(get_n_entries_top_key)
3428 
3429  def add_attribute(self, *args):
3430  """
3431  add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
3432  add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
3433  add_attribute(Transporting self, IntKey a0, IMP::Int a1)
3434  add_attribute(Transporting self, FloatsKey a0, IMP::Floats a1)
3435  add_attribute(Transporting self, IntsKey a0, IMP::Ints a1)
3436  add_attribute(Transporting self, StringKey a0, IMP::String a1)
3437  add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
3438  add_attribute(Transporting self, ObjectKey a0, Object a1)
3439  """
3440  return _IMP_npctransport.Transporting_add_attribute(self, *args)
3441 
3442 
3443  def get_value(self, *args):
3444  """
3445  get_value(Transporting self, FloatKey a0) -> IMP::Float
3446  get_value(Transporting self, IntKey a0) -> IMP::Int
3447  get_value(Transporting self, FloatsKey a0) -> IMP::Floats
3448  get_value(Transporting self, IntsKey a0) -> IMP::Ints
3449  get_value(Transporting self, StringKey a0) -> IMP::String
3450  get_value(Transporting self, ParticleIndexKey a0) -> Particle
3451  get_value(Transporting self, ObjectKey a0) -> Object
3452  """
3453  return _IMP_npctransport.Transporting_get_value(self, *args)
3454 
3455 
3456  def set_value(self, *args):
3457  """
3458  set_value(Transporting self, FloatKey a0, IMP::Float a1)
3459  set_value(Transporting self, IntKey a0, IMP::Int a1)
3460  set_value(Transporting self, FloatsKey a0, IMP::Floats a1)
3461  set_value(Transporting self, IntsKey a0, IMP::Ints a1)
3462  set_value(Transporting self, StringKey a0, IMP::String a1)
3463  set_value(Transporting self, ParticleIndexKey a0, Particle a1)
3464  set_value(Transporting self, ObjectKey a0, Object a1)
3465  """
3466  return _IMP_npctransport.Transporting_set_value(self, *args)
3467 
3468 
3469  def remove_attribute(self, *args):
3470  """
3471  remove_attribute(Transporting self, FloatKey a0)
3472  remove_attribute(Transporting self, IntKey a0)
3473  remove_attribute(Transporting self, FloatsKey a0)
3474  remove_attribute(Transporting self, IntsKey a0)
3475  remove_attribute(Transporting self, StringKey a0)
3476  remove_attribute(Transporting self, ParticleIndexKey a0)
3477  remove_attribute(Transporting self, ObjectKey a0)
3478  """
3479  return _IMP_npctransport.Transporting_remove_attribute(self, *args)
3480 
3481 
3482  def has_attribute(self, *args):
3483  """
3484  has_attribute(Transporting self, FloatKey a0) -> bool
3485  has_attribute(Transporting self, IntKey a0) -> bool
3486  has_attribute(Transporting self, FloatsKey a0) -> bool
3487  has_attribute(Transporting self, IntsKey a0) -> bool
3488  has_attribute(Transporting self, StringKey a0) -> bool
3489  has_attribute(Transporting self, ParticleIndexKey a0) -> bool
3490  has_attribute(Transporting self, ObjectKey a0) -> bool
3491  """
3492  return _IMP_npctransport.Transporting_has_attribute(self, *args)
3493 
3494 
3495  def get_derivative(self, a0):
3496  """get_derivative(Transporting self, FloatKey a0) -> double"""
3497  return _IMP_npctransport.Transporting_get_derivative(self, a0)
3498 
3499 
3500  def get_name(self):
3501  """get_name(Transporting self) -> std::string"""
3502  return _IMP_npctransport.Transporting_get_name(self)
3503 
3504 
3505  def clear_caches(self):
3506  """clear_caches(Transporting self)"""
3507  return _IMP_npctransport.Transporting_clear_caches(self)
3508 
3509 
3510  def set_name(self, a0):
3511  """set_name(Transporting self, std::string a0)"""
3512  return _IMP_npctransport.Transporting_set_name(self, a0)
3513 
3514 
3515  def set_check_level(self, a0):
3516  """set_check_level(Transporting self, IMP::CheckLevel a0)"""
3517  return _IMP_npctransport.Transporting_set_check_level(self, a0)
3518 
3519 
3520  def add_to_derivative(self, a0, a1, a2):
3521  """add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3522  return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
3523 
3524 
3525  def set_is_optimized(self, a0, a1):
3526  """set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
3527  return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
3528 
3529 
3530  def get_is_optimized(self, a0):
3531  """get_is_optimized(Transporting self, FloatKey a0) -> bool"""
3532  return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
3533 
3534 
3535  def get_check_level(self):
3536  """get_check_level(Transporting self) -> IMP::CheckLevel"""
3537  return _IMP_npctransport.Transporting_get_check_level(self)
3538 
3539 
3540  def __eq__(self, *args):
3541  """
3542  __eq__(Transporting self, Transporting o) -> bool
3543  __eq__(Transporting self, Particle d) -> bool
3544  """
3545  return _IMP_npctransport.Transporting___eq__(self, *args)
3546 
3547 
3548  def __ne__(self, *args):
3549  """
3550  __ne__(Transporting self, Transporting o) -> bool
3551  __ne__(Transporting self, Particle d) -> bool
3552  """
3553  return _IMP_npctransport.Transporting___ne__(self, *args)
3554 
3555 
3556  def __le__(self, *args):
3557  """
3558  __le__(Transporting self, Transporting o) -> bool
3559  __le__(Transporting self, Particle d) -> bool
3560  """
3561  return _IMP_npctransport.Transporting___le__(self, *args)
3562 
3563 
3564  def __lt__(self, *args):
3565  """
3566  __lt__(Transporting self, Transporting o) -> bool
3567  __lt__(Transporting self, Particle d) -> bool
3568  """
3569  return _IMP_npctransport.Transporting___lt__(self, *args)
3570 
3571 
3572  def __ge__(self, *args):
3573  """
3574  __ge__(Transporting self, Transporting o) -> bool
3575  __ge__(Transporting self, Particle d) -> bool
3576  """
3577  return _IMP_npctransport.Transporting___ge__(self, *args)
3578 
3579 
3580  def __gt__(self, *args):
3581  """
3582  __gt__(Transporting self, Transporting o) -> bool
3583  __gt__(Transporting self, Particle d) -> bool
3584  """
3585  return _IMP_npctransport.Transporting___gt__(self, *args)
3586 
3587 
3588  def __hash__(self):
3589  """__hash__(Transporting self) -> std::size_t"""
3590  return _IMP_npctransport.Transporting___hash__(self)
3591 
3592 
3593  def __str__(self):
3594  """__str__(Transporting self) -> std::string"""
3595  return _IMP_npctransport.Transporting___str__(self)
3596 
3597 
3598  def __repr__(self):
3599  """__repr__(Transporting self) -> std::string"""
3600  return _IMP_npctransport.Transporting___repr__(self)
3601 
3602  __swig_destroy__ = _IMP_npctransport.delete_Transporting
3603  __del__ = lambda self: None
3604 Transporting_swigregister = _IMP_npctransport.Transporting_swigregister
3605 Transporting_swigregister(Transporting)
3606 
3607 def Transporting_setup_particle(*args):
3608  """
3609  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
3610  setup_particle(Model m, ParticleIndex pi) -> Transporting
3611  setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
3612  Transporting_setup_particle(_ParticleAdaptor decorator) -> Transporting
3613  """
3614  return _IMP_npctransport.Transporting_setup_particle(*args)
3615 
3616 def Transporting_get_is_setup(*args):
3617  """
3618  get_is_setup(_ParticleAdaptor p) -> bool
3619  Transporting_get_is_setup(Model m, ParticleIndex pi) -> bool
3620  """
3621  return _IMP_npctransport.Transporting_get_is_setup(*args)
3622 
3623 def Transporting_get_is_last_entry_from_top_key():
3624  """Transporting_get_is_last_entry_from_top_key() -> IntKey"""
3625  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3626 
3627 def Transporting_get_last_tracked_z_key():
3628  """Transporting_get_last_tracked_z_key() -> FloatKey"""
3629  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3630 
3631 def Transporting_get_n_entries_bottom_key():
3632  """Transporting_get_n_entries_bottom_key() -> IntKey"""
3633  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3634 
3635 def Transporting_get_n_entries_top_key():
3636  """Transporting_get_n_entries_top_key() -> IntKey"""
3637  return _IMP_npctransport.Transporting_get_n_entries_top_key()
3638 
3639 
3640 def show_ranges(fname):
3641  """show_ranges(std::string fname)"""
3642  return _IMP_npctransport.show_ranges(fname)
3643 
3644 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
3645  """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"""
3646  return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
3647 
3648 def get_number_of_work_units(configuration_file):
3649  """get_number_of_work_units(std::string configuration_file) -> int"""
3650  return _IMP_npctransport.get_number_of_work_units(configuration_file)
3651 class SlabWithPore(IMP.Decorator):
3652  """Proxy of C++ IMP::npctransport::SlabWithPore class"""
3653  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3654 
3655  def __init__(self, *args):
3656  """
3657  __init__(IMP::npctransport::SlabWithPore self) -> SlabWithPore
3658  __init__(IMP::npctransport::SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
3659  __init__(IMP::npctransport::SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
3660  """
3661  this = _IMP_npctransport.new_SlabWithPore(*args)
3662  try:
3663  self.this.append(this)
3664  except:
3665  self.this = this
3666 
3667  def show(self, *args):
3668  """
3669  show(SlabWithPore self, _ostream out)
3670  show(SlabWithPore self)
3671  """
3672  return _IMP_npctransport.SlabWithPore_show(self, *args)
3673 
3674 
3675  def setup_particle(*args):
3676  """
3677  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3678  setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3679  """
3680  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3681 
3682  setup_particle = staticmethod(setup_particle)
3683 
3684  def get_is_setup(*args):
3685  """
3686  get_is_setup(_ParticleAdaptor p) -> bool
3687  get_is_setup(Model m, ParticleIndex pi) -> bool
3688  """
3689  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3690 
3691  get_is_setup = staticmethod(get_is_setup)
3692 
3693  def set_thickness(self, thickness):
3694  """set_thickness(SlabWithPore self, double thickness)"""
3695  return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
3696 
3697 
3698  def get_thickness(self):
3699  """get_thickness(SlabWithPore self) -> IMP::Float"""
3700  return _IMP_npctransport.SlabWithPore_get_thickness(self)
3701 
3702 
3703  def get_pore_radius(self):
3704  """get_pore_radius(SlabWithPore self) -> IMP::Float"""
3705  return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
3706 
3707 
3708  def set_pore_radius(self, r):
3709  """set_pore_radius(SlabWithPore self, double r)"""
3710  return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
3711 
3712 
3713  def add_to_pore_radius_derivative(self, v, d):
3714  """add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
3715  return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
3716 
3717 
3718  def get_pore_radius_is_optimized(self):
3719  """get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
3720  return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
3721 
3722 
3723  def set_pore_radius_is_optimized(self, tf):
3724  """set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
3725  return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
3726 
3727 
3728  def get_thickness_key():
3729  """get_thickness_key() -> FloatKey"""
3730  return _IMP_npctransport.SlabWithPore_get_thickness_key()
3731 
3732  get_thickness_key = staticmethod(get_thickness_key)
3733 
3734  def get_pore_radius_key():
3735  """get_pore_radius_key() -> FloatKey"""
3736  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3737 
3738  get_pore_radius_key = staticmethod(get_pore_radius_key)
3739 
3740  def add_attribute(self, *args):
3741  """
3742  add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
3743  add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
3744  add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
3745  add_attribute(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3746  add_attribute(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3747  add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
3748  add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3749  add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
3750  """
3751  return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
3752 
3753 
3754  def get_value(self, *args):
3755  """
3756  get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
3757  get_value(SlabWithPore self, IntKey a0) -> IMP::Int
3758  get_value(SlabWithPore self, FloatsKey a0) -> IMP::Floats
3759  get_value(SlabWithPore self, IntsKey a0) -> IMP::Ints
3760  get_value(SlabWithPore self, StringKey a0) -> IMP::String
3761  get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3762  get_value(SlabWithPore self, ObjectKey a0) -> Object
3763  """
3764  return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3765 
3766 
3767  def set_value(self, *args):
3768  """
3769  set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3770  set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3771  set_value(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3772  set_value(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3773  set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3774  set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3775  set_value(SlabWithPore self, ObjectKey a0, Object a1)
3776  """
3777  return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3778 
3779 
3780  def remove_attribute(self, *args):
3781  """
3782  remove_attribute(SlabWithPore self, FloatKey a0)
3783  remove_attribute(SlabWithPore self, IntKey a0)
3784  remove_attribute(SlabWithPore self, FloatsKey a0)
3785  remove_attribute(SlabWithPore self, IntsKey a0)
3786  remove_attribute(SlabWithPore self, StringKey a0)
3787  remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3788  remove_attribute(SlabWithPore self, ObjectKey a0)
3789  """
3790  return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3791 
3792 
3793  def has_attribute(self, *args):
3794  """
3795  has_attribute(SlabWithPore self, FloatKey a0) -> bool
3796  has_attribute(SlabWithPore self, IntKey a0) -> bool
3797  has_attribute(SlabWithPore self, FloatsKey a0) -> bool
3798  has_attribute(SlabWithPore self, IntsKey a0) -> bool
3799  has_attribute(SlabWithPore self, StringKey a0) -> bool
3800  has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3801  has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3802  """
3803  return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3804 
3805 
3806  def get_derivative(self, a0):
3807  """get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3808  return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3809 
3810 
3811  def get_name(self):
3812  """get_name(SlabWithPore self) -> std::string"""
3813  return _IMP_npctransport.SlabWithPore_get_name(self)
3814 
3815 
3816  def clear_caches(self):
3817  """clear_caches(SlabWithPore self)"""
3818  return _IMP_npctransport.SlabWithPore_clear_caches(self)
3819 
3820 
3821  def set_name(self, a0):
3822  """set_name(SlabWithPore self, std::string a0)"""
3823  return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3824 
3825 
3826  def set_check_level(self, a0):
3827  """set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3828  return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3829 
3830 
3831  def add_to_derivative(self, a0, a1, a2):
3832  """add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3833  return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3834 
3835 
3836  def set_is_optimized(self, a0, a1):
3837  """set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3838  return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3839 
3840 
3841  def get_is_optimized(self, a0):
3842  """get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3843  return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3844 
3845 
3846  def get_check_level(self):
3847  """get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3848  return _IMP_npctransport.SlabWithPore_get_check_level(self)
3849 
3850 
3851  def __eq__(self, *args):
3852  """
3853  __eq__(SlabWithPore self, SlabWithPore o) -> bool
3854  __eq__(SlabWithPore self, Particle d) -> bool
3855  """
3856  return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3857 
3858 
3859  def __ne__(self, *args):
3860  """
3861  __ne__(SlabWithPore self, SlabWithPore o) -> bool
3862  __ne__(SlabWithPore self, Particle d) -> bool
3863  """
3864  return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3865 
3866 
3867  def __le__(self, *args):
3868  """
3869  __le__(SlabWithPore self, SlabWithPore o) -> bool
3870  __le__(SlabWithPore self, Particle d) -> bool
3871  """
3872  return _IMP_npctransport.SlabWithPore___le__(self, *args)
3873 
3874 
3875  def __lt__(self, *args):
3876  """
3877  __lt__(SlabWithPore self, SlabWithPore o) -> bool
3878  __lt__(SlabWithPore self, Particle d) -> bool
3879  """
3880  return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3881 
3882 
3883  def __ge__(self, *args):
3884  """
3885  __ge__(SlabWithPore self, SlabWithPore o) -> bool
3886  __ge__(SlabWithPore self, Particle d) -> bool
3887  """
3888  return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3889 
3890 
3891  def __gt__(self, *args):
3892  """
3893  __gt__(SlabWithPore self, SlabWithPore o) -> bool
3894  __gt__(SlabWithPore self, Particle d) -> bool
3895  """
3896  return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3897 
3898 
3899  def __hash__(self):
3900  """__hash__(SlabWithPore self) -> std::size_t"""
3901  return _IMP_npctransport.SlabWithPore___hash__(self)
3902 
3903 
3904  def __str__(self):
3905  """__str__(SlabWithPore self) -> std::string"""
3906  return _IMP_npctransport.SlabWithPore___str__(self)
3907 
3908 
3909  def __repr__(self):
3910  """__repr__(SlabWithPore self) -> std::string"""
3911  return _IMP_npctransport.SlabWithPore___repr__(self)
3912 
3913  __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3914  __del__ = lambda self: None
3915 SlabWithPore_swigregister = _IMP_npctransport.SlabWithPore_swigregister
3916 SlabWithPore_swigregister(SlabWithPore)
3917 
3918 def SlabWithPore_setup_particle(*args):
3919  """
3920  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3921  SlabWithPore_setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3922  """
3923  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3924 
3925 def SlabWithPore_get_is_setup(*args):
3926  """
3927  get_is_setup(_ParticleAdaptor p) -> bool
3928  SlabWithPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3929  """
3930  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3931 
3932 def SlabWithPore_get_thickness_key():
3933  """SlabWithPore_get_thickness_key() -> FloatKey"""
3934  return _IMP_npctransport.SlabWithPore_get_thickness_key()
3935 
3936 def SlabWithPore_get_pore_radius_key():
3937  """SlabWithPore_get_pore_radius_key() -> FloatKey"""
3938  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3939 
3940 class SlabWithCylindricalPore(SlabWithPore):
3941  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class"""
3942  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3943 
3944  def __init__(self, *args):
3945  """
3946  __init__(IMP::npctransport::SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3947  __init__(IMP::npctransport::SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3948  __init__(IMP::npctransport::SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3949  """
3950  this = _IMP_npctransport.new_SlabWithCylindricalPore(*args)
3951  try:
3952  self.this.append(this)
3953  except:
3954  self.this = this
3955 
3956  def show(self, *args):
3957  """
3958  show(SlabWithCylindricalPore self, _ostream out)
3959  show(SlabWithCylindricalPore self)
3960  """
3961  return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3962 
3963 
3964  def setup_particle(*args):
3965  """
3966  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3967  setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3968  """
3969  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3970 
3971  setup_particle = staticmethod(setup_particle)
3972 
3973  def get_is_setup(*args):
3974  """
3975  get_is_setup(_ParticleAdaptor p) -> bool
3976  get_is_setup(Model m, ParticleIndex pi) -> bool
3977  """
3978  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3979 
3980  get_is_setup = staticmethod(get_is_setup)
3981 
3982  def get_cylindrical_pore_key():
3983  """get_cylindrical_pore_key() -> IntKey"""
3984  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3985 
3986  get_cylindrical_pore_key = staticmethod(get_cylindrical_pore_key)
3987 
3988  def add_attribute(self, *args):
3989  """
3990  add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3991  add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3992  add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3993  add_attribute(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3994  add_attribute(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3995  add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3996  add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3997  add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3998  """
3999  return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
4000 
4001 
4002  def get_value(self, *args):
4003  """
4004  get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
4005  get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
4006  get_value(SlabWithCylindricalPore self, FloatsKey a0) -> IMP::Floats
4007  get_value(SlabWithCylindricalPore self, IntsKey a0) -> IMP::Ints
4008  get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
4009  get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
4010  get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
4011  """
4012  return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
4013 
4014 
4015  def set_value(self, *args):
4016  """
4017  set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
4018  set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
4019  set_value(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
4020  set_value(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
4021  set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
4022  set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
4023  set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
4024  """
4025  return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
4026 
4027 
4028  def remove_attribute(self, *args):
4029  """
4030  remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
4031  remove_attribute(SlabWithCylindricalPore self, IntKey a0)
4032  remove_attribute(SlabWithCylindricalPore self, FloatsKey a0)
4033  remove_attribute(SlabWithCylindricalPore self, IntsKey a0)
4034  remove_attribute(SlabWithCylindricalPore self, StringKey a0)
4035  remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
4036  remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
4037  """
4038  return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
4039 
4040 
4041  def has_attribute(self, *args):
4042  """
4043  has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
4044  has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
4045  has_attribute(SlabWithCylindricalPore self, FloatsKey a0) -> bool
4046  has_attribute(SlabWithCylindricalPore self, IntsKey a0) -> bool
4047  has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
4048  has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
4049  has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
4050  """
4051  return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
4052 
4053 
4054  def get_derivative(self, a0):
4055  """get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
4056  return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
4057 
4058 
4059  def get_name(self):
4060  """get_name(SlabWithCylindricalPore self) -> std::string"""
4061  return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
4062 
4063 
4064  def clear_caches(self):
4065  """clear_caches(SlabWithCylindricalPore self)"""
4066  return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
4067 
4068 
4069  def set_name(self, a0):
4070  """set_name(SlabWithCylindricalPore self, std::string a0)"""
4071  return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
4072 
4073 
4074  def set_check_level(self, a0):
4075  """set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
4076  return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
4077 
4078 
4079  def add_to_derivative(self, a0, a1, a2):
4080  """add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4081  return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
4082 
4083 
4084  def set_is_optimized(self, a0, a1):
4085  """set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
4086  return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
4087 
4088 
4089  def get_is_optimized(self, a0):
4090  """get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
4091  return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
4092 
4093 
4094  def get_check_level(self):
4095  """get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
4096  return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
4097 
4098 
4099  def __eq__(self, *args):
4100  """
4101  __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
4102  __eq__(SlabWithCylindricalPore self, Particle d) -> bool
4103  """
4104  return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
4105 
4106 
4107  def __ne__(self, *args):
4108  """
4109  __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
4110  __ne__(SlabWithCylindricalPore self, Particle d) -> bool
4111  """
4112  return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
4113 
4114 
4115  def __le__(self, *args):
4116  """
4117  __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
4118  __le__(SlabWithCylindricalPore self, Particle d) -> bool
4119  """
4120  return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
4121 
4122 
4123  def __lt__(self, *args):
4124  """
4125  __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
4126  __lt__(SlabWithCylindricalPore self, Particle d) -> bool
4127  """
4128  return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
4129 
4130 
4131  def __ge__(self, *args):
4132  """
4133  __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
4134  __ge__(SlabWithCylindricalPore self, Particle d) -> bool
4135  """
4136  return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
4137 
4138 
4139  def __gt__(self, *args):
4140  """
4141  __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
4142  __gt__(SlabWithCylindricalPore self, Particle d) -> bool
4143  """
4144  return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
4145 
4146 
4147  def __hash__(self):
4148  """__hash__(SlabWithCylindricalPore self) -> std::size_t"""
4149  return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
4150 
4151 
4152  def __str__(self):
4153  """__str__(SlabWithCylindricalPore self) -> std::string"""
4154  return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
4155 
4156 
4157  def __repr__(self):
4158  """__repr__(SlabWithCylindricalPore self) -> std::string"""
4159  return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
4160 
4161  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
4162  __del__ = lambda self: None
4163 SlabWithCylindricalPore_swigregister = _IMP_npctransport.SlabWithCylindricalPore_swigregister
4164 SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
4165 
4166 def SlabWithCylindricalPore_setup_particle(*args):
4167  """
4168  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
4169  SlabWithCylindricalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
4170  """
4171  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
4172 
4173 def SlabWithCylindricalPore_get_is_setup(*args):
4174  """
4175  get_is_setup(_ParticleAdaptor p) -> bool
4176  SlabWithCylindricalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
4177  """
4178  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
4179 
4180 def SlabWithCylindricalPore_get_cylindrical_pore_key():
4181  """SlabWithCylindricalPore_get_cylindrical_pore_key() -> IntKey"""
4182  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
4183 
4184 class SlabWithToroidalPore(SlabWithPore):
4185  """Proxy of C++ IMP::npctransport::SlabWithToroidalPore class"""
4186  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4187 
4188  def __init__(self, *args):
4189  """
4190  __init__(IMP::npctransport::SlabWithToroidalPore self) -> SlabWithToroidalPore
4191  __init__(IMP::npctransport::SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
4192  __init__(IMP::npctransport::SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
4193  """
4194  this = _IMP_npctransport.new_SlabWithToroidalPore(*args)
4195  try:
4196  self.this.append(this)
4197  except:
4198  self.this = this
4199 
4200  def show(self, *args):
4201  """
4202  show(SlabWithToroidalPore self, _ostream out)
4203  show(SlabWithToroidalPore self)
4204  """
4205  return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
4206 
4207 
4208  def setup_particle(*args):
4209  """
4210  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
4211  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
4212  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4213  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4214  """
4215  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
4216 
4217  setup_particle = staticmethod(setup_particle)
4218 
4219  def get_is_setup(*args):
4220  """
4221  get_is_setup(_ParticleAdaptor p) -> bool
4222  get_is_setup(Model m, ParticleIndex pi) -> bool
4223  """
4224  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
4225 
4226  get_is_setup = staticmethod(get_is_setup)
4227 
4228  def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
4229  """set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
4230  return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
4231 
4232 
4233  def get_minor_radius_h2v_aspect_ratio(self):
4234  """get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
4235  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
4236 
4237 
4238  def get_vertical_minor_radius(self):
4239  """get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
4240  return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
4241 
4242 
4243  def set_vertical_minor_radius(self, rv):
4244  """set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
4245  return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
4246 
4247 
4248  def get_horizontal_minor_radius(self):
4249  """get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
4250  return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
4251 
4252 
4253  def set_horizontal_minor_radius(self, rh):
4254  """set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
4255  return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
4256 
4257 
4258  def get_minor_radius_h2v_aspect_ratio_key():
4259  """get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
4260  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
4261 
4262  get_minor_radius_h2v_aspect_ratio_key = staticmethod(get_minor_radius_h2v_aspect_ratio_key)
4263 
4264  def get_toroidal_pore_key():
4265  """get_toroidal_pore_key() -> IntKey"""
4266  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
4267 
4268  get_toroidal_pore_key = staticmethod(get_toroidal_pore_key)
4269 
4270  def add_attribute(self, *args):
4271  """
4272  add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
4273  add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
4274  add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
4275  add_attribute(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
4276  add_attribute(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
4277  add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
4278  add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
4279  add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
4280  """
4281  return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
4282 
4283 
4284  def get_value(self, *args):
4285  """
4286  get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
4287  get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
4288  get_value(SlabWithToroidalPore self, FloatsKey a0) -> IMP::Floats
4289  get_value(SlabWithToroidalPore self, IntsKey a0) -> IMP::Ints
4290  get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
4291  get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
4292  get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
4293  """
4294  return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
4295 
4296 
4297  def set_value(self, *args):
4298  """
4299  set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
4300  set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
4301  set_value(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
4302  set_value(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
4303  set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
4304  set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
4305  set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
4306  """
4307  return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
4308 
4309 
4310  def remove_attribute(self, *args):
4311  """
4312  remove_attribute(SlabWithToroidalPore self, FloatKey a0)
4313  remove_attribute(SlabWithToroidalPore self, IntKey a0)
4314  remove_attribute(SlabWithToroidalPore self, FloatsKey a0)
4315  remove_attribute(SlabWithToroidalPore self, IntsKey a0)
4316  remove_attribute(SlabWithToroidalPore self, StringKey a0)
4317  remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
4318  remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
4319  """
4320  return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
4321 
4322 
4323  def has_attribute(self, *args):
4324  """
4325  has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
4326  has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
4327  has_attribute(SlabWithToroidalPore self, FloatsKey a0) -> bool
4328  has_attribute(SlabWithToroidalPore self, IntsKey a0) -> bool
4329  has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
4330  has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
4331  has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
4332  """
4333  return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
4334 
4335 
4336  def get_derivative(self, a0):
4337  """get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
4338  return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
4339 
4340 
4341  def get_name(self):
4342  """get_name(SlabWithToroidalPore self) -> std::string"""
4343  return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
4344 
4345 
4346  def clear_caches(self):
4347  """clear_caches(SlabWithToroidalPore self)"""
4348  return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
4349 
4350 
4351  def set_name(self, a0):
4352  """set_name(SlabWithToroidalPore self, std::string a0)"""
4353  return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
4354 
4355 
4356  def set_check_level(self, a0):
4357  """set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
4358  return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
4359 
4360 
4361  def add_to_derivative(self, a0, a1, a2):
4362  """add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
4363  return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
4364 
4365 
4366  def set_is_optimized(self, a0, a1):
4367  """set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
4368  return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
4369 
4370 
4371  def get_is_optimized(self, a0):
4372  """get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
4373  return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
4374 
4375 
4376  def get_check_level(self):
4377  """get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
4378  return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
4379 
4380 
4381  def __eq__(self, *args):
4382  """
4383  __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4384  __eq__(SlabWithToroidalPore self, Particle d) -> bool
4385  """
4386  return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
4387 
4388 
4389  def __ne__(self, *args):
4390  """
4391  __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4392  __ne__(SlabWithToroidalPore self, Particle d) -> bool
4393  """
4394  return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
4395 
4396 
4397  def __le__(self, *args):
4398  """
4399  __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4400  __le__(SlabWithToroidalPore self, Particle d) -> bool
4401  """
4402  return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
4403 
4404 
4405  def __lt__(self, *args):
4406  """
4407  __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4408  __lt__(SlabWithToroidalPore self, Particle d) -> bool
4409  """
4410  return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
4411 
4412 
4413  def __ge__(self, *args):
4414  """
4415  __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4416  __ge__(SlabWithToroidalPore self, Particle d) -> bool
4417  """
4418  return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
4419 
4420 
4421  def __gt__(self, *args):
4422  """
4423  __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4424  __gt__(SlabWithToroidalPore self, Particle d) -> bool
4425  """
4426  return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
4427 
4428 
4429  def __hash__(self):
4430  """__hash__(SlabWithToroidalPore self) -> std::size_t"""
4431  return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
4432 
4433 
4434  def __str__(self):
4435  """__str__(SlabWithToroidalPore self) -> std::string"""
4436  return _IMP_npctransport.SlabWithToroidalPore___str__(self)
4437 
4438 
4439  def __repr__(self):
4440  """__repr__(SlabWithToroidalPore self) -> std::string"""
4441  return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
4442 
4443  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
4444  __del__ = lambda self: None
4445 SlabWithToroidalPore_swigregister = _IMP_npctransport.SlabWithToroidalPore_swigregister
4446 SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
4447 
4448 def SlabWithToroidalPore_setup_particle(*args):
4449  """
4450  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
4451  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
4452  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4453  SlabWithToroidalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4454  """
4455  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
4456 
4457 def SlabWithToroidalPore_get_is_setup(*args):
4458  """
4459  get_is_setup(_ParticleAdaptor p) -> bool
4460  SlabWithToroidalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
4461  """
4462  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
4463 
4464 def SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key():
4465  """SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
4466  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
4467 
4468 def SlabWithToroidalPore_get_toroidal_pore_key():
4469  """SlabWithToroidalPore_get_toroidal_pore_key() -> IntKey"""
4470  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
4471 
4472 
4473 def __lshift__(*args):
4474  """
4475  __lshift__(_ostream out, RelaxingSpring n) -> _ostream
4476  __lshift__(_ostream out, Transporting n) -> _ostream
4477  __lshift__(_ostream out, SlabWithPore n) -> _ostream
4478  __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
4479  __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
4480  """
4481  return _IMP_npctransport.__lshift__(*args)
4482 class SlabWithCylindricalPorePairScore(IMP.PairScore):
4483  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class"""
4484  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4485 
4486  def __init__(self, k):
4487  """__init__(IMP::npctransport::SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
4488  this = _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k)
4489  try:
4490  self.this.append(this)
4491  except:
4492  self.this = this
4493 
4494  def get_displacement_direction(self, slab, v):
4495  """get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
4496  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
4497 
4498 
4499  def get_displacement_magnitude(self, slab, v):
4500  """get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
4501  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
4502 
4503 
4504  def do_get_inputs(self, m, pis):
4505  """do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4506  return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
4507 
4508 
4509  def get_version_info(self):
4510  """get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
4511  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
4512 
4513 
4514  def __str__(self):
4515  """__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
4516  return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
4517 
4518 
4519  def __repr__(self):
4520  """__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
4521  return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
4522 
4523 
4524  @staticmethod
4525  def get_from(o):
4526  return _object_cast_to_SlabWithCylindricalPorePairScore(o)
4527 
4528 SlabWithCylindricalPorePairScore_swigregister = _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister
4529 SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
4530 
4531 class SlabWithToroidalPorePairScore(IMP.PairScore):
4532  """Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class"""
4533  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4534 
4535  def __init__(self, k):
4536  """__init__(IMP::npctransport::SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
4537  this = _IMP_npctransport.new_SlabWithToroidalPorePairScore(k)
4538  try:
4539  self.this.append(this)
4540  except:
4541  self.this = this
4542 
4543  def do_get_inputs(self, m, pis):
4544  """do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4545  return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
4546 
4547 
4548  def get_version_info(self):
4549  """get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
4550  return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
4551 
4552 
4553  def __str__(self):
4554  """__str__(SlabWithToroidalPorePairScore self) -> std::string"""
4555  return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
4556 
4557 
4558  def __repr__(self):
4559  """__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
4560  return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
4561 
4562 
4563  @staticmethod
4564  def get_from(o):
4565  return _object_cast_to_SlabWithToroidalPorePairScore(o)
4566 
4567 SlabWithToroidalPorePairScore_swigregister = _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister
4568 SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
4569 
4570 class SlabWithCylindricalPoreWireGeometry(IMP.display.Geometry):
4571  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class"""
4572  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4573 
4574  def __init__(self, height, radius, length):
4575  """__init__(IMP::npctransport::SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
4576  this = _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length)
4577  try:
4578  self.this.append(this)
4579  except:
4580  self.this = this
4581 
4582  def get_version_info(self):
4583  """get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
4584  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
4585 
4586 
4587  def __str__(self):
4588  """__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4589  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
4590 
4591 
4592  def __repr__(self):
4593  """__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4594  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
4595 
4596 
4597  @staticmethod
4598  def get_from(o):
4599  return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
4600 
4601 SlabWithCylindricalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister
4602 SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
4603 
4604 class SlabWithCylindricalPoreSurfaceGeometry(IMP.display.SurfaceMeshGeometry):
4605  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class"""
4606  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4607 
4608  def __init__(self, height, radius, length):
4609  """__init__(IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
4610  this = _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length)
4611  try:
4612  self.this.append(this)
4613  except:
4614  self.this = this
4615 
4616  def __str__(self):
4617  """__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4618  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
4619 
4620 
4621  def __repr__(self):
4622  """__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4623  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
4624 
4625 
4626  @staticmethod
4627  def get_from(o):
4628  return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
4629 
4630  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
4631  __del__ = lambda self: None
4632 SlabWithCylindricalPoreSurfaceGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister
4633 SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
4634 
4635 class SlabWithToroidalPoreWireGeometry(IMP.display.Geometry):
4636  """Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class"""
4637  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4638 
4639  def __init__(self, *args):
4640  """
4641  __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
4642  __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
4643  """
4644  this = _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args)
4645  try:
4646  self.this.append(this)
4647  except:
4648  self.this = this
4649 
4650  def get_version_info(self):
4651  """get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
4652  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
4653 
4654 
4655  def __str__(self):
4656  """__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4657  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
4658 
4659 
4660  def __repr__(self):
4661  """__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4662  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
4663 
4664 
4665  @staticmethod
4666  def get_from(o):
4667  return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
4668 
4669 SlabWithToroidalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister
4670 SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
4671 
4672 class _GenericAttributeSingletonScoreForPoreRadus(IMP.SingletonScore):
4673  """Proxy of C++ IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> class"""
4674  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4675  __repr__ = _swig_repr
4676 
4677  def __init__(self, f, k):
4678  """__init__(IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
4679  this = _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k)
4680  try:
4681  self.this.append(this)
4682  except:
4683  self.this = this
4684 
4685  def do_get_inputs(self, m, pis):
4686  """do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4687  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
4688 
4689 
4690  def get_unary_function(self):
4691  """get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
4692  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
4693 
4694 
4695  def get_version_info(self):
4696  """get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
4697  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
4698 
4699 _GenericAttributeSingletonScoreForPoreRadus_swigregister = _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister
4700 _GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
4701 
4702 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
4703  """Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class"""
4704  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4705 
4706  def __init__(self, mean, k):
4707  """__init__(IMP::npctransport::PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
4708  this = _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k)
4709  try:
4710  self.this.append(this)
4711  except:
4712  self.this = this
4713 
4714  def set_k(self, k):
4715  """set_k(PoreRadiusSingletonScore self, double k)"""
4716  return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
4717 
4718 
4719  def __str__(self):
4720  """__str__(PoreRadiusSingletonScore self) -> std::string"""
4721  return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
4722 
4723 
4724  def __repr__(self):
4725  """__repr__(PoreRadiusSingletonScore self) -> std::string"""
4726  return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
4727 
4728 
4729  @staticmethod
4730  def get_from(o):
4731  return _object_cast_to_PoreRadiusSingletonScore(o)
4732 
4733 PoreRadiusSingletonScore_swigregister = _IMP_npctransport.PoreRadiusSingletonScore_swigregister
4734 PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
4735 
4736 class ExcludeZRangeSingletonScore(IMP.SingletonScore):
4737  """Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class"""
4738  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4739 
4740  def __init__(self, bottom, top, k):
4741  """__init__(IMP::npctransport::ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
4742  this = _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k)
4743  try:
4744  self.this.append(this)
4745  except:
4746  self.this = this
4747 
4748  def get_bottom_z(self):
4749  """get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
4750  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
4751 
4752 
4753  def get_top_z(self):
4754  """get_top_z(ExcludeZRangeSingletonScore self) -> double"""
4755  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
4756 
4757 
4758  def get_k(self):
4759  """get_k(ExcludeZRangeSingletonScore self) -> double"""
4760  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
4761 
4762 
4763  def do_get_inputs(self, m, pis):
4764  """do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4765  return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
4766 
4767 
4768  def get_version_info(self):
4769  """get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
4770  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
4771 
4772 
4773  def __str__(self):
4774  """__str__(ExcludeZRangeSingletonScore self) -> std::string"""
4775  return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
4776 
4777 
4778  def __repr__(self):
4779  """__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
4780  return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
4781 
4782 
4783  @staticmethod
4784  def get_from(o):
4785  return _object_cast_to_ExcludeZRangeSingletonScore(o)
4786 
4787 ExcludeZRangeSingletonScore_swigregister = _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister
4788 ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
4789 
4790 class ZBiasSingletonScore(IMP.SingletonScore):
4791  """Proxy of C++ IMP::npctransport::ZBiasSingletonScore class"""
4792  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4793 
4794  def __init__(self, *args):
4795  """
4796  __init__(IMP::npctransport::ZBiasSingletonScore self, double k, double max_r) -> ZBiasSingletonScore
4797  __init__(IMP::npctransport::ZBiasSingletonScore self, double k) -> ZBiasSingletonScore
4798  """
4799  this = _IMP_npctransport.new_ZBiasSingletonScore(*args)
4800  try:
4801  self.this.append(this)
4802  except:
4803  self.this = this
4804 
4805  def get_k(self):
4806  """get_k(ZBiasSingletonScore self) -> double"""
4807  return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
4808 
4809 
4810  def set_k(self, k):
4811  """set_k(ZBiasSingletonScore self, double k)"""
4812  return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
4813 
4814 
4815  def do_get_inputs(self, m, pis):
4816  """do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4817  return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
4818 
4819 
4820  def get_version_info(self):
4821  """get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
4822  return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
4823 
4824 
4825  def __str__(self):
4826  """__str__(ZBiasSingletonScore self) -> std::string"""
4827  return _IMP_npctransport.ZBiasSingletonScore___str__(self)
4828 
4829 
4830  def __repr__(self):
4831  """__repr__(ZBiasSingletonScore self) -> std::string"""
4832  return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
4833 
4834 
4835  @staticmethod
4836  def get_from(o):
4837  return _object_cast_to_ZBiasSingletonScore(o)
4838 
4839 ZBiasSingletonScore_swigregister = _IMP_npctransport.ZBiasSingletonScore_swigregister
4840 ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
4841 
4842 class BodyStatisticsOptimizerState(IMP.OptimizerState):
4843  """Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class"""
4844  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4845 
4846  def __init__(self, p, statistics_manager=None, periodicity=1):
4847  """
4848  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState
4849  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None) -> BodyStatisticsOptimizerState
4850  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p) -> BodyStatisticsOptimizerState
4851  """
4852  this = _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity)
4853  try:
4854  self.this.append(this)
4855  except:
4856  self.this = this
4857 
4858  def get_correlation_time(self):
4859  """get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4860  return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4861 
4862 
4863  def get_diffusion_coefficient(self):
4864  """get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4865  return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4866 
4867 
4868  def update_particle_type_zr_distribution_map(self):
4869  """update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4870  return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4871 
4872 
4873  def do_update(self, call_num):
4874  """do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4875  return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4876 
4877 
4878  def get_version_info(self):
4879  """get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4880  return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4881 
4882 
4883  def __str__(self):
4884  """__str__(BodyStatisticsOptimizerState self) -> std::string"""
4885  return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4886 
4887 
4888  def __repr__(self):
4889  """__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4890  return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4891 
4892 
4893  @staticmethod
4894  def get_from(o):
4895  return _object_cast_to_BodyStatisticsOptimizerState(o)
4896 
4897 BodyStatisticsOptimizerState_swigregister = _IMP_npctransport.BodyStatisticsOptimizerState_swigregister
4898 BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4899 
4900 class ParticleTransportStatisticsOptimizerState(IMP.OptimizerState):
4901  """Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class"""
4902  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4903 
4904  def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4905  """
4906  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0, WeakPointer< IMP::atom::Simulator > owner=0) -> ParticleTransportStatisticsOptimizerState
4907  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0) -> ParticleTransportStatisticsOptimizerState
4908  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z) -> ParticleTransportStatisticsOptimizerState
4909  """
4910  this = _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner)
4911  try:
4912  self.this.append(this)
4913  except:
4914  self.this = this
4915 
4916  def set_owner(self, owner):
4917  """set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4918  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4919 
4920 
4921  def get_owner(self):
4922  """get_owner(ParticleTransportStatisticsOptimizerState self) -> Simulator"""
4923  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4924 
4925 
4926  def get_n_transports_up(self):
4927  """get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4928  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4929 
4930 
4931  def get_n_transports_down(self):
4932  """get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4933  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4934 
4935 
4936  def get_total_n_transports(self):
4937  """get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4938  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4939 
4940 
4941  def get_transport_time_points_in_ns(self):
4942  """get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4943  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4944 
4945 
4946  def do_update(self, call_num):
4947  """do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4948  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4949 
4950 
4951  def get_version_info(self):
4952  """get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4953  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4954 
4955 
4956  def __str__(self):
4957  """__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4958  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4959 
4960 
4961  def __repr__(self):
4962  """__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4963  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4964 
4965 
4966  @staticmethod
4967  def get_from(o):
4968  return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4969 
4970 ParticleTransportStatisticsOptimizerState_swigregister = _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister
4971 ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4972 
4973 class ChainStatisticsOptimizerState(IMP.OptimizerState):
4974  """Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class"""
4975  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4976 
4977  def __init__(self, ps, periodicity=1):
4978  """
4979  __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState
4980  __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps) -> ChainStatisticsOptimizerState
4981  """
4982  this = _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity)
4983  try:
4984  self.this.append(this)
4985  except:
4986  self.this = this
4987 
4988  def get_correlation_time(self):
4989  """get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4990  return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4991 
4992 
4993  def get_local_diffusion_coefficients(self):
4994  """get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4995  return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4996 
4997 
4998  def get_diffusion_coefficient(self):
4999  """get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
5000  return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
5001 
5002 
5003  def get_mean_radius_of_gyration(self):
5004  """get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
5005  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
5006 
5007 
5008  def get_mean_square_radius_of_gyration(self):
5009  """get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
5010  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
5011 
5012 
5013  def get_mean_end_to_end_distance(self):
5014  """get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
5015  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
5016 
5017 
5018  def get_mean_square_end_to_end_distance(self):
5019  """get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
5020  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
5021 
5022 
5023  def get_mean_bond_distance(self):
5024  """get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
5025  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
5026 
5027 
5028  def get_mean_square_bond_distance(self):
5029  """get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
5030  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
5031 
5032 
5033  def do_update(self, call_num):
5034  """do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
5035  return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
5036 
5037 
5038  def get_version_info(self):
5039  """get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
5040  return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
5041 
5042 
5043  def __str__(self):
5044  """__str__(ChainStatisticsOptimizerState self) -> std::string"""
5045  return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
5046 
5047 
5048  def __repr__(self):
5049  """__repr__(ChainStatisticsOptimizerState self) -> std::string"""
5050  return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
5051 
5052 
5053  @staticmethod
5054  def get_from(o):
5055  return _object_cast_to_ChainStatisticsOptimizerState(o)
5056 
5057 ChainStatisticsOptimizerState_swigregister = _IMP_npctransport.ChainStatisticsOptimizerState_swigregister
5058 ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
5059 
5060 class BipartitePairsStatisticsOptimizerState(IMP.OptimizerState):
5061  """Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class"""
5062  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5063 
5064  def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
5065  """
5066  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0, double slack=1.0) -> BipartitePairsStatisticsOptimizerState
5067  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0) -> BipartitePairsStatisticsOptimizerState
5068  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII) -> BipartitePairsStatisticsOptimizerState
5069  """
5070  this = _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack)
5071  try:
5072  self.this.append(this)
5073  except:
5074  self.this = this
5075 
5076  def get_interaction_type(self):
5077  """get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
5078  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
5079 
5080 
5081  def get_average_number_of_contacts(self):
5082  """get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
5083  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
5084 
5085 
5086  def get_average_off_per_contact_per_ns(self):
5087  """get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5088  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
5089 
5090 
5091  def get_average_off_per_bound_I_per_ns(self):
5092  """get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5093  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
5094 
5095 
5096  def get_average_off_per_bound_II_per_ns(self):
5097  """get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5098  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
5099 
5100 
5101  def get_average_on_per_missing_contact_per_ns(self):
5102  """get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5103  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
5104 
5105 
5106  def get_average_on_per_unbound_I_per_ns(self):
5107  """get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5108  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
5109 
5110 
5111  def get_average_on_per_unbound_II_per_ns(self):
5112  """get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5113  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
5114 
5115 
5116  def get_average_fraction_bound_particles_I(self):
5117  """get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
5118  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
5119 
5120 
5121  def get_average_fraction_bound_particles_II(self):
5122  """get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
5123  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
5124 
5125 
5126  def get_average_fraction_bound_particle_sites_I(self):
5127  """get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
5128  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
5129 
5130 
5131  def get_average_fraction_bound_particle_sites_II(self):
5132  """get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
5133  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
5134 
5135 
5136  def get_average_fraction_nonspecific_interactions_I(self):
5137  """get_average_fraction_nonspecific_interactions_I(BipartitePairsStatisticsOptimizerState self) -> double"""
5138  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_I(self)
5139 
5140 
5141  def get_average_fraction_nonspecific_interactions_II(self):
5142  """get_average_fraction_nonspecific_interactions_II(BipartitePairsStatisticsOptimizerState self) -> double"""
5143  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_II(self)
5144 
5145 
5146  def get_number_of_particles_1(self):
5147  """get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
5148  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
5149 
5150 
5151  def get_number_of_particles_2(self):
5152  """get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
5153  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
5154 
5155 
5156  def get_misc_stats_period_ns(self):
5157  """get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5158  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
5159 
5160 
5161  def get_off_stats_period_ns(self):
5162  """get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5163  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
5164 
5165 
5166  def get_off_I_stats_period_ns(self):
5167  """get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5168  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
5169 
5170 
5171  def get_off_II_stats_period_ns(self):
5172  """get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5173  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
5174 
5175 
5176  def get_on_stats_period_ns(self):
5177  """get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5178  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
5179 
5180 
5181  def get_on_I_stats_period_ns(self):
5182  """get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5183  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
5184 
5185 
5186  def get_on_II_stats_period_ns(self):
5187  """get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
5188  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
5189 
5190 
5191  def get_version_info(self):
5192  """get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
5193  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
5194 
5195 
5196  def __str__(self):
5197  """__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
5198  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
5199 
5200 
5201  def __repr__(self):
5202  """__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
5203  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
5204 
5205 
5206  @staticmethod
5207  def get_from(o):
5208  return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
5209 
5210 BipartitePairsStatisticsOptimizerState_swigregister = _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister
5211 BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
5212 
5213 
5214 def get_close_pairs_range(*args):
5215  """
5216  get_close_pairs_range(double max_range, double max_range_factor) -> double
5217  get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
5218  """
5219  return _IMP_npctransport.get_close_pairs_range(*args)
5220 
5221 def get_time_step(*args):
5222  """
5223  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
5224  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
5225  get_time_step(double max_d_factor, double max_k, double min_radius, double min_range) -> double
5226  get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
5227  get_time_step(::npctransport_proto::Assignment const & config) -> double
5228  """
5229  return _IMP_npctransport.get_time_step(*args)
5230 
5231 def get_frames_from_ns(ns, time_step):
5232  """get_frames_from_ns(double ns, double time_step) -> int"""
5233  return _IMP_npctransport.get_frames_from_ns(ns, time_step)
5234 
5235 def get_number_of_frames(config, time_step):
5236  """get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
5237  return _IMP_npctransport.get_number_of_frames(config, time_step)
5238 
5239 def get_dump_interval_in_frames(config, time_step):
5240  """get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
5241  return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
5242 
5243 def get_statistics_interval_in_frames(assign, time_step, default_value_ns=0.1):
5244  """
5245  get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int
5246  get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
5247  """
5248  return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
5249 
5250 def get_output_statistics_interval_in_frames(assign, time_step, default_value_ns=1.0):
5251  """
5252  get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int
5253  get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
5254  """
5255  return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
5256 
5257 def initialize_positions(*args):
5258  """
5259  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False, bool are_fgs_pre_initialized=False)
5260  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False)
5261  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0)
5262  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False)
5263  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints)
5264  initialize_positions(SimulationData sd)
5265  """
5266  return _IMP_npctransport.initialize_positions(*args)
5267 class Avro2PBReader(object):
5268  """Proxy of C++ IMP::npctransport::Avro2PBReader class"""
5269  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
5270 
5271  def __init__(self, *args):
5272  """
5273  __init__(IMP::npctransport::Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
5274  __init__(IMP::npctransport::Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
5275  """
5276  this = _IMP_npctransport.new_Avro2PBReader(*args)
5277  try:
5278  self.this.append(this)
5279  except:
5280  self.this = this
5281  __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
5282  __del__ = lambda self: None
5283 
5284  def read_next(self):
5285  """read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
5286  return _IMP_npctransport.Avro2PBReader_read_next(self)
5287 
5288 
5289  def get_is_valid(self):
5290  """get_is_valid(Avro2PBReader self) -> bool"""
5291  return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
5292 
5293 
5294  def get_cur_file_name(self):
5295  """get_cur_file_name(Avro2PBReader self) -> std::string"""
5296  return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
5297 
5298 
5299  def show(self, *args):
5300  """
5301  show(Avro2PBReader self, _ostream out)
5302  show(Avro2PBReader self)
5303  """
5304  return _IMP_npctransport.Avro2PBReader_show(self, *args)
5305 
5306 
5307  def __str__(self):
5308  """__str__(Avro2PBReader self) -> std::string"""
5309  return _IMP_npctransport.Avro2PBReader___str__(self)
5310 
5311 
5312  def __repr__(self):
5313  """__repr__(Avro2PBReader self) -> std::string"""
5314  return _IMP_npctransport.Avro2PBReader___repr__(self)
5315 
5316 Avro2PBReader_swigregister = _IMP_npctransport.Avro2PBReader_swigregister
5317 Avro2PBReader_swigregister(Avro2PBReader)
5318 
5319 
5320 def get_optimizable_particles(particles):
5321  """get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
5322  return _IMP_npctransport.get_optimizable_particles(particles)
5323 
5324 def get_non_optimizable_particles(particles):
5325  """get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
5326  return _IMP_npctransport.get_non_optimizable_particles(particles)
5327 
5328 def get_particle_indexes(particles):
5329  """get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
5330  return _IMP_npctransport.get_particle_indexes(particles)
5331 
5332 def get_protobuf_configuration_from_text(config_txt, config_pb):
5333  """get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
5334  return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
5335 
5336 def get_spheres_from_vectors(vs, radius):
5337  """get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
5338  return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
5339 
5340 def get_spheres_centers(spheres):
5341  """get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
5342  return _IMP_npctransport.get_spheres_centers(spheres)
5343 
5344 def copy_particle_reference_frame_if_applicable(src_p, trg_p):
5345  """copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
5346  return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
5347 
5348 def copy_hierarchy_reference_frame_recursive(src_p, trg_p):
5349  """copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
5350  return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
5351 
5352 def copy_FGs_coordinates(src_sd, trg_sd):
5353  """copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
5354  return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
5355 
5356 try:
5357  from .npctransport_pb2 import *
5358  import google.protobuf
5359 except ImportError:
5360  print("no protobuf support in python")
5361 from ._configuration import *
5362 
5363 
5364 def get_module_version():
5365  """get_module_version() -> std::string const"""
5366  return _IMP_npctransport.get_module_version()
5367 
5368 def get_example_path(fname):
5369  """get_example_path(std::string fname) -> std::string"""
5370  return _IMP_npctransport.get_example_path(fname)
5371 
5372 def get_data_path(fname):
5373  """get_data_path(std::string fname) -> std::string"""
5374  return _IMP_npctransport.get_data_path(fname)
5375 
5376 from . import _version_check
5377 _version_check.check_version(get_module_version())
5378 __version__ = get_module_version()
5379 
5380 
5381 
IMP::PairScore
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:42
IMP::get_check_level
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:80
IMP::npctransport::create_fg_chain
FGChain * create_fg_chain(IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)
IMP::modeller::get_example_path
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
IMP::npctransport::add_hierarchy_with_sites
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
IMP::container
Various classes to hold sets of particles.
IMP::npctransport::assign_ranges
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)
IMP::display::Geometry
The base class for geometry.
Definition: declare_Geometry.h:26
IMP::npctransport::get_output_statistics_interval_in_frames
int get_output_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)
IMP::npctransport::make_unordered_particle_index_pair
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
Definition: typedefs.h:45
IMP::display::SingletonsGeometry
A base class for geometry from a set of particles.
Definition: particle_geometry.h:50
IMP::npctransport::get_time_step
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)
IMP::cgal
Make CGAL functionality available to IMP.
IMP::npctransport::copy_FGs_coordinates
void copy_FGs_coordinates(SimulationData const *src_sd, SimulationData *trg_sd)
copy coordinates of src_sd to trg_sd for FG repeats only
IMP::modeller::get_module_version
std::string get_module_version()
Return the version of this module, as a string.
Definition: EMageFit/__init__.py:5
IMP::modeller::get_data_path
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
IMP::npctransport::get_statistics_interval_in_frames
int get_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)
IMP::npctransport::get_protobuf_configuration_from_text
void get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)
IMP::npctransport::copy_hierarchy_reference_frame_recursive
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
IMP::atom::BrownianDynamicsTAMD
Simple Brownian dynamics simulator.
Definition: BrownianDynamicsTAMD.h:72
IMP::score_functor
Composable functors to implement scores via compile-time composition.
IMP::statistics
Code to compute statistical measures.
IMP::npctransport::link_hierarchies_with_sites
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
IMP::npctransport::get_non_optimizable_particles
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
IMP::npctransport::copy_particle_reference_frame_if_applicable
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
IMP::Object
Common base class for heavy weight IMP objects.
Definition: Object.h:106
IMP::npctransport::get_particle_indexes
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
IMP::npctransport::get_number_of_frames
int get_number_of_frames(const ::npctransport_proto::Assignment &config, double time_step)
IMP::SingletonScore
Abstract class for scoring object(s) of type ParticleIndex.
Definition: SingletonScore.h:42
IMP::npctransport::get_frames_from_ns
int get_frames_from_ns(double ns, double time_step)
IMP::em
Basic utilities for handling cryo-electron microscopy 3D density maps.
IMP::npctransport::initialize_positions
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)
IMP::Decorator
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
IMP::core::show
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
Definition: core/Hierarchy.h:411
IMP::npctransport::get_optimizable_particles
ParticlesTemp get_optimizable_particles(ParticlesTemp const &particles)
IMP::core
Basic functionality that is expected to be used by a wide variety of IMP users.
IMP::algebra
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
IMP::npctransport::get_dump_interval_in_frames
int get_dump_interval_in_frames(const ::npctransport_proto::Assignment &config, double time_step)
IMP::npctransport::create_hierarchies_with_sites
atom::Hierarchies create_hierarchies_with_sites(RMF::FileConstHandle fh, Model *m)
IMP::OptimizerState
Shared optimizer state that is invoked upon commitment of new coordinates.
Definition: OptimizerState.h:43
IMP::core::get_root
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
Definition: core/Hierarchy.h:550
IMP::npctransport::add_hierarchies_with_sites
void add_hierarchies_with_sites(RMF::FileHandle fh, const atom::Hierarchies &hs)
IMP::npctransport::make_unordered_interaction_type
InteractionType make_unordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
Definition: typedefs.h:35
IMP::atom::get_diffusion_coefficient
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
IMP::npctransport::get_fg_chain
FGChain * get_fg_chain(atom::Hierarchy root)
IMP::display
Output IMP model data in various file formats.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::benchmark
Support for developing and analyzing benchmarks of IMP code.
IMP::npctransport::make_ordered_interaction_type
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
IMP::rmf
Support for the RMF file format for storing hierarchical molecular data and markup.
IMP::saxs
Support for small angle X-ray scattering (SAXS) data.
IMP::set_check_level
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:72
IMP::core::XYZRGeometry
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:151
IMP::npctransport::add_test_sites
void add_test_sites(RMF::FileHandle fh, core::ParticleType t, double display_radius, algebra::Vector3Ds sites)
IMP::isd
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
IMP::npctransport::get_spheres_from_vectors
algebra::Sphere3Ds get_spheres_from_vectors(V3iter first, V3iter last, double radius)
convert vectors to spheres of passed radius
Definition: util.h:169