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IMP Reference Guide  2.10.0
The Integrative Modeling Platform
npctransport/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
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 # This wrapper is part of IMP,
8 # Copyright 2007-2018 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_npctransport')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_npctransport')
25  _IMP_npctransport = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_npctransport', [dirname(__file__)])
34  except ImportError:
35  import _IMP_npctransport
36  return _IMP_npctransport
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_npctransport', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_npctransport = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_npctransport
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_NPCTRANSPORT_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_NPCTRANSPORT_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_npctransport.delete_IMP_NPCTRANSPORT_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
126  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
132  incr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
133  """
134  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
140  decr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
141  """
142  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
152  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator"""
157  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
162  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
167  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
172  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
177  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
182  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
187  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
192  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
197  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
202  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator
208  __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_NPCTRANSPORT_SwigPyIterator_swigregister = _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_swigregister
215 IMP_NPCTRANSPORT_SwigPyIterator_swigregister(IMP_NPCTRANSPORT_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_npctransport.IMP_DEBUG
224 IMP_RELEASE = _IMP_npctransport.IMP_RELEASE
225 IMP_SILENT = _IMP_npctransport.IMP_SILENT
226 IMP_PROGRESS = _IMP_npctransport.IMP_PROGRESS
227 IMP_TERSE = _IMP_npctransport.IMP_TERSE
228 IMP_VERBOSE = _IMP_npctransport.IMP_VERBOSE
229 IMP_MEMORY = _IMP_npctransport.IMP_MEMORY
230 IMP_NONE = _IMP_npctransport.IMP_NONE
231 IMP_USAGE = _IMP_npctransport.IMP_USAGE
232 IMP_INTERNAL = _IMP_npctransport.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_npctransport.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_npctransport.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_npctransport._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_npctransport._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_npctransport.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_npctransport.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_npctransport.IMP_HAS_NOEXCEPT
288 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
289 import IMP
290 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
291 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
292 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
293 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
294 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
295 import IMP.benchmark
296 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
297 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
298 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
299 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
300 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
301 import IMP.cgal
302 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
303 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
304 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
305 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
306 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
307 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
308 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
309 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
310 import IMP.algebra
311 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
312 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
313 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
314 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
315 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
316 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
317 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
318 import IMP.display
319 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
320 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
322 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
323 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
324 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
325 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
326 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
327 import IMP.score_functor
328 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
329 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
330 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
331 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
332 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
333 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
335 import IMP.statistics
336 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
344 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
345 import IMP.core
346 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
347 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
348 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
349 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
350 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
351 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
352 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
353 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
354 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
355 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
356 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
357 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
358 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
359 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
361 import IMP.container
362 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
363 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
364 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
365 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
366 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
367 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
368 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
369 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
370 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
371 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
372 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
373 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
374 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
375 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
376 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
377 import IMP.atom
378 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
379 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
380 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
381 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
382 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
383 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
384 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
385 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
386 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
387 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
388 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
389 import IMP.rmf
390 import RMF
391 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
392 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
393 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
394 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
395 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
396 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
397 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
398 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
399 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
400 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
401 
402 _object_types.append("SitesPairScore")
403 
404 
405 def _object_cast_to_SitesPairScore(o):
406  """_object_cast_to_SitesPairScore(Object o) -> SitesPairScore"""
407  return _IMP_npctransport._object_cast_to_SitesPairScore(o)
408 
409 _object_types.append("Scoring")
410 
411 
412 def _object_cast_to_Scoring(o):
413  """_object_cast_to_Scoring(Object o) -> Scoring"""
414  return _IMP_npctransport._object_cast_to_Scoring(o)
415 
416 _object_types.append("BrownianDynamicsTAMDWithSlabSupport")
417 
418 
419 def _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o):
420  """_object_cast_to_BrownianDynamicsTAMDWithSlabSupport(Object o) -> BrownianDynamicsTAMDWithSlabSupport"""
421  return _IMP_npctransport._object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
422 
423 _object_types.append("Statistics")
424 
425 
426 def _object_cast_to_Statistics(o):
427  """_object_cast_to_Statistics(Object o) -> Statistics"""
428  return _IMP_npctransport._object_cast_to_Statistics(o)
429 
430 _object_types.append("SimulationData")
431 
432 
433 def _object_cast_to_SimulationData(o):
434  """_object_cast_to_SimulationData(Object o) -> SimulationData"""
435  return _IMP_npctransport._object_cast_to_SimulationData(o)
436 
437 _object_types.append("SitesGeometry")
438 
439 
440 def _object_cast_to_SitesGeometry(o):
441  """_object_cast_to_SitesGeometry(Object o) -> SitesGeometry"""
442  return _IMP_npctransport._object_cast_to_SitesGeometry(o)
443 
444 _object_types.append("TypedSitesGeometry")
445 
446 
447 def _object_cast_to_TypedSitesGeometry(o):
448  """_object_cast_to_TypedSitesGeometry(Object o) -> TypedSitesGeometry"""
449  return _IMP_npctransport._object_cast_to_TypedSitesGeometry(o)
450 
451 _object_types.append("SlabWithCylindricalPorePairScore")
452 
453 
454 def _object_cast_to_SlabWithCylindricalPorePairScore(o):
455  """_object_cast_to_SlabWithCylindricalPorePairScore(Object o) -> SlabWithCylindricalPorePairScore"""
456  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPorePairScore(o)
457 
458 _object_types.append("SlabWithToroidalPorePairScore")
459 
460 
461 def _object_cast_to_SlabWithToroidalPorePairScore(o):
462  """_object_cast_to_SlabWithToroidalPorePairScore(Object o) -> SlabWithToroidalPorePairScore"""
463  return _IMP_npctransport._object_cast_to_SlabWithToroidalPorePairScore(o)
464 
465 _object_types.append("PoreRadiusSingletonScore")
466 
467 
468 def _object_cast_to_PoreRadiusSingletonScore(o):
469  """_object_cast_to_PoreRadiusSingletonScore(Object o) -> PoreRadiusSingletonScore"""
470  return _IMP_npctransport._object_cast_to_PoreRadiusSingletonScore(o)
471 
472 _object_types.append("ExcludeZRangeSingletonScore")
473 
474 
475 def _object_cast_to_ExcludeZRangeSingletonScore(o):
476  """_object_cast_to_ExcludeZRangeSingletonScore(Object o) -> ExcludeZRangeSingletonScore"""
477  return _IMP_npctransport._object_cast_to_ExcludeZRangeSingletonScore(o)
478 
479 _object_types.append("ZBiasSingletonScore")
480 
481 
482 def _object_cast_to_ZBiasSingletonScore(o):
483  """_object_cast_to_ZBiasSingletonScore(Object o) -> ZBiasSingletonScore"""
484  return _IMP_npctransport._object_cast_to_ZBiasSingletonScore(o)
485 
486 _object_types.append("SlabWithCylindricalPoreWireGeometry")
487 
488 
489 def _object_cast_to_SlabWithCylindricalPoreWireGeometry(o):
490  """_object_cast_to_SlabWithCylindricalPoreWireGeometry(Object o) -> SlabWithCylindricalPoreWireGeometry"""
491  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
492 
493 _object_types.append("SlabWithCylindricalPoreSurfaceGeometry")
494 
495 
496 def _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o):
497  """_object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(Object o) -> SlabWithCylindricalPoreSurfaceGeometry"""
498  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
499 
500 _object_types.append("SlabWithToroidalPoreWireGeometry")
501 
502 
503 def _object_cast_to_SlabWithToroidalPoreWireGeometry(o):
504  """_object_cast_to_SlabWithToroidalPoreWireGeometry(Object o) -> SlabWithToroidalPoreWireGeometry"""
505  return _IMP_npctransport._object_cast_to_SlabWithToroidalPoreWireGeometry(o)
506 
507 _object_types.append("LinearSoftSpherePairScore")
508 
509 
510 def _object_cast_to_LinearSoftSpherePairScore(o):
511  """_object_cast_to_LinearSoftSpherePairScore(Object o) -> LinearSoftSpherePairScore"""
512  return _IMP_npctransport._object_cast_to_LinearSoftSpherePairScore(o)
513 
514 _object_types.append("FunctorLinearSoftSpherePairScore")
515 
516 
517 def _object_cast_to_FunctorLinearSoftSpherePairScore(o):
518  """_object_cast_to_FunctorLinearSoftSpherePairScore(Object o) -> FunctorLinearSoftSpherePairScore"""
519  return _IMP_npctransport._object_cast_to_FunctorLinearSoftSpherePairScore(o)
520 
521 _object_types.append("LinearInteractionPairScore")
522 
523 
524 def _object_cast_to_LinearInteractionPairScore(o):
525  """_object_cast_to_LinearInteractionPairScore(Object o) -> LinearInteractionPairScore"""
526  return _IMP_npctransport._object_cast_to_LinearInteractionPairScore(o)
527 
528 _object_types.append("FunctorLinearInteractionPairScore")
529 
530 
531 def _object_cast_to_FunctorLinearInteractionPairScore(o):
532  """_object_cast_to_FunctorLinearInteractionPairScore(Object o) -> FunctorLinearInteractionPairScore"""
533  return _IMP_npctransport._object_cast_to_FunctorLinearInteractionPairScore(o)
534 
535 _object_types.append("LinearWellPairScore")
536 
537 
538 def _object_cast_to_LinearWellPairScore(o):
539  """_object_cast_to_LinearWellPairScore(Object o) -> LinearWellPairScore"""
540  return _IMP_npctransport._object_cast_to_LinearWellPairScore(o)
541 
542 _object_types.append("HarmonicSpringSingletonScore")
543 
544 
545 def _object_cast_to_HarmonicSpringSingletonScore(o):
546  """_object_cast_to_HarmonicSpringSingletonScore(Object o) -> HarmonicSpringSingletonScore"""
547  return _IMP_npctransport._object_cast_to_HarmonicSpringSingletonScore(o)
548 
549 _object_types.append("HierarchyWithSitesSaveLink")
550 
551 
552 def _object_cast_to_HierarchyWithSitesSaveLink(o):
553  """_object_cast_to_HierarchyWithSitesSaveLink(Object o) -> HierarchyWithSitesSaveLink"""
554  return _IMP_npctransport._object_cast_to_HierarchyWithSitesSaveLink(o)
555 
556 _object_types.append("HierarchyWithSitesLoadLink")
557 
558 
559 def _object_cast_to_HierarchyWithSitesLoadLink(o):
560  """_object_cast_to_HierarchyWithSitesLoadLink(Object o) -> HierarchyWithSitesLoadLink"""
561  return _IMP_npctransport._object_cast_to_HierarchyWithSitesLoadLink(o)
562 
563 _object_types.append("ChainStatisticsOptimizerState")
564 
565 
566 def _object_cast_to_ChainStatisticsOptimizerState(o):
567  """_object_cast_to_ChainStatisticsOptimizerState(Object o) -> ChainStatisticsOptimizerState"""
568  return _IMP_npctransport._object_cast_to_ChainStatisticsOptimizerState(o)
569 
570 _object_types.append("BodyStatisticsOptimizerState")
571 
572 
573 def _object_cast_to_BodyStatisticsOptimizerState(o):
574  """_object_cast_to_BodyStatisticsOptimizerState(Object o) -> BodyStatisticsOptimizerState"""
575  return _IMP_npctransport._object_cast_to_BodyStatisticsOptimizerState(o)
576 
577 _object_types.append("BipartitePairsStatisticsOptimizerState")
578 
579 
580 def _object_cast_to_BipartitePairsStatisticsOptimizerState(o):
581  """_object_cast_to_BipartitePairsStatisticsOptimizerState(Object o) -> BipartitePairsStatisticsOptimizerState"""
582  return _IMP_npctransport._object_cast_to_BipartitePairsStatisticsOptimizerState(o)
583 
584 _object_types.append("ParticleTransportStatisticsOptimizerState")
585 
586 
587 def _object_cast_to_ParticleTransportStatisticsOptimizerState(o):
588  """_object_cast_to_ParticleTransportStatisticsOptimizerState(Object o) -> ParticleTransportStatisticsOptimizerState"""
589  return _IMP_npctransport._object_cast_to_ParticleTransportStatisticsOptimizerState(o)
590 
591 _object_types.append("FGChain")
592 
593 
594 def _object_cast_to_FGChain(o):
595  """_object_cast_to_FGChain(Object o) -> FGChain"""
596  return _IMP_npctransport._object_cast_to_FGChain(o)
597 
598 _object_types.append("ParticleFactory")
599 
600 
601 def _object_cast_to_ParticleFactory(o):
602  """_object_cast_to_ParticleFactory(Object o) -> ParticleFactory"""
603  return _IMP_npctransport._object_cast_to_ParticleFactory(o)
604 
605 Avro2PBReaders=list
606 _plural_types.append("Avro2PBReaders")
607 _value_types.append("Avro2PBReader")
608 
609 
610 SitesPairScoreParametersList=list
611 _plural_types.append("SitesPairScoreParametersList")
612 _value_types.append("SitesPairScoreParameters")
613 
614 
615 def Transportings(l=[]):
616  return [Transporting(x) for x in l]
617 _plural_types.append("Transportings")
618 
619 
620 _value_types.append("Transporting")
621 
622 
623 def SlabWithPores(l=[]):
624  return [SlabWithPore(x) for x in l]
625 _plural_types.append("SlabWithPores")
626 
627 
628 _value_types.append("SlabWithPore")
629 
630 
631 def SlabWithCylindricalPores(l=[]):
632  return [SlabWithCylindricalPore(x) for x in l]
633 _plural_types.append("SlabWithCylindricalPores")
634 
635 
636 _value_types.append("SlabWithCylindricalPore")
637 
638 
639 def RelaxingSprings(l=[]):
640  return [RelaxingSpring(x) for x in l]
641 _plural_types.append("RelaxingSprings")
642 
643 
644 _value_types.append("RelaxingSpring")
645 
646 
647 def SlabWithToroidalPores(l=[]):
648  return [SlabWithToroidalPore(x) for x in l]
649 _plural_types.append("SlabWithToroidalPores")
650 
651 
652 _value_types.append("SlabWithToroidalPore")
653 
654 class _DoubleParameter(object):
655  """Proxy of C++ IMP::npctransport::Parameter<(double)> class."""
656 
657  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
658  __repr__ = _swig_repr
659 
660  def __init__(self, *args):
661  """
662  __init__(IMP::npctransport::Parameter<(double)> self) -> _DoubleParameter
663  __init__(IMP::npctransport::Parameter<(double)> self, double t) -> _DoubleParameter
664  """
665  this = _IMP_npctransport.new__DoubleParameter(*args)
666  try:
667  self.this.append(this)
668  except __builtin__.Exception:
669  self.this = this
670 
671  def get_value(self):
672  """get_value(_DoubleParameter self) -> double"""
673  return _IMP_npctransport._DoubleParameter_get_value(self)
674 
675 
676  def is_init(self):
677  """is_init(_DoubleParameter self) -> bool"""
678  return _IMP_npctransport._DoubleParameter_is_init(self)
679 
680  __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
681  __del__ = lambda self: None
682 _DoubleParameter_swigregister = _IMP_npctransport._DoubleParameter_swigregister
683 _DoubleParameter_swigregister(_DoubleParameter)
684 
685 class _IntParameter(object):
686  """Proxy of C++ IMP::npctransport::Parameter<(int)> class."""
687 
688  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
689  __repr__ = _swig_repr
690 
691  def __init__(self, *args):
692  """
693  __init__(IMP::npctransport::Parameter<(int)> self) -> _IntParameter
694  __init__(IMP::npctransport::Parameter<(int)> self, int t) -> _IntParameter
695  """
696  this = _IMP_npctransport.new__IntParameter(*args)
697  try:
698  self.this.append(this)
699  except __builtin__.Exception:
700  self.this = this
701 
702  def get_value(self):
703  """get_value(_IntParameter self) -> int"""
704  return _IMP_npctransport._IntParameter_get_value(self)
705 
706 
707  def is_init(self):
708  """is_init(_IntParameter self) -> bool"""
709  return _IMP_npctransport._IntParameter_is_init(self)
710 
711  __swig_destroy__ = _IMP_npctransport.delete__IntParameter
712  __del__ = lambda self: None
713 _IntParameter_swigregister = _IMP_npctransport._IntParameter_swigregister
714 _IntParameter_swigregister(_IntParameter)
715 
716 class _BoolParameter(object):
717  """Proxy of C++ IMP::npctransport::Parameter<(bool)> class."""
718 
719  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
720  __repr__ = _swig_repr
721 
722  def __init__(self, *args):
723  """
724  __init__(IMP::npctransport::Parameter<(bool)> self) -> _BoolParameter
725  __init__(IMP::npctransport::Parameter<(bool)> self, bool t) -> _BoolParameter
726  """
727  this = _IMP_npctransport.new__BoolParameter(*args)
728  try:
729  self.this.append(this)
730  except __builtin__.Exception:
731  self.this = this
732 
733  def get_value(self):
734  """get_value(_BoolParameter self) -> bool"""
735  return _IMP_npctransport._BoolParameter_get_value(self)
736 
737 
738  def is_init(self):
739  """is_init(_BoolParameter self) -> bool"""
740  return _IMP_npctransport._BoolParameter_is_init(self)
741 
742  __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
743  __del__ = lambda self: None
744 _BoolParameter_swigregister = _IMP_npctransport._BoolParameter_swigregister
745 _BoolParameter_swigregister(_BoolParameter)
746 
747 
749  """make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
750  return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
751 
753  """make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
754  return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
755 
757  """
758  make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
759  make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
760  """
761  return _IMP_npctransport.make_unordered_particle_index_pair(*args)
762 class LinearSoftSpherePairScore(IMP.PairScore):
763  """Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class."""
764 
765  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
766 
767  def __init__(self, *args):
768  """
769  __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k, std::string name) -> LinearSoftSpherePairScore
770  __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k) -> LinearSoftSpherePairScore
771  """
772  this = _IMP_npctransport.new_LinearSoftSpherePairScore(*args)
773  try:
774  self.this.append(this)
775  except __builtin__.Exception:
776  self.this = this
777 
778  def do_get_inputs(self, m, pis):
779  """do_get_inputs(LinearSoftSpherePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
780  return _IMP_npctransport.LinearSoftSpherePairScore_do_get_inputs(self, m, pis)
781 
782 
783  def get_k(self):
784  """get_k(LinearSoftSpherePairScore self) -> double"""
785  return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
786 
787 
788  def get_version_info(self):
789  """get_version_info(LinearSoftSpherePairScore self) -> VersionInfo"""
790  return _IMP_npctransport.LinearSoftSpherePairScore_get_version_info(self)
791 
792 
793  def __str__(self):
794  """__str__(LinearSoftSpherePairScore self) -> std::string"""
795  return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
796 
797 
798  def __repr__(self):
799  """__repr__(LinearSoftSpherePairScore self) -> std::string"""
800  return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
801 
802 
803  @staticmethod
804  def get_from(o):
805  return _object_cast_to_LinearSoftSpherePairScore(o)
806 
807 LinearSoftSpherePairScore_swigregister = _IMP_npctransport.LinearSoftSpherePairScore_swigregister
808 LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
809 
810 class LinearInteractionPairScore(IMP.PairScore):
811  """Proxy of C++ IMP::npctransport::LinearInteractionPairScore class."""
812 
813  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
814 
815  def __init__(self, *args):
816  """
817  __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr, std::string name) -> LinearInteractionPairScore
818  __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr) -> LinearInteractionPairScore
819  """
820  this = _IMP_npctransport.new_LinearInteractionPairScore(*args)
821  try:
822  self.this.append(this)
823  except __builtin__.Exception:
824  self.this = this
825 
826  def evaluate_if_good_index(self, *args):
827  """
828  evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPair const & p, DerivativeAccumulator da, double max) -> double
829  evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound) -> double
830  """
831  return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
832 
833 
834  def do_get_inputs(self, m, pis):
835  """do_get_inputs(LinearInteractionPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
836  return _IMP_npctransport.LinearInteractionPairScore_do_get_inputs(self, m, pis)
837 
838 
839  def get_range_attraction(self):
840  """get_range_attraction(LinearInteractionPairScore self) -> double"""
841  return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
842 
843 
844  def get_k_attraction(self):
845  """get_k_attraction(LinearInteractionPairScore self) -> double"""
846  return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
847 
848 
849  def set_k_attraction(self, k_attr):
850  """set_k_attraction(LinearInteractionPairScore self, double k_attr)"""
851  return _IMP_npctransport.LinearInteractionPairScore_set_k_attraction(self, k_attr)
852 
853 
854  def get_k_repulsion(self):
855  """get_k_repulsion(LinearInteractionPairScore self) -> double"""
856  return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
857 
858 
859  def set_k_repulsion(self, k_rep):
860  """set_k_repulsion(LinearInteractionPairScore self, double k_rep)"""
861  return _IMP_npctransport.LinearInteractionPairScore_set_k_repulsion(self, k_rep)
862 
863 
864  def get_version_info(self):
865  """get_version_info(LinearInteractionPairScore self) -> VersionInfo"""
866  return _IMP_npctransport.LinearInteractionPairScore_get_version_info(self)
867 
868 
869  def __str__(self):
870  """__str__(LinearInteractionPairScore self) -> std::string"""
871  return _IMP_npctransport.LinearInteractionPairScore___str__(self)
872 
873 
874  def __repr__(self):
875  """__repr__(LinearInteractionPairScore self) -> std::string"""
876  return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
877 
878 
879  @staticmethod
880  def get_from(o):
881  return _object_cast_to_LinearInteractionPairScore(o)
882 
883 LinearInteractionPairScore_swigregister = _IMP_npctransport.LinearInteractionPairScore_swigregister
884 LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
885 
886 class LinearWellPairScore(IMP.PairScore):
887  """Proxy of C++ IMP::npctransport::LinearWellPairScore class."""
888 
889  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
890 
891  def __init__(self, *args):
892  """
893  __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k, std::string name) -> LinearWellPairScore
894  __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k) -> LinearWellPairScore
895  """
896  this = _IMP_npctransport.new_LinearWellPairScore(*args)
897  try:
898  self.this.append(this)
899  except __builtin__.Exception:
900  self.this = this
901 
902  def set_rest_length_factor(self, rest_length_factor):
903  """set_rest_length_factor(LinearWellPairScore self, double rest_length_factor)"""
904  return _IMP_npctransport.LinearWellPairScore_set_rest_length_factor(self, rest_length_factor)
905 
906 
907  def get_rest_length_factor(self):
908  """get_rest_length_factor(LinearWellPairScore self) -> double"""
909  return _IMP_npctransport.LinearWellPairScore_get_rest_length_factor(self)
910 
911 
912  def set_k(self, k):
913  """set_k(LinearWellPairScore self, double k)"""
914  return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
915 
916 
917  def get_k(self):
918  """get_k(LinearWellPairScore self) -> double"""
919  return _IMP_npctransport.LinearWellPairScore_get_k(self)
920 
921 
922  def do_get_inputs(self, m, pis):
923  """do_get_inputs(LinearWellPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
924  return _IMP_npctransport.LinearWellPairScore_do_get_inputs(self, m, pis)
925 
926 
927  def get_version_info(self):
928  """get_version_info(LinearWellPairScore self) -> VersionInfo"""
929  return _IMP_npctransport.LinearWellPairScore_get_version_info(self)
930 
931 
932  def __str__(self):
933  """__str__(LinearWellPairScore self) -> std::string"""
934  return _IMP_npctransport.LinearWellPairScore___str__(self)
935 
936 
937  def __repr__(self):
938  """__repr__(LinearWellPairScore self) -> std::string"""
939  return _IMP_npctransport.LinearWellPairScore___repr__(self)
940 
941 
942  @staticmethod
943  def get_from(o):
944  return _object_cast_to_LinearWellPairScore(o)
945 
946 LinearWellPairScore_swigregister = _IMP_npctransport.LinearWellPairScore_swigregister
947 LinearWellPairScore_swigregister(LinearWellPairScore)
948 
949 class RelaxingSpring(IMP.Decorator):
950  """Proxy of C++ IMP::npctransport::RelaxingSpring class."""
951 
952  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
953 
954  def __init__(self, *args):
955  """
956  __init__(IMP::npctransport::RelaxingSpring self) -> RelaxingSpring
957  __init__(IMP::npctransport::RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
958  __init__(IMP::npctransport::RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
959  """
960  this = _IMP_npctransport.new_RelaxingSpring(*args)
961  try:
962  self.this.append(this)
963  except __builtin__.Exception:
964  self.this = this
965 
966  def show(self, *args):
967  """
968  show(RelaxingSpring self, _ostream out)
969  show(RelaxingSpring self)
970  """
971  return _IMP_npctransport.RelaxingSpring_show(self, *args)
972 
973 
974  def setup_particle(*args):
975  """
976  setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
977  setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
978  """
979  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
980 
981  setup_particle = staticmethod(setup_particle)
982 
983  def get_is_setup(*args):
984  """
985  get_is_setup(_ParticleAdaptor p) -> bool
986  get_is_setup(Model m, ParticleIndex pi) -> bool
987  """
988  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
989 
990  get_is_setup = staticmethod(get_is_setup)
991 
992  def get_bonded_particle_0_key():
993  """get_bonded_particle_0_key() -> ParticleIndexKey"""
994  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
995 
996  get_bonded_particle_0_key = staticmethod(get_bonded_particle_0_key)
997 
998  def get_bonded_particle_1_key():
999  """get_bonded_particle_1_key() -> ParticleIndexKey"""
1000  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1001 
1002  get_bonded_particle_1_key = staticmethod(get_bonded_particle_1_key)
1003 
1004  def get_equilibrium_rest_length_factor_key():
1005  """get_equilibrium_rest_length_factor_key() -> FloatKey"""
1006  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1007 
1008  get_equilibrium_rest_length_factor_key = staticmethod(get_equilibrium_rest_length_factor_key)
1009 
1010  def get_rest_length_key():
1011  """get_rest_length_key() -> FloatKey"""
1012  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1013 
1014  get_rest_length_key = staticmethod(get_rest_length_key)
1015 
1016  def get_rest_length_diffusion_coefficient_key():
1017  """get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1018  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1019 
1020  get_rest_length_diffusion_coefficient_key = staticmethod(get_rest_length_diffusion_coefficient_key)
1021 
1022  def get_bonded_particle_0(self):
1023  """get_bonded_particle_0(RelaxingSpring self) -> Particle"""
1024  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0(self)
1025 
1026 
1027  def get_bonded_particle_1(self):
1028  """get_bonded_particle_1(RelaxingSpring self) -> Particle"""
1029  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1(self)
1030 
1031 
1032  def get_bonded_particle_index_0(self):
1033  """get_bonded_particle_index_0(RelaxingSpring self) -> ParticleIndex"""
1034  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_0(self)
1035 
1036 
1037  def get_bonded_particle_index_1(self):
1038  """get_bonded_particle_index_1(RelaxingSpring self) -> ParticleIndex"""
1039  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_1(self)
1040 
1041 
1042  def get_equilibrium_rest_length_factor(self):
1043  """get_equilibrium_rest_length_factor(RelaxingSpring self) -> IMP::Float"""
1044  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor(self)
1045 
1046 
1047  def set_equilibrium_rest_length_factor(self, t):
1048  """set_equilibrium_rest_length_factor(RelaxingSpring self, IMP::Float t)"""
1049  return _IMP_npctransport.RelaxingSpring_set_equilibrium_rest_length_factor(self, t)
1050 
1051 
1052  def get_rest_length(self):
1053  """get_rest_length(RelaxingSpring self) -> IMP::Float"""
1054  return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1055 
1056 
1057  def set_rest_length(self, t):
1058  """set_rest_length(RelaxingSpring self, IMP::Float t)"""
1059  return _IMP_npctransport.RelaxingSpring_set_rest_length(self, t)
1060 
1061 
1062  def get_rest_length_diffusion_coefficient(self):
1063  """get_rest_length_diffusion_coefficient(RelaxingSpring self) -> IMP::Float"""
1064  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient(self)
1065 
1066 
1067  def set_rest_length_diffusion_coefficient(self, t):
1068  """set_rest_length_diffusion_coefficient(RelaxingSpring self, IMP::Float t)"""
1069  return _IMP_npctransport.RelaxingSpring_set_rest_length_diffusion_coefficient(self, t)
1070 
1071 
1072  def add_to_rest_length_derivative(self, d, da):
1073  """add_to_rest_length_derivative(RelaxingSpring self, double d, DerivativeAccumulator da)"""
1074  return _IMP_npctransport.RelaxingSpring_add_to_rest_length_derivative(self, d, da)
1075 
1076 
1077  def get_rest_length_derivative(self):
1078  """get_rest_length_derivative(RelaxingSpring self) -> double"""
1079  return _IMP_npctransport.RelaxingSpring_get_rest_length_derivative(self)
1080 
1081 
1082  def add_attribute(self, *args):
1083  """
1084  add_attribute(RelaxingSpring self, FloatKey k, IMP::Float v, bool opt)
1085  add_attribute(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1086  add_attribute(RelaxingSpring self, IntKey a0, IMP::Int a1)
1087  add_attribute(RelaxingSpring self, StringKey a0, IMP::String a1)
1088  add_attribute(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1089  add_attribute(RelaxingSpring self, ObjectKey a0, Object a1)
1090  """
1091  return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1092 
1093 
1094  def get_value(self, *args):
1095  """
1096  get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1097  get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1098  get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1099  get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1100  get_value(RelaxingSpring self, ObjectKey a0) -> Object
1101  """
1102  return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1103 
1104 
1105  def set_value(self, *args):
1106  """
1107  set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1108  set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1109  set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1110  set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1111  set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1112  """
1113  return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1114 
1115 
1116  def remove_attribute(self, *args):
1117  """
1118  remove_attribute(RelaxingSpring self, FloatKey a0)
1119  remove_attribute(RelaxingSpring self, IntKey a0)
1120  remove_attribute(RelaxingSpring self, StringKey a0)
1121  remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1122  remove_attribute(RelaxingSpring self, ObjectKey a0)
1123  """
1124  return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1125 
1126 
1127  def has_attribute(self, *args):
1128  """
1129  has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1130  has_attribute(RelaxingSpring self, IntKey a0) -> bool
1131  has_attribute(RelaxingSpring self, StringKey a0) -> bool
1132  has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1133  has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1134  """
1135  return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1136 
1137 
1138  def get_derivative(self, a0):
1139  """get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1140  return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1141 
1142 
1143  def get_name(self):
1144  """get_name(RelaxingSpring self) -> std::string"""
1145  return _IMP_npctransport.RelaxingSpring_get_name(self)
1146 
1147 
1148  def clear_caches(self):
1149  """clear_caches(RelaxingSpring self)"""
1150  return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1151 
1152 
1153  def set_name(self, a0):
1154  """set_name(RelaxingSpring self, std::string a0)"""
1155  return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1156 
1157 
1158  def set_check_level(self, a0):
1159  """set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1160  return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1161 
1162 
1163  def add_to_derivative(self, a0, a1, a2):
1164  """add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1165  return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1166 
1167 
1168  def set_is_optimized(self, a0, a1):
1169  """set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1170  return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1171 
1172 
1173  def get_is_optimized(self, a0):
1174  """get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1175  return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1176 
1177 
1178  def get_check_level(self):
1179  """get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1180  return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1181 
1182 
1183  def __eq__(self, *args):
1184  """
1185  __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1186  __eq__(RelaxingSpring self, Particle d) -> bool
1187  """
1188  return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1189 
1190 
1191  def __ne__(self, *args):
1192  """
1193  __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1194  __ne__(RelaxingSpring self, Particle d) -> bool
1195  """
1196  return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1197 
1198 
1199  def __le__(self, *args):
1200  """
1201  __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1202  __le__(RelaxingSpring self, Particle d) -> bool
1203  """
1204  return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1205 
1206 
1207  def __lt__(self, *args):
1208  """
1209  __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1210  __lt__(RelaxingSpring self, Particle d) -> bool
1211  """
1212  return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1213 
1214 
1215  def __ge__(self, *args):
1216  """
1217  __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1218  __ge__(RelaxingSpring self, Particle d) -> bool
1219  """
1220  return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1221 
1222 
1223  def __gt__(self, *args):
1224  """
1225  __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1226  __gt__(RelaxingSpring self, Particle d) -> bool
1227  """
1228  return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1229 
1230 
1231  def __hash__(self):
1232  """__hash__(RelaxingSpring self) -> std::size_t"""
1233  return _IMP_npctransport.RelaxingSpring___hash__(self)
1234 
1235 
1236  def __str__(self):
1237  """__str__(RelaxingSpring self) -> std::string"""
1238  return _IMP_npctransport.RelaxingSpring___str__(self)
1239 
1240 
1241  def __repr__(self):
1242  """__repr__(RelaxingSpring self) -> std::string"""
1243  return _IMP_npctransport.RelaxingSpring___repr__(self)
1244 
1245  __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1246  __del__ = lambda self: None
1247 RelaxingSpring_swigregister = _IMP_npctransport.RelaxingSpring_swigregister
1248 RelaxingSpring_swigregister(RelaxingSpring)
1249 
1250 def RelaxingSpring_setup_particle(*args):
1251  """
1252  setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1253  RelaxingSpring_setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1254  """
1255  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1256 
1257 def RelaxingSpring_get_is_setup(*args):
1258  """
1259  get_is_setup(_ParticleAdaptor p) -> bool
1260  RelaxingSpring_get_is_setup(Model m, ParticleIndex pi) -> bool
1261  """
1262  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1263 
1264 def RelaxingSpring_get_bonded_particle_0_key():
1265  """RelaxingSpring_get_bonded_particle_0_key() -> ParticleIndexKey"""
1266  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1267 
1268 def RelaxingSpring_get_bonded_particle_1_key():
1269  """RelaxingSpring_get_bonded_particle_1_key() -> ParticleIndexKey"""
1270  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1271 
1272 def RelaxingSpring_get_equilibrium_rest_length_factor_key():
1273  """RelaxingSpring_get_equilibrium_rest_length_factor_key() -> FloatKey"""
1274  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1275 
1276 def RelaxingSpring_get_rest_length_key():
1277  """RelaxingSpring_get_rest_length_key() -> FloatKey"""
1278  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1279 
1280 def RelaxingSpring_get_rest_length_diffusion_coefficient_key():
1281  """RelaxingSpring_get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1282  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1283 
1284 class HarmonicSpringSingletonScore(IMP.SingletonScore):
1285  """Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1286 
1287  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1288 
1289  def __init__(self, *args):
1290  """
1291  __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2, std::string name) -> HarmonicSpringSingletonScore
1292  __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2) -> HarmonicSpringSingletonScore
1293  """
1294  this = _IMP_npctransport.new_HarmonicSpringSingletonScore(*args)
1295  try:
1296  self.this.append(this)
1297  except __builtin__.Exception:
1298  self.this = this
1299 
1300  def set_k1(self, k1):
1301  """set_k1(HarmonicSpringSingletonScore self, double k1)"""
1302  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1303 
1304 
1305  def get_k1(self):
1306  """get_k1(HarmonicSpringSingletonScore self) -> double"""
1307  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1308 
1309 
1310  def set_k2(self, k2):
1311  """set_k2(HarmonicSpringSingletonScore self, double k2)"""
1312  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1313 
1314 
1315  def get_k2(self):
1316  """get_k2(HarmonicSpringSingletonScore self) -> double"""
1317  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1318 
1319 
1320  def do_get_inputs(self, m, pis):
1321  """do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1322  return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1323 
1324 
1325  def get_version_info(self):
1326  """get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1327  return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1328 
1329 
1330  def __str__(self):
1331  """__str__(HarmonicSpringSingletonScore self) -> std::string"""
1332  return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1333 
1334 
1335  def __repr__(self):
1336  """__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1337  return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1338 
1339 
1340  @staticmethod
1341  def get_from(o):
1342  return _object_cast_to_HarmonicSpringSingletonScore(o)
1343 
1344 HarmonicSpringSingletonScore_swigregister = _IMP_npctransport.HarmonicSpringSingletonScore_swigregister
1345 HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1346 
1347 class LinearInteraction(object):
1348  """Proxy of C++ IMP::npctransport::LinearInteraction class."""
1349 
1350  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1351  __repr__ = _swig_repr
1352 
1353  def __init__(self, krep, attr_range, kattr):
1354  """__init__(IMP::npctransport::LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction"""
1355  this = _IMP_npctransport.new_LinearInteraction(krep, attr_range, kattr)
1356  try:
1357  self.this.append(this)
1358  except __builtin__.Exception:
1359  self.this = this
1360 
1361  def show(self, *args):
1362  """
1363  show(LinearInteraction self, _ostream out)
1364  show(LinearInteraction self)
1365  """
1366  return _IMP_npctransport.LinearInteraction_show(self, *args)
1367 
1368  __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1369  __del__ = lambda self: None
1370 LinearInteraction_swigregister = _IMP_npctransport.LinearInteraction_swigregister
1371 LinearInteraction_swigregister(LinearInteraction)
1372 
1373 class _DistancePairScoreForLinearSoftSphere(IMP.PairScore):
1374  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> class."""
1375 
1376  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1377  __repr__ = _swig_repr
1378 
1379  def __init__(self, *args):
1380  """
1381  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearSoftSphere
1382  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0) -> _DistancePairScoreForLinearSoftSphere
1383  """
1384  this = _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args)
1385  try:
1386  self.this.append(this)
1387  except __builtin__.Exception:
1388  self.this = this
1389 
1390  def do_get_inputs(self, m, pis):
1391  """do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1392  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1393 
1394 
1395  def get_score_functor(self):
1396  """get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1397  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1398 
1399 
1400  def get_version_info(self):
1401  """get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1402  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1403 
1404 _DistancePairScoreForLinearSoftSphere_swigregister = _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister
1405 _DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1406 
1407 class _DistancePairScoreForLinearInteraction(IMP.PairScore):
1408  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> class."""
1409 
1410  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1411  __repr__ = _swig_repr
1412 
1413  def __init__(self, *args):
1414  """
1415  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearInteraction
1416  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0) -> _DistancePairScoreForLinearInteraction
1417  """
1418  this = _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args)
1419  try:
1420  self.this.append(this)
1421  except __builtin__.Exception:
1422  self.this = this
1423 
1424  def do_get_inputs(self, m, pis):
1425  """do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1426  return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1427 
1428 
1429  def get_score_functor(self):
1430  """get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1431  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1432 
1433 
1434  def get_version_info(self):
1435  """get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1436  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1437 
1438 _DistancePairScoreForLinearInteraction_swigregister = _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister
1439 _DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1440 
1441 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1442  """Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1443 
1444  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1445 
1446  def __init__(self, *args):
1447  """
1448  __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k, std::string name) -> FunctorLinearSoftSpherePairScore
1449  __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k) -> FunctorLinearSoftSpherePairScore
1450  """
1451  this = _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args)
1452  try:
1453  self.this.append(this)
1454  except __builtin__.Exception:
1455  self.this = this
1456 
1457  def __str__(self):
1458  """__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1459  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1460 
1461 
1462  def __repr__(self):
1463  """__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1464  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1465 
1466 
1467  @staticmethod
1468  def get_from(o):
1469  return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1470 
1471 FunctorLinearSoftSpherePairScore_swigregister = _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister
1472 FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1473 
1474 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1475  """Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1476 
1477  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1478 
1479  def __init__(self, *args):
1480  """
1481  __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name) -> FunctorLinearInteractionPairScore
1482  __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr) -> FunctorLinearInteractionPairScore
1483  """
1484  this = _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args)
1485  try:
1486  self.this.append(this)
1487  except __builtin__.Exception:
1488  self.this = this
1489 
1490  def __str__(self):
1491  """__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1492  return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1493 
1494 
1495  def __repr__(self):
1496  """__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1497  return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1498 
1499 
1500  @staticmethod
1501  def get_from(o):
1502  return _object_cast_to_FunctorLinearInteractionPairScore(o)
1503 
1504 FunctorLinearInteractionPairScore_swigregister = _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister
1505 FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1506 
1507 class BrownianDynamicsTAMDWithSlabSupport(IMP.atom.BrownianDynamicsTAMD):
1508  """Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1509 
1510  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1511 
1512  def __init__(self, *args):
1513  """
1514  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport
1515  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name) -> BrownianDynamicsTAMDWithSlabSupport
1516  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m) -> BrownianDynamicsTAMDWithSlabSupport
1517  """
1518  this = _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args)
1519  try:
1520  self.this.append(this)
1521  except __builtin__.Exception:
1522  self.this = this
1523 
1524  def __str__(self):
1525  """__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1526  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1527 
1528 
1529  def __repr__(self):
1530  """__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1531  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1532 
1533 
1534  @staticmethod
1535  def get_from(o):
1536  return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1537 
1538  __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1539  __del__ = lambda self: None
1540 BrownianDynamicsTAMDWithSlabSupport_swigregister = _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister
1541 BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1542 
1543 class SitesPairScoreParameters(object):
1544  """Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1545 
1546  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1547  r = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set)
1548  k = _swig_property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set)
1549  r2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set)
1550  kr = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set)
1551  kr2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set)
1552  cosSigma1_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set)
1553  cosSigma2_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set)
1554  is_orientational = _swig_property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set)
1555 
1556  def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1557  """
1558  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters
1559  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0) -> SitesPairScoreParameters
1560  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient) -> SitesPairScoreParameters
1561  """
1562  this = _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg)
1563  try:
1564  self.this.append(this)
1565  except __builtin__.Exception:
1566  self.this = this
1567 
1568  def set_range(self, r):
1569  """set_range(SitesPairScoreParameters self, double r)"""
1570  return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1571 
1572 
1573  def set_force_coefficient(self, k):
1574  """set_force_coefficient(SitesPairScoreParameters self, double k)"""
1575  return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1576 
1577 
1578  def set_sigma1_max(self, sigma1_max_deg):
1579  """set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1580  return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1581 
1582 
1583  def set_sigma2_max(self, sigma2_max_deg):
1584  """set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1585  return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1586 
1587 
1588  def update_is_orientational(self):
1589  """update_is_orientational(SitesPairScoreParameters self)"""
1590  return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1591 
1592 
1593  def show(self, *args):
1594  """
1595  show(SitesPairScoreParameters self, _ostream out)
1596  show(SitesPairScoreParameters self)
1597  """
1598  return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1599 
1600 
1601  def __str__(self):
1602  """__str__(SitesPairScoreParameters self) -> std::string"""
1603  return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1604 
1605 
1606  def __repr__(self):
1607  """__repr__(SitesPairScoreParameters self) -> std::string"""
1608  return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1609 
1610  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1611  __del__ = lambda self: None
1612 SitesPairScoreParameters_swigregister = _IMP_npctransport.SitesPairScoreParameters_swigregister
1613 SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1614 
1615 class SitesGeometry(IMP.core.XYZRGeometry):
1616  """Proxy of C++ IMP::npctransport::SitesGeometry class."""
1617 
1618  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1619 
1620  def __init__(self, p, sites):
1621  """__init__(IMP::npctransport::SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1622  this = _IMP_npctransport.new_SitesGeometry(p, sites)
1623  try:
1624  self.this.append(this)
1625  except __builtin__.Exception:
1626  self.this = this
1627 
1628  def __str__(self):
1629  """__str__(SitesGeometry self) -> std::string"""
1630  return _IMP_npctransport.SitesGeometry___str__(self)
1631 
1632 
1633  def __repr__(self):
1634  """__repr__(SitesGeometry self) -> std::string"""
1635  return _IMP_npctransport.SitesGeometry___repr__(self)
1636 
1637 
1638  @staticmethod
1639  def get_from(o):
1640  return _object_cast_to_SitesGeometry(o)
1641 
1642 SitesGeometry_swigregister = _IMP_npctransport.SitesGeometry_swigregister
1643 SitesGeometry_swigregister(SitesGeometry)
1644 
1645 class TypedSitesGeometry(IMP.display.SingletonsGeometry):
1646  """Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1647 
1648  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1649 
1650  def __init__(self, sc):
1651  """__init__(IMP::npctransport::TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1652  this = _IMP_npctransport.new_TypedSitesGeometry(sc)
1653  try:
1654  self.this.append(this)
1655  except __builtin__.Exception:
1656  self.this = this
1657 
1658  def set_sites(self, t, s):
1659  """set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1660  return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1661 
1662 
1663  def get_version_info(self):
1664  """get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1665  return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1666 
1667 
1668  def __str__(self):
1669  """__str__(TypedSitesGeometry self) -> std::string"""
1670  return _IMP_npctransport.TypedSitesGeometry___str__(self)
1671 
1672 
1673  def __repr__(self):
1674  """__repr__(TypedSitesGeometry self) -> std::string"""
1675  return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1676 
1677 
1678  @staticmethod
1679  def get_from(o):
1680  return _object_cast_to_TypedSitesGeometry(o)
1681 
1682 TypedSitesGeometry_swigregister = _IMP_npctransport.TypedSitesGeometry_swigregister
1683 TypedSitesGeometry_swigregister(TypedSitesGeometry)
1684 
1685 class SitesPairScore(LinearInteractionPairScore):
1686  """Proxy of C++ IMP::npctransport::SitesPairScore class."""
1687 
1688  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1689 
1690  def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1691  """__init__(IMP::npctransport::SitesPairScore self, double range, double k, double sigma0_deg, double sigma1_deg, double range_nonspec_attraction, double k_nonspec_attraction, double k_nonspec_repulsion, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1) -> SitesPairScore"""
1692  this = _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1)
1693  try:
1694  self.this.append(this)
1695  except __builtin__.Exception:
1696  self.this = this
1697 
1698  def get_sites_range(self):
1699  """get_sites_range(SitesPairScore self) -> double"""
1700  return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1701 
1702 
1703  def get_sites_k(self):
1704  """get_sites_k(SitesPairScore self) -> double"""
1705  return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1706 
1707 
1708  def get_parameters(self):
1709  """get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1710  return _IMP_npctransport.SitesPairScore_get_parameters(self)
1711 
1712 
1713  def set_sites(self, sites0, sites1):
1714  """set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1715  return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1716 
1717 
1718  def set_sites0(self, sites0):
1719  """set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1720  return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1721 
1722 
1723  def set_sites1(self, sites1):
1724  """set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1725  return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1726 
1727 
1728  def __str__(self):
1729  """__str__(SitesPairScore self) -> std::string"""
1730  return _IMP_npctransport.SitesPairScore___str__(self)
1731 
1732 
1733  def __repr__(self):
1734  """__repr__(SitesPairScore self) -> std::string"""
1735  return _IMP_npctransport.SitesPairScore___repr__(self)
1736 
1737 
1738  @staticmethod
1739  def get_from(o):
1740  return _object_cast_to_SitesPairScore(o)
1741 
1742 SitesPairScore_swigregister = _IMP_npctransport.SitesPairScore_swigregister
1743 SitesPairScore_swigregister(SitesPairScore)
1744 
1745 class FGChain(IMP.Object):
1746  """Proxy of C++ IMP::npctransport::FGChain class."""
1747 
1748  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1749 
1750  def __init__(self, *args):
1751  """
1752  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name) -> FGChain
1753  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0) -> FGChain
1754  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0) -> FGChain
1755  __init__(IMP::npctransport::FGChain self, Particle root) -> FGChain
1756  """
1757  this = _IMP_npctransport.new_FGChain(*args)
1758  try:
1759  self.this.append(this)
1760  except __builtin__.Exception:
1761  self.this = this
1762 
1763  def get_root(self):
1764  """get_root(FGChain self) -> Hierarchy"""
1765  return _IMP_npctransport.FGChain_get_root(self)
1766 
1767 
1768  def get_beads(self):
1769  """get_beads(FGChain self) -> IMP::ParticlesTemp"""
1770  return _IMP_npctransport.FGChain_get_beads(self)
1771 
1772 
1773  def get_bead(self, i):
1774  """get_bead(FGChain self, unsigned int i) -> Particle"""
1775  return _IMP_npctransport.FGChain_get_bead(self, i)
1776 
1777 
1778  def get_bead_index(self, i):
1779  """get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1780  return _IMP_npctransport.FGChain_get_bead_index(self, i)
1781 
1782 
1783  def get_number_of_beads(self):
1784  """get_number_of_beads(FGChain self) -> unsigned int"""
1785  return _IMP_npctransport.FGChain_get_number_of_beads(self)
1786 
1787 
1788  def get_chain_restraints(self, scoring_manager):
1789  """get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1790  return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1791 
1792 
1793  def set_rest_length_factor(self, rlf):
1794  """set_rest_length_factor(FGChain self, double rlf)"""
1795  return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1796 
1797 
1798  def set_backbone_k(self, k):
1799  """set_backbone_k(FGChain self, double k)"""
1800  return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1801 
1802 
1803  def get_rest_length_factor(self):
1804  """get_rest_length_factor(FGChain self) -> double"""
1805  return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1806 
1807 
1808  def get_backbone_k(self):
1809  """get_backbone_k(FGChain self) -> double"""
1810  return _IMP_npctransport.FGChain_get_backbone_k(self)
1811 
1812 
1813  def get_version_info(self):
1814  """get_version_info(FGChain self) -> VersionInfo"""
1815  return _IMP_npctransport.FGChain_get_version_info(self)
1816 
1817 
1818  def __str__(self):
1819  """__str__(FGChain self) -> std::string"""
1820  return _IMP_npctransport.FGChain___str__(self)
1821 
1822 
1823  def __repr__(self):
1824  """__repr__(FGChain self) -> std::string"""
1825  return _IMP_npctransport.FGChain___repr__(self)
1826 
1827 
1828  @staticmethod
1829  def get_from(o):
1830  return _object_cast_to_FGChain(o)
1831 
1832 FGChain_swigregister = _IMP_npctransport.FGChain_swigregister
1833 FGChain_swigregister(FGChain)
1834 
1835 
1836 def create_fg_chain(sd, parent, fg_data, c):
1837  """create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1838  return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1839 
1840 def get_fg_chain(*args):
1841  """
1842  get_fg_chain(Hierarchy root) -> FGChain
1843  get_fg_chain(Particle p_root) -> FGChain
1844  """
1845  return _IMP_npctransport.get_fg_chain(*args)
1846 class Scoring(IMP.Object):
1847  """Proxy of C++ IMP::npctransport::Scoring class."""
1848 
1849  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1850 
1851  def __init__(self, owner_sd, data):
1852  """__init__(IMP::npctransport::Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1853  this = _IMP_npctransport.new_Scoring(owner_sd, data)
1854  try:
1855  self.this.append(this)
1856  except __builtin__.Exception:
1857  self.this = this
1858 
1859  def get_scoring_function(self, force_update=False):
1860  """
1861  get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction
1862  get_scoring_function(Scoring self) -> ScoringFunction
1863  """
1864  return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1865 
1866 
1867  def get_scoring_function_restraints(self, force_update=False):
1868  """
1869  get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints
1870  get_scoring_function_restraints(Scoring self) -> IMP::Restraints
1871  """
1872  return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1873 
1874 
1875  def get_custom_scoring_function(self, *args):
1876  """
1877  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1878  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1879  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1880  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1881  """
1882  return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1883 
1884 
1885  def get_close_beads_container(self, update=False):
1886  """
1887  get_close_beads_container(Scoring self, bool update=False) -> PairContainer
1888  get_close_beads_container(Scoring self) -> PairContainer
1889  """
1890  return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1891 
1892 
1893  def get_predicates_pair_restraint(self, update=False):
1894  """
1895  get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint
1896  get_predicates_pair_restraint(Scoring self) -> PredicatePairsRestraint
1897  """
1898  return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1899 
1900 
1901  def get_bounding_box_restraint(self, update=False):
1902  """
1903  get_bounding_box_restraint(Scoring self, bool update=False) -> Restraint
1904  get_bounding_box_restraint(Scoring self) -> Restraint
1905  """
1906  return _IMP_npctransport.Scoring_get_bounding_box_restraint(self, update)
1907 
1908 
1909  def get_slab_restraint(self, update=False):
1910  """
1911  get_slab_restraint(Scoring self, bool update=False) -> Restraint
1912  get_slab_restraint(Scoring self) -> Restraint
1913  """
1914  return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1915 
1916 
1917  def add_interaction(self, idata):
1918  """add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1919  return _IMP_npctransport.Scoring_add_interaction(self, idata)
1920 
1921 
1922  def create_close_beads_container(self, *args):
1923  """
1924  create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1925  create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1926  """
1927  return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
1928 
1929 
1930  def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
1931  """
1932  create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint
1933  create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs) -> PredicatePairsRestraint
1934  """
1935  return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
1936 
1937 
1938  def create_bounding_box_restraint(self, beads):
1939  """create_bounding_box_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1940  return _IMP_npctransport.Scoring_create_bounding_box_restraint(self, beads)
1941 
1942 
1943  def create_slab_restraint(self, beads):
1944  """create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
1945  return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
1946 
1947 
1948  def get_model(self):
1949  """get_model(Scoring self) -> Model"""
1950  return _IMP_npctransport.Scoring_get_model(self)
1951 
1952 
1953  def get_sd(self):
1954  """get_sd(Scoring self) -> SimulationData"""
1955  return _IMP_npctransport.Scoring_get_sd(self)
1956 
1957 
1958  def get_has_bounding_box(self):
1959  """get_has_bounding_box(Scoring self) -> bool"""
1960  return _IMP_npctransport.Scoring_get_has_bounding_box(self)
1961 
1962 
1963  def get_default_backbone_k(self):
1964  """get_default_backbone_k(Scoring self) -> double"""
1965  return _IMP_npctransport.Scoring_get_default_backbone_k(self)
1966 
1967 
1968  def get_is_backbone_harmonic(self):
1969  """get_is_backbone_harmonic(Scoring self) -> bool"""
1970  return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
1971 
1972 
1973  def get_excluded_volume_k(self):
1974  """get_excluded_volume_k(Scoring self) -> double"""
1975  return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
1976 
1977 
1978  def get_interaction_k(self):
1979  """get_interaction_k(Scoring self) -> double"""
1980  return _IMP_npctransport.Scoring_get_interaction_k(self)
1981 
1982 
1983  def get_predicate_pair_score(self, *args):
1984  """
1985  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1986  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
1987  """
1988  return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
1989 
1990 
1991  def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
1992  """
1993  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double
1994  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True) -> double
1995  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2) -> double
1996  """
1997  return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
1998 
1999 
2000  def get_ordered_type_pair_predicate(self):
2001  """get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
2002  return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
2003 
2004 
2005  def add_chain_restraints(self, chain):
2006  """add_chain_restraints(Scoring self, FGChain chain)"""
2007  return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
2008 
2009 
2010  def get_chain_restraints_on(self, beads):
2011  """get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
2012  return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
2013 
2014 
2015  def get_all_chain_restraints(self):
2016  """get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
2017  return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
2018 
2019 
2020  def remove_particle_type(self, pt):
2021  """remove_particle_type(Scoring self, ParticleType pt)"""
2022  return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
2023 
2024 
2025  def add_z_bias_restraint(self, *args):
2026  """
2027  add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
2028  add_z_bias_restraint(Scoring self, Particle p, double k)
2029  """
2030  return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
2031 
2032 
2033  def get_z_bias_restraints(self):
2034  """get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
2035  return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
2036 
2037 
2038  def create_z_bias_restraint(self, ps, k):
2039  """create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
2040  return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
2041 
2042 
2043  def add_custom_restraint(self, r):
2044  """add_custom_restraint(Scoring self, Restraint r)"""
2045  return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
2046 
2047 
2048  def add_custom_restraints(self, R):
2049  """add_custom_restraints(Scoring self, IMP::Restraints R)"""
2050  return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
2051 
2052 
2053  def clear_custom_restraints(self):
2054  """clear_custom_restraints(Scoring self)"""
2055  return _IMP_npctransport.Scoring_clear_custom_restraints(self)
2056 
2057 
2058  def get_custom_restraints(self):
2059  """get_custom_restraints(Scoring self) -> IMP::Restraints"""
2060  return _IMP_npctransport.Scoring_get_custom_restraints(self)
2061 
2062 
2063  def add_restrained_anchor_bead(self, p):
2064  """add_restrained_anchor_bead(Scoring self, Particle p)"""
2065  return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
2066 
2067 
2068  def get_pore_radius_restraint(self):
2069  """get_pore_radius_restraint(Scoring self) -> Restraint"""
2070  return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
2071 
2072 
2073  def get_range(self):
2074  """get_range(Scoring self) -> double"""
2075  return _IMP_npctransport.Scoring_get_range(self)
2076 
2077 
2078  def set_interaction_range_factor(self, type, value):
2079  """set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
2080  return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
2081 
2082 
2083  def set_interaction_k_factor(self, type, value):
2084  """set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
2085  return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
2086 
2087 
2088  def get_version_info(self):
2089  """get_version_info(Scoring self) -> VersionInfo"""
2090  return _IMP_npctransport.Scoring_get_version_info(self)
2091 
2092 
2093  def __str__(self):
2094  """__str__(Scoring self) -> std::string"""
2095  return _IMP_npctransport.Scoring___str__(self)
2096 
2097 
2098  def __repr__(self):
2099  """__repr__(Scoring self) -> std::string"""
2100  return _IMP_npctransport.Scoring___repr__(self)
2101 
2102 
2103  @staticmethod
2104  def get_from(o):
2105  return _object_cast_to_Scoring(o)
2106 
2107 Scoring_swigregister = _IMP_npctransport.Scoring_swigregister
2108 Scoring_swigregister(Scoring)
2109 
2110 class timer(object):
2111  """Proxy of C++ boost::timer class."""
2112 
2113  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2114  __repr__ = _swig_repr
2115 
2116  def __init__(self):
2117  """__init__(boost::timer self) -> timer"""
2118  this = _IMP_npctransport.new_timer()
2119  try:
2120  self.this.append(this)
2121  except __builtin__.Exception:
2122  self.this = this
2123  __swig_destroy__ = _IMP_npctransport.delete_timer
2124  __del__ = lambda self: None
2125 timer_swigregister = _IMP_npctransport.timer_swigregister
2126 timer_swigregister(timer)
2127 
2128 class Statistics(IMP.Object):
2129  """Proxy of C++ IMP::npctransport::Statistics class."""
2130 
2131  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2132 
2133  def remove_particle_type(self, pt):
2134  """remove_particle_type(Statistics self, ParticleType pt)"""
2135  return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2136 
2137 
2138  def __init__(self, sd, statistics_interval_frames, output_file_name):
2139  """__init__(IMP::npctransport::Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2140  this = _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name)
2141  try:
2142  self.this.append(this)
2143  except __builtin__.Exception:
2144  self.this = this
2145 
2146  def add_fg_chain_stats(self, fg_chain):
2147  """add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2148  return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2149 
2150 
2151  def add_floater_stats(self, p):
2152  """add_floater_stats(Statistics self, Particle p)"""
2153  return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2154 
2155 
2156  def add_interaction_stats(self, type0, type1):
2157  """add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2158  return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2159 
2160 
2161  def add_optimizer_states(self, o=None):
2162  """
2163  add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates
2164  add_optimizer_states(Statistics self) -> IMP::OptimizerStates
2165  """
2166  return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2167 
2168 
2169  def update_particle_type_zr_distribution_map(self, p):
2170  """update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2171  return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2172 
2173 
2174  def update_particle_type_xyz_distribution_map(self, p):
2175  """update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2176  return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2177 
2178 
2179  def update(self, timer, nf_new=1):
2180  """
2181  update(Statistics self, timer timer, unsigned int nf_new=1)
2182  update(Statistics self, timer timer)
2183  """
2184  return _IMP_npctransport.Statistics_update(self, timer, nf_new)
2185 
2186 
2187  def reset_statistics_optimizer_states(self):
2188  """reset_statistics_optimizer_states(Statistics self)"""
2189  return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2190 
2191 
2192  def set_interrupted(self, tf):
2193  """set_interrupted(Statistics self, bool tf)"""
2194  return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2195 
2196 
2197  def get_model(self):
2198  """get_model(Statistics self) -> Model"""
2199  return _IMP_npctransport.Statistics_get_model(self)
2200 
2201 
2202  def get_sd(self):
2203  """get_sd(Statistics self) -> SimulationData"""
2204  return _IMP_npctransport.Statistics_get_sd(self)
2205 
2206 
2207  def get_is_activated(self):
2208  """get_is_activated(Statistics self) -> bool"""
2209  return _IMP_npctransport.Statistics_get_is_activated(self)
2210 
2211 
2212  def get_output_file_name(self):
2213  """get_output_file_name(Statistics self) -> std::string"""
2214  return _IMP_npctransport.Statistics_get_output_file_name(self)
2215 
2216 
2217  def get_version_info(self):
2218  """get_version_info(Statistics self) -> VersionInfo"""
2219  return _IMP_npctransport.Statistics_get_version_info(self)
2220 
2221 
2222  def __str__(self):
2223  """__str__(Statistics self) -> std::string"""
2224  return _IMP_npctransport.Statistics___str__(self)
2225 
2226 
2227  def __repr__(self):
2228  """__repr__(Statistics self) -> std::string"""
2229  return _IMP_npctransport.Statistics___repr__(self)
2230 
2231 
2232  @staticmethod
2233  def get_from(o):
2234  return _object_cast_to_Statistics(o)
2235 
2236 Statistics_swigregister = _IMP_npctransport.Statistics_swigregister
2237 Statistics_swigregister(Statistics)
2238 
2239 
2240 def create_boost_timer():
2241  """create_boost_timer() -> timer"""
2242  return _IMP_npctransport.create_boost_timer()
2243 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2244 class SimulationData(IMP.Object):
2245  """Proxy of C++ IMP::npctransport::SimulationData class."""
2246 
2247  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2248 
2249  def get_output_npctransport_version(self):
2250  """get_output_npctransport_version(SimulationData self) -> double"""
2251  return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2252 
2253 
2254  def get_range(self):
2255  """get_range(SimulationData self) -> double"""
2256  return _IMP_npctransport.SimulationData_get_range(self)
2257 
2258 
2259  def get_output_statistics_interval_frames(self):
2260  """get_output_statistics_interval_frames(SimulationData self) -> int"""
2261  return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2262 
2263 
2264  def get_is_exclude_floaters_from_slab_initially(self):
2265  """get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2266  return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2267 
2268 
2269  def get_are_floaters_on_one_slab_side(self):
2270  """get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2271  return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2272 
2273 
2274  def get_is_xyz_hist_stats(self):
2275  """get_is_xyz_hist_stats(SimulationData self) -> bool"""
2276  return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2277 
2278 
2279  def get_angular_d_factor(self):
2280  """get_angular_d_factor(SimulationData self) -> double"""
2281  return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2282 
2283 
2284  def __init__(self, *args):
2285  """
2286  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name, std::string new_output_file) -> SimulationData
2287  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name) -> SimulationData
2288  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick) -> SimulationData
2289  """
2290  this = _IMP_npctransport.new_SimulationData(*args)
2291  try:
2292  self.this.append(this)
2293  except __builtin__.Exception:
2294  self.this = this
2295 
2296  def get_model(self):
2297  """get_model(SimulationData self) -> Model"""
2298  return _IMP_npctransport.SimulationData_get_model(self)
2299 
2300 
2301  def get_scoring(self):
2302  """get_scoring(SimulationData self) -> Scoring"""
2303  return _IMP_npctransport.SimulationData_get_scoring(self)
2304 
2305 
2306  def get_statistics(self):
2307  """get_statistics(SimulationData self) -> Statistics"""
2308  return _IMP_npctransport.SimulationData_get_statistics(self)
2309 
2310 
2311  def get_bd(self, recreate=False):
2312  """
2313  get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics
2314  get_bd(SimulationData self) -> BrownianDynamics
2315  """
2316  return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2317 
2318 
2319  def activate_statistics(self):
2320  """activate_statistics(SimulationData self)"""
2321  return _IMP_npctransport.SimulationData_activate_statistics(self)
2322 
2323 
2324  def get_statistics_fraction(self):
2325  """get_statistics_fraction(SimulationData self) -> double"""
2326  return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2327 
2328 
2329  def get_is_fg_bead(self, *args):
2330  """
2331  get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2332  get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2333  """
2334  return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2335 
2336 
2337  def get_is_fg_chain(self, *args):
2338  """
2339  get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2340  get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2341  """
2342  return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2343 
2344 
2345  def get_fg_bead_types(self):
2346  """get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2347  return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2348 
2349 
2350  def get_fg_chain_types(self):
2351  """get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2352  return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2353 
2354 
2355  def get_floater_types(self):
2356  """get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2357  return _IMP_npctransport.SimulationData_get_floater_types(self)
2358 
2359 
2360  def get_obstacle_types(self):
2361  """get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2362  return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2363 
2364 
2365  def get_fg_chain_roots(self):
2366  """get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2367  return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2368 
2369 
2370  def get_fg_chains(self):
2371  """get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2372  return _IMP_npctransport.SimulationData_get_fg_chains(self)
2373 
2374 
2375  def get_obstacle_particles(self):
2376  """get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2377  return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2378 
2379 
2380  def get_beads(self):
2381  """get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2382  return _IMP_npctransport.SimulationData_get_beads(self)
2383 
2384 
2385  def get_optimizable_beads(self):
2386  """get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2387  return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2388 
2389 
2390  def get_non_optimizable_beads(self):
2391  """get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2392  return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2393 
2394 
2395  def get_is_backbone_harmonic(self):
2396  """get_is_backbone_harmonic(SimulationData self) -> bool"""
2397  return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2398 
2399 
2400  def get_backbone_tau_ns(self):
2401  """get_backbone_tau_ns(SimulationData self) -> double"""
2402  return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2403 
2404 
2405  def get_temperature_k(self):
2406  """get_temperature_k(SimulationData self) -> double"""
2407  return _IMP_npctransport.SimulationData_get_temperature_k(self)
2408 
2409 
2410  def get_initial_simulation_time_ns(self):
2411  """get_initial_simulation_time_ns(SimulationData self) -> double"""
2412  return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2413 
2414 
2415  def get_site_centers(self, t0):
2416  """get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2417  return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2418 
2419 
2420  def get_sites(self, t0):
2421  """get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2422  return _IMP_npctransport.SimulationData_get_sites(self, t0)
2423 
2424 
2425  def set_sites(self, *args):
2426  """
2427  set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2428  set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2429  """
2430  return _IMP_npctransport.SimulationData_set_sites(self, *args)
2431 
2432 
2433  def get_site_display_radius(self, arg2):
2434  """get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2435  return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2436 
2437 
2438  def get_maximum_number_of_minutes(self):
2439  """get_maximum_number_of_minutes(SimulationData self) -> double"""
2440  return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2441 
2442 
2443  def remove_particle_type(self, pt):
2444  """remove_particle_type(SimulationData self, ParticleType pt)"""
2445  return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2446 
2447 
2448  def remove_fgs_with_prefix(self, s_fg_type):
2449  """remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2450  return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2451 
2452 
2453  def get_box(self):
2454  """get_box(SimulationData self) -> BoundingBox3D"""
2455  return _IMP_npctransport.SimulationData_get_box(self)
2456 
2457 
2458  def get_box_size(self):
2459  """get_box_size(SimulationData self) -> double"""
2460  return _IMP_npctransport.SimulationData_get_box_size(self)
2461 
2462 
2463  def set_box_size(self, box_size):
2464  """set_box_size(SimulationData self, double box_size)"""
2465  return _IMP_npctransport.SimulationData_set_box_size(self, box_size)
2466 
2467 
2468  def get_has_slab(self):
2469  """get_has_slab(SimulationData self) -> bool"""
2470  return _IMP_npctransport.SimulationData_get_has_slab(self)
2471 
2472 
2473  def get_is_slab_with_cylindrical_pore(self):
2474  """get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2475  return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2476 
2477 
2478  def get_is_slab_with_toroidal_pore(self):
2479  """get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2480  return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2481 
2482 
2483  def get_slab_particle(self):
2484  """get_slab_particle(SimulationData self) -> Particle"""
2485  return _IMP_npctransport.SimulationData_get_slab_particle(self)
2486 
2487 
2488  def get_cylinder(self):
2489  """get_cylinder(SimulationData self) -> Cylinder3D"""
2490  return _IMP_npctransport.SimulationData_get_cylinder(self)
2491 
2492 
2493  def get_has_bounding_box(self):
2494  """get_has_bounding_box(SimulationData self) -> bool"""
2495  return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2496 
2497 
2498  def initialize_positions_from_rmf(self, fh, frame_number=-1):
2499  """
2500  initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)
2501  initialize_positions_from_rmf(SimulationData self, FileConstHandle fh)
2502  """
2503  return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2504 
2505 
2506  def link_rmf_file_handle(self, fh, is_restraints=True):
2507  """
2508  link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)
2509  link_rmf_file_handle(SimulationData self, FileHandle fh)
2510  """
2511  return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2512 
2513 
2514  def get_rmf_sos_writer(self):
2515  """get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2516  return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2517 
2518 
2519  def reset_rmf(self):
2520  """reset_rmf(SimulationData self)"""
2521  return _IMP_npctransport.SimulationData_reset_rmf(self)
2522 
2523 
2524  def switch_suspend_rmf(self, suspend):
2525  """switch_suspend_rmf(SimulationData self, bool suspend)"""
2526  return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2527 
2528 
2529  def write_geometry(self, out):
2530  """write_geometry(SimulationData self, std::string out)"""
2531  return _IMP_npctransport.SimulationData_write_geometry(self, out)
2532 
2533 
2534  def dump_geometry(self):
2535  """dump_geometry(SimulationData self)"""
2536  return _IMP_npctransport.SimulationData_dump_geometry(self)
2537 
2538 
2539  def get_root_of_type(self, type):
2540  """get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2541  return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2542 
2543 
2544  def get_number_of_frames(self):
2545  """get_number_of_frames(SimulationData self) -> unsigned int"""
2546  return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2547 
2548 
2549  def get_number_of_trials(self):
2550  """get_number_of_trials(SimulationData self) -> unsigned int"""
2551  return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2552 
2553 
2554  def get_root(self):
2555  """get_root(SimulationData self) -> Hierarchy"""
2556  return _IMP_npctransport.SimulationData_get_root(self)
2557 
2558 
2559  def get_slab_thickness(self):
2560  """get_slab_thickness(SimulationData self) -> double"""
2561  return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2562 
2563 
2564  def get_tunnel_radius(self):
2565  """get_tunnel_radius(SimulationData self) -> double"""
2566  return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2567 
2568 
2569  def get_pore_radius(self):
2570  """get_pore_radius(SimulationData self) -> double"""
2571  return _IMP_npctransport.SimulationData_get_pore_radius(self)
2572 
2573 
2574  def get_tunnel_radius_k(self):
2575  """get_tunnel_radius_k(SimulationData self) -> double"""
2576  return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2577 
2578 
2579  def get_pore_radius_k(self):
2580  """get_pore_radius_k(SimulationData self) -> double"""
2581  return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2582 
2583 
2584  def get_is_pore_radius_dynamic(self):
2585  """get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2586  return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2587 
2588 
2589  def get_pore_anchored_beads_k(self):
2590  """get_pore_anchored_beads_k(SimulationData self) -> double"""
2591  return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2592 
2593 
2594  def get_static_geometry(self):
2595  """get_static_geometry(SimulationData self) -> Geometry"""
2596  return _IMP_npctransport.SimulationData_get_static_geometry(self)
2597 
2598 
2599  def get_rmf_dump_interval_frames(self):
2600  """get_rmf_dump_interval_frames(SimulationData self) -> int"""
2601  return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2602 
2603 
2604  def get_rmf_file_name(self):
2605  """get_rmf_file_name(SimulationData self) -> std::string"""
2606  return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2607 
2608 
2609  def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2610  """
2611  set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)
2612  set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True)
2613  set_rmf_file(SimulationData self, std::string const & new_name)
2614  """
2615  return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2616 
2617 
2618  def get_version_info(self):
2619  """get_version_info(SimulationData self) -> VersionInfo"""
2620  return _IMP_npctransport.SimulationData_get_version_info(self)
2621 
2622 
2623  def __str__(self):
2624  """__str__(SimulationData self) -> std::string"""
2625  return _IMP_npctransport.SimulationData___str__(self)
2626 
2627 
2628  def __repr__(self):
2629  """__repr__(SimulationData self) -> std::string"""
2630  return _IMP_npctransport.SimulationData___repr__(self)
2631 
2632 
2633  @staticmethod
2634  def get_from(o):
2635  return _object_cast_to_SimulationData(o)
2636 
2637 SimulationData_swigregister = _IMP_npctransport.SimulationData_swigregister
2638 SimulationData_swigregister(SimulationData)
2639 
2640 
2641 def get_simulation_data_key():
2642  """get_simulation_data_key() -> IMP::WeakObjectKey"""
2643  return _IMP_npctransport.get_simulation_data_key()
2644 
2645 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2646  """write_geometry(IMP::ParticlesTemp const & kaps, IMP::algebra::Sphere3Ds const & kap_sites, IMP::ParticlesTemp const & chains, IMP::algebra::Sphere3Ds const & chain_sites, IMP::RestraintsTemp const & rs, Writer out)"""
2647  return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2648 class ParticleFactory(IMP.Object):
2649  """Proxy of C++ IMP::npctransport::ParticleFactory class."""
2650 
2651  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2652  sd_ = _swig_property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set)
2653  radius_ = _swig_property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set)
2654  D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set)
2655  angular_D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set)
2656  color_ = _swig_property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set)
2657  type_ = _swig_property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set)
2658 
2659  def __init__(self, *args):
2660  """
2661  __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name) -> ParticleFactory
2662  __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type) -> ParticleFactory
2663  """
2664  this = _IMP_npctransport.new_ParticleFactory(*args)
2665  try:
2666  self.this.append(this)
2667  except __builtin__.Exception:
2668  self.this = this
2669 
2670  def create(self, *args):
2671  """
2672  create(ParticleFactory self, std::string name) -> Particle
2673  create(ParticleFactory self) -> Particle
2674  """
2675  return _IMP_npctransport.ParticleFactory_create(self, *args)
2676 
2677 
2678  def get_model(self):
2679  """get_model(ParticleFactory self) -> Model"""
2680  return _IMP_npctransport.ParticleFactory_get_model(self)
2681 
2682 
2683  def get_simulation_data(self):
2684  """get_simulation_data(ParticleFactory self) -> SimulationData"""
2685  return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2686 
2687 
2688  def get_radius(self):
2689  """get_radius(ParticleFactory self) -> double"""
2690  return _IMP_npctransport.ParticleFactory_get_radius(self)
2691 
2692 
2693  def get_version_info(self):
2694  """get_version_info(ParticleFactory self) -> VersionInfo"""
2695  return _IMP_npctransport.ParticleFactory_get_version_info(self)
2696 
2697 
2698  def __str__(self):
2699  """__str__(ParticleFactory self) -> std::string"""
2700  return _IMP_npctransport.ParticleFactory___str__(self)
2701 
2702 
2703  def __repr__(self):
2704  """__repr__(ParticleFactory self) -> std::string"""
2705  return _IMP_npctransport.ParticleFactory___repr__(self)
2706 
2707 
2708  @staticmethod
2709  def get_from(o):
2710  return _object_cast_to_ParticleFactory(o)
2711 
2712 ParticleFactory_swigregister = _IMP_npctransport.ParticleFactory_swigregister
2713 ParticleFactory_swigregister(ParticleFactory)
2714 
2715 class HierarchyWithSitesLoadLink(IMP.rmf.HierarchyLoadLink):
2716  """Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2717 
2718  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2719 
2720  def __init__(self, fh):
2721  """__init__(IMP::npctransport::HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2722  this = _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh)
2723  try:
2724  self.this.append(this)
2725  except __builtin__.Exception:
2726  self.this = this
2727 
2728  def get_name():
2729  """get_name() -> char const *"""
2730  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2731 
2732  get_name = staticmethod(get_name)
2733 
2734  def __str__(self):
2735  """__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2736  return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2737 
2738 
2739  def __repr__(self):
2740  """__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2741  return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2742 
2743 
2744  @staticmethod
2745  def get_from(o):
2746  return _object_cast_to_HierarchyWithSitesLoadLink(o)
2747 
2748  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2749  __del__ = lambda self: None
2750 HierarchyWithSitesLoadLink_swigregister = _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister
2751 HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2752 
2753 def HierarchyWithSitesLoadLink_get_name():
2754  """HierarchyWithSitesLoadLink_get_name() -> char const *"""
2755  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2756 
2757 class HierarchyWithSitesSaveLink(IMP.rmf.HierarchySaveLink):
2758  """Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2759 
2760  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2761 
2762  def __init__(self, fh):
2763  """__init__(IMP::npctransport::HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2764  this = _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh)
2765  try:
2766  self.this.append(this)
2767  except __builtin__.Exception:
2768  self.this = this
2769 
2770  def get_name():
2771  """get_name() -> char const *"""
2772  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2773 
2774  get_name = staticmethod(get_name)
2775 
2776  def __str__(self):
2777  """__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2778  return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2779 
2780 
2781  def __repr__(self):
2782  """__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2783  return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2784 
2785 
2786  @staticmethod
2787  def get_from(o):
2788  return _object_cast_to_HierarchyWithSitesSaveLink(o)
2789 
2790  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2791  __del__ = lambda self: None
2792 HierarchyWithSitesSaveLink_swigregister = _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister
2793 HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2794 
2795 def HierarchyWithSitesSaveLink_get_name():
2796  """HierarchyWithSitesSaveLink_get_name() -> char const *"""
2797  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2798 
2799 
2800 def add_test_sites(*args):
2801  """
2802  add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2803  add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2804  """
2805  return _IMP_npctransport.add_test_sites(*args)
2806 
2807 def add_hierarchies_with_sites(*args):
2808  """
2809  add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2810  add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2811  """
2812  return _IMP_npctransport.add_hierarchies_with_sites(*args)
2813 
2814 def add_hierarchy_with_sites(fh, hs):
2815  """add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2816  return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2817 
2819  """create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2820  return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2821 
2822 def link_hierarchies_with_sites(fh, hs):
2823  """link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2824  return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2825 class Transporting(IMP.Decorator):
2826  """Proxy of C++ IMP::npctransport::Transporting class."""
2827 
2828  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2829 
2830  def __init__(self, *args):
2831  """
2832  __init__(IMP::npctransport::Transporting self) -> Transporting
2833  __init__(IMP::npctransport::Transporting self, Model m, ParticleIndex id) -> Transporting
2834  __init__(IMP::npctransport::Transporting self, _ParticleAdaptor d) -> Transporting
2835  """
2836  this = _IMP_npctransport.new_Transporting(*args)
2837  try:
2838  self.this.append(this)
2839  except __builtin__.Exception:
2840  self.this = this
2841 
2842  def show(self, *args):
2843  """
2844  show(Transporting self, _ostream out)
2845  show(Transporting self)
2846  """
2847  return _IMP_npctransport.Transporting_show(self, *args)
2848 
2849 
2850  def setup_particle(*args):
2851  """
2852  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2853  setup_particle(Model m, ParticleIndex pi) -> Transporting
2854  setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
2855  setup_particle(_ParticleAdaptor decorator) -> Transporting
2856  """
2857  return _IMP_npctransport.Transporting_setup_particle(*args)
2858 
2859  setup_particle = staticmethod(setup_particle)
2860 
2861  def get_is_setup(*args):
2862  """
2863  get_is_setup(_ParticleAdaptor p) -> bool
2864  get_is_setup(Model m, ParticleIndex pi) -> bool
2865  """
2866  return _IMP_npctransport.Transporting_get_is_setup(*args)
2867 
2868  get_is_setup = staticmethod(get_is_setup)
2869 
2870  def set_is_last_entry_from_top(self, is_last_entry_from_top):
2871  """set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2872  return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2873 
2874 
2875  def get_is_last_entry_from_top(self):
2876  """get_is_last_entry_from_top(Transporting self) -> bool"""
2877  return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2878 
2879 
2880  def get_is_last_entry_from_top_key():
2881  """get_is_last_entry_from_top_key() -> IntKey"""
2882  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
2883 
2884  get_is_last_entry_from_top_key = staticmethod(get_is_last_entry_from_top_key)
2885 
2886  def set_last_tracked_z(self, last_tracked_z):
2887  """set_last_tracked_z(Transporting self, double last_tracked_z)"""
2888  return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
2889 
2890 
2891  def get_last_tracked_z(self):
2892  """get_last_tracked_z(Transporting self) -> double"""
2893  return _IMP_npctransport.Transporting_get_last_tracked_z(self)
2894 
2895 
2896  def get_last_tracked_z_key():
2897  """get_last_tracked_z_key() -> FloatKey"""
2898  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
2899 
2900  get_last_tracked_z_key = staticmethod(get_last_tracked_z_key)
2901 
2902  def set_n_entries_bottom(self, n):
2903  """set_n_entries_bottom(Transporting self, int n)"""
2904  return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
2905 
2906 
2907  def get_n_entries_bottom(self):
2908  """get_n_entries_bottom(Transporting self) -> int"""
2909  return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
2910 
2911 
2912  def get_n_entries_bottom_key():
2913  """get_n_entries_bottom_key() -> IntKey"""
2914  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
2915 
2916  get_n_entries_bottom_key = staticmethod(get_n_entries_bottom_key)
2917 
2918  def set_n_entries_top(self, n):
2919  """set_n_entries_top(Transporting self, int n)"""
2920  return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
2921 
2922 
2923  def get_n_entries_top(self):
2924  """get_n_entries_top(Transporting self) -> int"""
2925  return _IMP_npctransport.Transporting_get_n_entries_top(self)
2926 
2927 
2928  def get_n_entries_top_key():
2929  """get_n_entries_top_key() -> IntKey"""
2930  return _IMP_npctransport.Transporting_get_n_entries_top_key()
2931 
2932  get_n_entries_top_key = staticmethod(get_n_entries_top_key)
2933 
2934  def add_attribute(self, *args):
2935  """
2936  add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
2937  add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
2938  add_attribute(Transporting self, IntKey a0, IMP::Int a1)
2939  add_attribute(Transporting self, StringKey a0, IMP::String a1)
2940  add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
2941  add_attribute(Transporting self, ObjectKey a0, Object a1)
2942  """
2943  return _IMP_npctransport.Transporting_add_attribute(self, *args)
2944 
2945 
2946  def get_value(self, *args):
2947  """
2948  get_value(Transporting self, FloatKey a0) -> IMP::Float
2949  get_value(Transporting self, IntKey a0) -> IMP::Int
2950  get_value(Transporting self, StringKey a0) -> IMP::String
2951  get_value(Transporting self, ParticleIndexKey a0) -> Particle
2952  get_value(Transporting self, ObjectKey a0) -> Object
2953  """
2954  return _IMP_npctransport.Transporting_get_value(self, *args)
2955 
2956 
2957  def set_value(self, *args):
2958  """
2959  set_value(Transporting self, FloatKey a0, IMP::Float a1)
2960  set_value(Transporting self, IntKey a0, IMP::Int a1)
2961  set_value(Transporting self, StringKey a0, IMP::String a1)
2962  set_value(Transporting self, ParticleIndexKey a0, Particle a1)
2963  set_value(Transporting self, ObjectKey a0, Object a1)
2964  """
2965  return _IMP_npctransport.Transporting_set_value(self, *args)
2966 
2967 
2968  def remove_attribute(self, *args):
2969  """
2970  remove_attribute(Transporting self, FloatKey a0)
2971  remove_attribute(Transporting self, IntKey a0)
2972  remove_attribute(Transporting self, StringKey a0)
2973  remove_attribute(Transporting self, ParticleIndexKey a0)
2974  remove_attribute(Transporting self, ObjectKey a0)
2975  """
2976  return _IMP_npctransport.Transporting_remove_attribute(self, *args)
2977 
2978 
2979  def has_attribute(self, *args):
2980  """
2981  has_attribute(Transporting self, FloatKey a0) -> bool
2982  has_attribute(Transporting self, IntKey a0) -> bool
2983  has_attribute(Transporting self, StringKey a0) -> bool
2984  has_attribute(Transporting self, ParticleIndexKey a0) -> bool
2985  has_attribute(Transporting self, ObjectKey a0) -> bool
2986  """
2987  return _IMP_npctransport.Transporting_has_attribute(self, *args)
2988 
2989 
2990  def get_derivative(self, a0):
2991  """get_derivative(Transporting self, FloatKey a0) -> double"""
2992  return _IMP_npctransport.Transporting_get_derivative(self, a0)
2993 
2994 
2995  def get_name(self):
2996  """get_name(Transporting self) -> std::string"""
2997  return _IMP_npctransport.Transporting_get_name(self)
2998 
2999 
3000  def clear_caches(self):
3001  """clear_caches(Transporting self)"""
3002  return _IMP_npctransport.Transporting_clear_caches(self)
3003 
3004 
3005  def set_name(self, a0):
3006  """set_name(Transporting self, std::string a0)"""
3007  return _IMP_npctransport.Transporting_set_name(self, a0)
3008 
3009 
3010  def set_check_level(self, a0):
3011  """set_check_level(Transporting self, IMP::CheckLevel a0)"""
3012  return _IMP_npctransport.Transporting_set_check_level(self, a0)
3013 
3014 
3015  def add_to_derivative(self, a0, a1, a2):
3016  """add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3017  return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
3018 
3019 
3020  def set_is_optimized(self, a0, a1):
3021  """set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
3022  return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
3023 
3024 
3025  def get_is_optimized(self, a0):
3026  """get_is_optimized(Transporting self, FloatKey a0) -> bool"""
3027  return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
3028 
3029 
3030  def get_check_level(self):
3031  """get_check_level(Transporting self) -> IMP::CheckLevel"""
3032  return _IMP_npctransport.Transporting_get_check_level(self)
3033 
3034 
3035  def __eq__(self, *args):
3036  """
3037  __eq__(Transporting self, Transporting o) -> bool
3038  __eq__(Transporting self, Particle d) -> bool
3039  """
3040  return _IMP_npctransport.Transporting___eq__(self, *args)
3041 
3042 
3043  def __ne__(self, *args):
3044  """
3045  __ne__(Transporting self, Transporting o) -> bool
3046  __ne__(Transporting self, Particle d) -> bool
3047  """
3048  return _IMP_npctransport.Transporting___ne__(self, *args)
3049 
3050 
3051  def __le__(self, *args):
3052  """
3053  __le__(Transporting self, Transporting o) -> bool
3054  __le__(Transporting self, Particle d) -> bool
3055  """
3056  return _IMP_npctransport.Transporting___le__(self, *args)
3057 
3058 
3059  def __lt__(self, *args):
3060  """
3061  __lt__(Transporting self, Transporting o) -> bool
3062  __lt__(Transporting self, Particle d) -> bool
3063  """
3064  return _IMP_npctransport.Transporting___lt__(self, *args)
3065 
3066 
3067  def __ge__(self, *args):
3068  """
3069  __ge__(Transporting self, Transporting o) -> bool
3070  __ge__(Transporting self, Particle d) -> bool
3071  """
3072  return _IMP_npctransport.Transporting___ge__(self, *args)
3073 
3074 
3075  def __gt__(self, *args):
3076  """
3077  __gt__(Transporting self, Transporting o) -> bool
3078  __gt__(Transporting self, Particle d) -> bool
3079  """
3080  return _IMP_npctransport.Transporting___gt__(self, *args)
3081 
3082 
3083  def __hash__(self):
3084  """__hash__(Transporting self) -> std::size_t"""
3085  return _IMP_npctransport.Transporting___hash__(self)
3086 
3087 
3088  def __str__(self):
3089  """__str__(Transporting self) -> std::string"""
3090  return _IMP_npctransport.Transporting___str__(self)
3091 
3092 
3093  def __repr__(self):
3094  """__repr__(Transporting self) -> std::string"""
3095  return _IMP_npctransport.Transporting___repr__(self)
3096 
3097  __swig_destroy__ = _IMP_npctransport.delete_Transporting
3098  __del__ = lambda self: None
3099 Transporting_swigregister = _IMP_npctransport.Transporting_swigregister
3100 Transporting_swigregister(Transporting)
3101 
3102 def Transporting_setup_particle(*args):
3103  """
3104  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
3105  setup_particle(Model m, ParticleIndex pi) -> Transporting
3106  setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
3107  Transporting_setup_particle(_ParticleAdaptor decorator) -> Transporting
3108  """
3109  return _IMP_npctransport.Transporting_setup_particle(*args)
3110 
3111 def Transporting_get_is_setup(*args):
3112  """
3113  get_is_setup(_ParticleAdaptor p) -> bool
3114  Transporting_get_is_setup(Model m, ParticleIndex pi) -> bool
3115  """
3116  return _IMP_npctransport.Transporting_get_is_setup(*args)
3117 
3118 def Transporting_get_is_last_entry_from_top_key():
3119  """Transporting_get_is_last_entry_from_top_key() -> IntKey"""
3120  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3121 
3122 def Transporting_get_last_tracked_z_key():
3123  """Transporting_get_last_tracked_z_key() -> FloatKey"""
3124  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3125 
3126 def Transporting_get_n_entries_bottom_key():
3127  """Transporting_get_n_entries_bottom_key() -> IntKey"""
3128  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3129 
3130 def Transporting_get_n_entries_top_key():
3131  """Transporting_get_n_entries_top_key() -> IntKey"""
3132  return _IMP_npctransport.Transporting_get_n_entries_top_key()
3133 
3134 
3135 def show_ranges(fname):
3136  """show_ranges(std::string fname)"""
3137  return _IMP_npctransport.show_ranges(fname)
3138 
3139 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
3140  """assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed) -> int"""
3141  return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
3142 
3143 def get_number_of_work_units(configuration_file):
3144  """get_number_of_work_units(std::string configuration_file) -> int"""
3145  return _IMP_npctransport.get_number_of_work_units(configuration_file)
3146 class SlabWithPore(IMP.Decorator):
3147  """Proxy of C++ IMP::npctransport::SlabWithPore class."""
3148 
3149  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3150 
3151  def __init__(self, *args):
3152  """
3153  __init__(IMP::npctransport::SlabWithPore self) -> SlabWithPore
3154  __init__(IMP::npctransport::SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
3155  __init__(IMP::npctransport::SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
3156  """
3157  this = _IMP_npctransport.new_SlabWithPore(*args)
3158  try:
3159  self.this.append(this)
3160  except __builtin__.Exception:
3161  self.this = this
3162 
3163  def show(self, *args):
3164  """
3165  show(SlabWithPore self, _ostream out)
3166  show(SlabWithPore self)
3167  """
3168  return _IMP_npctransport.SlabWithPore_show(self, *args)
3169 
3170 
3171  def setup_particle(*args):
3172  """
3173  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3174  setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3175  """
3176  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3177 
3178  setup_particle = staticmethod(setup_particle)
3179 
3180  def get_is_setup(*args):
3181  """
3182  get_is_setup(_ParticleAdaptor p) -> bool
3183  get_is_setup(Model m, ParticleIndex pi) -> bool
3184  """
3185  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3186 
3187  get_is_setup = staticmethod(get_is_setup)
3188 
3189  def set_thickness(self, thickness):
3190  """set_thickness(SlabWithPore self, double thickness)"""
3191  return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
3192 
3193 
3194  def get_thickness(self):
3195  """get_thickness(SlabWithPore self) -> IMP::Float"""
3196  return _IMP_npctransport.SlabWithPore_get_thickness(self)
3197 
3198 
3199  def get_pore_radius(self):
3200  """get_pore_radius(SlabWithPore self) -> IMP::Float"""
3201  return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
3202 
3203 
3204  def set_pore_radius(self, r):
3205  """set_pore_radius(SlabWithPore self, double r)"""
3206  return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
3207 
3208 
3209  def add_to_pore_radius_derivative(self, v, d):
3210  """add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
3211  return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
3212 
3213 
3214  def get_pore_radius_is_optimized(self):
3215  """get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
3216  return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
3217 
3218 
3219  def set_pore_radius_is_optimized(self, tf):
3220  """set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
3221  return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
3222 
3223 
3224  def get_thickness_key():
3225  """get_thickness_key() -> FloatKey"""
3226  return _IMP_npctransport.SlabWithPore_get_thickness_key()
3227 
3228  get_thickness_key = staticmethod(get_thickness_key)
3229 
3230  def get_pore_radius_key():
3231  """get_pore_radius_key() -> FloatKey"""
3232  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3233 
3234  get_pore_radius_key = staticmethod(get_pore_radius_key)
3235 
3236  def add_attribute(self, *args):
3237  """
3238  add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
3239  add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
3240  add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
3241  add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
3242  add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3243  add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
3244  """
3245  return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
3246 
3247 
3248  def get_value(self, *args):
3249  """
3250  get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
3251  get_value(SlabWithPore self, IntKey a0) -> IMP::Int
3252  get_value(SlabWithPore self, StringKey a0) -> IMP::String
3253  get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3254  get_value(SlabWithPore self, ObjectKey a0) -> Object
3255  """
3256  return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3257 
3258 
3259  def set_value(self, *args):
3260  """
3261  set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3262  set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3263  set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3264  set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3265  set_value(SlabWithPore self, ObjectKey a0, Object a1)
3266  """
3267  return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3268 
3269 
3270  def remove_attribute(self, *args):
3271  """
3272  remove_attribute(SlabWithPore self, FloatKey a0)
3273  remove_attribute(SlabWithPore self, IntKey a0)
3274  remove_attribute(SlabWithPore self, StringKey a0)
3275  remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3276  remove_attribute(SlabWithPore self, ObjectKey a0)
3277  """
3278  return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3279 
3280 
3281  def has_attribute(self, *args):
3282  """
3283  has_attribute(SlabWithPore self, FloatKey a0) -> bool
3284  has_attribute(SlabWithPore self, IntKey a0) -> bool
3285  has_attribute(SlabWithPore self, StringKey a0) -> bool
3286  has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3287  has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3288  """
3289  return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3290 
3291 
3292  def get_derivative(self, a0):
3293  """get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3294  return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3295 
3296 
3297  def get_name(self):
3298  """get_name(SlabWithPore self) -> std::string"""
3299  return _IMP_npctransport.SlabWithPore_get_name(self)
3300 
3301 
3302  def clear_caches(self):
3303  """clear_caches(SlabWithPore self)"""
3304  return _IMP_npctransport.SlabWithPore_clear_caches(self)
3305 
3306 
3307  def set_name(self, a0):
3308  """set_name(SlabWithPore self, std::string a0)"""
3309  return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3310 
3311 
3312  def set_check_level(self, a0):
3313  """set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3314  return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3315 
3316 
3317  def add_to_derivative(self, a0, a1, a2):
3318  """add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3319  return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3320 
3321 
3322  def set_is_optimized(self, a0, a1):
3323  """set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3324  return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3325 
3326 
3327  def get_is_optimized(self, a0):
3328  """get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3329  return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3330 
3331 
3332  def get_check_level(self):
3333  """get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3334  return _IMP_npctransport.SlabWithPore_get_check_level(self)
3335 
3336 
3337  def __eq__(self, *args):
3338  """
3339  __eq__(SlabWithPore self, SlabWithPore o) -> bool
3340  __eq__(SlabWithPore self, Particle d) -> bool
3341  """
3342  return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3343 
3344 
3345  def __ne__(self, *args):
3346  """
3347  __ne__(SlabWithPore self, SlabWithPore o) -> bool
3348  __ne__(SlabWithPore self, Particle d) -> bool
3349  """
3350  return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3351 
3352 
3353  def __le__(self, *args):
3354  """
3355  __le__(SlabWithPore self, SlabWithPore o) -> bool
3356  __le__(SlabWithPore self, Particle d) -> bool
3357  """
3358  return _IMP_npctransport.SlabWithPore___le__(self, *args)
3359 
3360 
3361  def __lt__(self, *args):
3362  """
3363  __lt__(SlabWithPore self, SlabWithPore o) -> bool
3364  __lt__(SlabWithPore self, Particle d) -> bool
3365  """
3366  return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3367 
3368 
3369  def __ge__(self, *args):
3370  """
3371  __ge__(SlabWithPore self, SlabWithPore o) -> bool
3372  __ge__(SlabWithPore self, Particle d) -> bool
3373  """
3374  return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3375 
3376 
3377  def __gt__(self, *args):
3378  """
3379  __gt__(SlabWithPore self, SlabWithPore o) -> bool
3380  __gt__(SlabWithPore self, Particle d) -> bool
3381  """
3382  return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3383 
3384 
3385  def __hash__(self):
3386  """__hash__(SlabWithPore self) -> std::size_t"""
3387  return _IMP_npctransport.SlabWithPore___hash__(self)
3388 
3389 
3390  def __str__(self):
3391  """__str__(SlabWithPore self) -> std::string"""
3392  return _IMP_npctransport.SlabWithPore___str__(self)
3393 
3394 
3395  def __repr__(self):
3396  """__repr__(SlabWithPore self) -> std::string"""
3397  return _IMP_npctransport.SlabWithPore___repr__(self)
3398 
3399  __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3400  __del__ = lambda self: None
3401 SlabWithPore_swigregister = _IMP_npctransport.SlabWithPore_swigregister
3402 SlabWithPore_swigregister(SlabWithPore)
3403 
3404 def SlabWithPore_setup_particle(*args):
3405  """
3406  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3407  SlabWithPore_setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3408  """
3409  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3410 
3411 def SlabWithPore_get_is_setup(*args):
3412  """
3413  get_is_setup(_ParticleAdaptor p) -> bool
3414  SlabWithPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3415  """
3416  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3417 
3418 def SlabWithPore_get_thickness_key():
3419  """SlabWithPore_get_thickness_key() -> FloatKey"""
3420  return _IMP_npctransport.SlabWithPore_get_thickness_key()
3421 
3422 def SlabWithPore_get_pore_radius_key():
3423  """SlabWithPore_get_pore_radius_key() -> FloatKey"""
3424  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3425 
3426 class SlabWithCylindricalPore(SlabWithPore):
3427  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3428 
3429  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3430 
3431  def __init__(self, *args):
3432  """
3433  __init__(IMP::npctransport::SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3434  __init__(IMP::npctransport::SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3435  __init__(IMP::npctransport::SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3436  """
3437  this = _IMP_npctransport.new_SlabWithCylindricalPore(*args)
3438  try:
3439  self.this.append(this)
3440  except __builtin__.Exception:
3441  self.this = this
3442 
3443  def show(self, *args):
3444  """
3445  show(SlabWithCylindricalPore self, _ostream out)
3446  show(SlabWithCylindricalPore self)
3447  """
3448  return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3449 
3450 
3451  def setup_particle(*args):
3452  """
3453  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3454  setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3455  """
3456  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3457 
3458  setup_particle = staticmethod(setup_particle)
3459 
3460  def get_is_setup(*args):
3461  """
3462  get_is_setup(_ParticleAdaptor p) -> bool
3463  get_is_setup(Model m, ParticleIndex pi) -> bool
3464  """
3465  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3466 
3467  get_is_setup = staticmethod(get_is_setup)
3468 
3469  def get_cylindrical_pore_key():
3470  """get_cylindrical_pore_key() -> IntKey"""
3471  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3472 
3473  get_cylindrical_pore_key = staticmethod(get_cylindrical_pore_key)
3474 
3475  def add_attribute(self, *args):
3476  """
3477  add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3478  add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3479  add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3480  add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3481  add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3482  add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3483  """
3484  return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3485 
3486 
3487  def get_value(self, *args):
3488  """
3489  get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3490  get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3491  get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3492  get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3493  get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3494  """
3495  return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3496 
3497 
3498  def set_value(self, *args):
3499  """
3500  set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3501  set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3502  set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3503  set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3504  set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3505  """
3506  return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3507 
3508 
3509  def remove_attribute(self, *args):
3510  """
3511  remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3512  remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3513  remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3514  remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3515  remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3516  """
3517  return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3518 
3519 
3520  def has_attribute(self, *args):
3521  """
3522  has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3523  has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3524  has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3525  has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3526  has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3527  """
3528  return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3529 
3530 
3531  def get_derivative(self, a0):
3532  """get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3533  return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3534 
3535 
3536  def get_name(self):
3537  """get_name(SlabWithCylindricalPore self) -> std::string"""
3538  return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3539 
3540 
3541  def clear_caches(self):
3542  """clear_caches(SlabWithCylindricalPore self)"""
3543  return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3544 
3545 
3546  def set_name(self, a0):
3547  """set_name(SlabWithCylindricalPore self, std::string a0)"""
3548  return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3549 
3550 
3551  def set_check_level(self, a0):
3552  """set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3553  return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3554 
3555 
3556  def add_to_derivative(self, a0, a1, a2):
3557  """add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3558  return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3559 
3560 
3561  def set_is_optimized(self, a0, a1):
3562  """set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3563  return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3564 
3565 
3566  def get_is_optimized(self, a0):
3567  """get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3568  return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3569 
3570 
3571  def get_check_level(self):
3572  """get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3573  return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3574 
3575 
3576  def __eq__(self, *args):
3577  """
3578  __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3579  __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3580  """
3581  return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3582 
3583 
3584  def __ne__(self, *args):
3585  """
3586  __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3587  __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3588  """
3589  return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3590 
3591 
3592  def __le__(self, *args):
3593  """
3594  __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3595  __le__(SlabWithCylindricalPore self, Particle d) -> bool
3596  """
3597  return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3598 
3599 
3600  def __lt__(self, *args):
3601  """
3602  __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3603  __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3604  """
3605  return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3606 
3607 
3608  def __ge__(self, *args):
3609  """
3610  __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3611  __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3612  """
3613  return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3614 
3615 
3616  def __gt__(self, *args):
3617  """
3618  __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3619  __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3620  """
3621  return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3622 
3623 
3624  def __hash__(self):
3625  """__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3626  return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3627 
3628 
3629  def __str__(self):
3630  """__str__(SlabWithCylindricalPore self) -> std::string"""
3631  return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3632 
3633 
3634  def __repr__(self):
3635  """__repr__(SlabWithCylindricalPore self) -> std::string"""
3636  return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3637 
3638  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3639  __del__ = lambda self: None
3640 SlabWithCylindricalPore_swigregister = _IMP_npctransport.SlabWithCylindricalPore_swigregister
3641 SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3642 
3643 def SlabWithCylindricalPore_setup_particle(*args):
3644  """
3645  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3646  SlabWithCylindricalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3647  """
3648  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3649 
3650 def SlabWithCylindricalPore_get_is_setup(*args):
3651  """
3652  get_is_setup(_ParticleAdaptor p) -> bool
3653  SlabWithCylindricalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3654  """
3655  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3656 
3657 def SlabWithCylindricalPore_get_cylindrical_pore_key():
3658  """SlabWithCylindricalPore_get_cylindrical_pore_key() -> IntKey"""
3659  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3660 
3661 class SlabWithToroidalPore(SlabWithPore):
3662  """Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3663 
3664  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3665 
3666  def __init__(self, *args):
3667  """
3668  __init__(IMP::npctransport::SlabWithToroidalPore self) -> SlabWithToroidalPore
3669  __init__(IMP::npctransport::SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3670  __init__(IMP::npctransport::SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3671  """
3672  this = _IMP_npctransport.new_SlabWithToroidalPore(*args)
3673  try:
3674  self.this.append(this)
3675  except __builtin__.Exception:
3676  self.this = this
3677 
3678  def show(self, *args):
3679  """
3680  show(SlabWithToroidalPore self, _ostream out)
3681  show(SlabWithToroidalPore self)
3682  """
3683  return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3684 
3685 
3686  def setup_particle(*args):
3687  """
3688  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3689  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
3690  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3691  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3692  """
3693  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3694 
3695  setup_particle = staticmethod(setup_particle)
3696 
3697  def get_is_setup(*args):
3698  """
3699  get_is_setup(_ParticleAdaptor p) -> bool
3700  get_is_setup(Model m, ParticleIndex pi) -> bool
3701  """
3702  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3703 
3704  get_is_setup = staticmethod(get_is_setup)
3705 
3706  def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3707  """set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3708  return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3709 
3710 
3711  def get_minor_radius_h2v_aspect_ratio(self):
3712  """get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3713  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3714 
3715 
3716  def get_vertical_minor_radius(self):
3717  """get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3718  return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3719 
3720 
3721  def set_vertical_minor_radius(self, rv):
3722  """set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3723  return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3724 
3725 
3726  def get_horizontal_minor_radius(self):
3727  """get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3728  return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3729 
3730 
3731  def set_horizontal_minor_radius(self, rh):
3732  """set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3733  return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3734 
3735 
3736  def get_minor_radius_h2v_aspect_ratio_key():
3737  """get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3738  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3739 
3740  get_minor_radius_h2v_aspect_ratio_key = staticmethod(get_minor_radius_h2v_aspect_ratio_key)
3741 
3742  def get_toroidal_pore_key():
3743  """get_toroidal_pore_key() -> IntKey"""
3744  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3745 
3746  get_toroidal_pore_key = staticmethod(get_toroidal_pore_key)
3747 
3748  def add_attribute(self, *args):
3749  """
3750  add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3751  add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3752  add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3753  add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3754  add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3755  add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3756  """
3757  return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3758 
3759 
3760  def get_value(self, *args):
3761  """
3762  get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3763  get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3764  get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3765  get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3766  get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3767  """
3768  return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3769 
3770 
3771  def set_value(self, *args):
3772  """
3773  set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3774  set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3775  set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3776  set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3777  set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3778  """
3779  return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3780 
3781 
3782  def remove_attribute(self, *args):
3783  """
3784  remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3785  remove_attribute(SlabWithToroidalPore self, IntKey a0)
3786  remove_attribute(SlabWithToroidalPore self, StringKey a0)
3787  remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3788  remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3789  """
3790  return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3791 
3792 
3793  def has_attribute(self, *args):
3794  """
3795  has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3796  has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3797  has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3798  has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3799  has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3800  """
3801  return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3802 
3803 
3804  def get_derivative(self, a0):
3805  """get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3806  return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3807 
3808 
3809  def get_name(self):
3810  """get_name(SlabWithToroidalPore self) -> std::string"""
3811  return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3812 
3813 
3814  def clear_caches(self):
3815  """clear_caches(SlabWithToroidalPore self)"""
3816  return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3817 
3818 
3819  def set_name(self, a0):
3820  """set_name(SlabWithToroidalPore self, std::string a0)"""
3821  return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3822 
3823 
3824  def set_check_level(self, a0):
3825  """set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3826  return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3827 
3828 
3829  def add_to_derivative(self, a0, a1, a2):
3830  """add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3831  return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3832 
3833 
3834  def set_is_optimized(self, a0, a1):
3835  """set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3836  return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3837 
3838 
3839  def get_is_optimized(self, a0):
3840  """get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3841  return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
3842 
3843 
3844  def get_check_level(self):
3845  """get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
3846  return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
3847 
3848 
3849  def __eq__(self, *args):
3850  """
3851  __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3852  __eq__(SlabWithToroidalPore self, Particle d) -> bool
3853  """
3854  return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
3855 
3856 
3857  def __ne__(self, *args):
3858  """
3859  __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3860  __ne__(SlabWithToroidalPore self, Particle d) -> bool
3861  """
3862  return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
3863 
3864 
3865  def __le__(self, *args):
3866  """
3867  __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3868  __le__(SlabWithToroidalPore self, Particle d) -> bool
3869  """
3870  return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
3871 
3872 
3873  def __lt__(self, *args):
3874  """
3875  __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3876  __lt__(SlabWithToroidalPore self, Particle d) -> bool
3877  """
3878  return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
3879 
3880 
3881  def __ge__(self, *args):
3882  """
3883  __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3884  __ge__(SlabWithToroidalPore self, Particle d) -> bool
3885  """
3886  return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
3887 
3888 
3889  def __gt__(self, *args):
3890  """
3891  __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
3892  __gt__(SlabWithToroidalPore self, Particle d) -> bool
3893  """
3894  return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
3895 
3896 
3897  def __hash__(self):
3898  """__hash__(SlabWithToroidalPore self) -> std::size_t"""
3899  return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
3900 
3901 
3902  def __str__(self):
3903  """__str__(SlabWithToroidalPore self) -> std::string"""
3904  return _IMP_npctransport.SlabWithToroidalPore___str__(self)
3905 
3906 
3907  def __repr__(self):
3908  """__repr__(SlabWithToroidalPore self) -> std::string"""
3909  return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
3910 
3911  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
3912  __del__ = lambda self: None
3913 SlabWithToroidalPore_swigregister = _IMP_npctransport.SlabWithToroidalPore_swigregister
3914 SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
3915 
3916 def SlabWithToroidalPore_setup_particle(*args):
3917  """
3918  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3919  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
3920  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3921  SlabWithToroidalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3922  """
3923  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3924 
3925 def SlabWithToroidalPore_get_is_setup(*args):
3926  """
3927  get_is_setup(_ParticleAdaptor p) -> bool
3928  SlabWithToroidalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3929  """
3930  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3931 
3932 def SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key():
3933  """SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3934  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3935 
3936 def SlabWithToroidalPore_get_toroidal_pore_key():
3937  """SlabWithToroidalPore_get_toroidal_pore_key() -> IntKey"""
3938  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3939 
3940 
3941 def __lshift__(*args):
3942  """
3943  __lshift__(_ostream out, RelaxingSpring n) -> _ostream
3944  __lshift__(_ostream out, Transporting n) -> _ostream
3945  __lshift__(_ostream out, SlabWithPore n) -> _ostream
3946  __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
3947  __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
3948  """
3949  return _IMP_npctransport.__lshift__(*args)
3950 class SlabWithCylindricalPorePairScore(IMP.PairScore):
3951  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
3952 
3953  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3954 
3955  def __init__(self, k):
3956  """__init__(IMP::npctransport::SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
3957  this = _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k)
3958  try:
3959  self.this.append(this)
3960  except __builtin__.Exception:
3961  self.this = this
3962 
3963  def get_displacement_direction(self, slab, v):
3964  """get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
3965  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
3966 
3967 
3968  def get_displacement_magnitude(self, slab, v):
3969  """get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
3970  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
3971 
3972 
3973  def do_get_inputs(self, m, pis):
3974  """do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3975  return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
3976 
3977 
3978  def get_version_info(self):
3979  """get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
3980  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
3981 
3982 
3983  def __str__(self):
3984  """__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
3985  return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
3986 
3987 
3988  def __repr__(self):
3989  """__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
3990  return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
3991 
3992 
3993  @staticmethod
3994  def get_from(o):
3995  return _object_cast_to_SlabWithCylindricalPorePairScore(o)
3996 
3997 SlabWithCylindricalPorePairScore_swigregister = _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister
3998 SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
3999 
4000 class SlabWithToroidalPorePairScore(IMP.PairScore):
4001  """Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
4002 
4003  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4004 
4005  def __init__(self, k):
4006  """__init__(IMP::npctransport::SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
4007  this = _IMP_npctransport.new_SlabWithToroidalPorePairScore(k)
4008  try:
4009  self.this.append(this)
4010  except __builtin__.Exception:
4011  self.this = this
4012 
4013  def do_get_inputs(self, m, pis):
4014  """do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4015  return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
4016 
4017 
4018  def get_version_info(self):
4019  """get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
4020  return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
4021 
4022 
4023  def __str__(self):
4024  """__str__(SlabWithToroidalPorePairScore self) -> std::string"""
4025  return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
4026 
4027 
4028  def __repr__(self):
4029  """__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
4030  return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
4031 
4032 
4033  @staticmethod
4034  def get_from(o):
4035  return _object_cast_to_SlabWithToroidalPorePairScore(o)
4036 
4037 SlabWithToroidalPorePairScore_swigregister = _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister
4038 SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
4039 
4040 class SlabWithCylindricalPoreWireGeometry(IMP.display.Geometry):
4041  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
4042 
4043  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4044 
4045  def __init__(self, height, radius, length):
4046  """__init__(IMP::npctransport::SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
4047  this = _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length)
4048  try:
4049  self.this.append(this)
4050  except __builtin__.Exception:
4051  self.this = this
4052 
4053  def get_version_info(self):
4054  """get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
4055  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
4056 
4057 
4058  def __str__(self):
4059  """__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4060  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
4061 
4062 
4063  def __repr__(self):
4064  """__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4065  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
4066 
4067 
4068  @staticmethod
4069  def get_from(o):
4070  return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
4071 
4072 SlabWithCylindricalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister
4073 SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
4074 
4075 class SlabWithCylindricalPoreSurfaceGeometry(IMP.display.SurfaceMeshGeometry):
4076  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
4077 
4078  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4079 
4080  def __init__(self, height, radius, length):
4081  """__init__(IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
4082  this = _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length)
4083  try:
4084  self.this.append(this)
4085  except __builtin__.Exception:
4086  self.this = this
4087 
4088  def __str__(self):
4089  """__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4090  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
4091 
4092 
4093  def __repr__(self):
4094  """__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4095  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
4096 
4097 
4098  @staticmethod
4099  def get_from(o):
4100  return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
4101 
4102  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
4103  __del__ = lambda self: None
4104 SlabWithCylindricalPoreSurfaceGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister
4105 SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
4106 
4107 class SlabWithToroidalPoreWireGeometry(IMP.display.Geometry):
4108  """Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
4109 
4110  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4111 
4112  def __init__(self, *args):
4113  """
4114  __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
4115  __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
4116  """
4117  this = _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args)
4118  try:
4119  self.this.append(this)
4120  except __builtin__.Exception:
4121  self.this = this
4122 
4123  def get_version_info(self):
4124  """get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
4125  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
4126 
4127 
4128  def __str__(self):
4129  """__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4130  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
4131 
4132 
4133  def __repr__(self):
4134  """__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4135  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
4136 
4137 
4138  @staticmethod
4139  def get_from(o):
4140  return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
4141 
4142 SlabWithToroidalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister
4143 SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
4144 
4145 class _GenericAttributeSingletonScoreForPoreRadus(IMP.SingletonScore):
4146  """Proxy of C++ IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> class."""
4147 
4148  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4149  __repr__ = _swig_repr
4150 
4151  def __init__(self, f, k):
4152  """__init__(IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
4153  this = _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k)
4154  try:
4155  self.this.append(this)
4156  except __builtin__.Exception:
4157  self.this = this
4158 
4159  def do_get_inputs(self, m, pis):
4160  """do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4161  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
4162 
4163 
4164  def get_unary_function(self):
4165  """get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
4166  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
4167 
4168 
4169  def get_version_info(self):
4170  """get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
4171  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
4172 
4173 _GenericAttributeSingletonScoreForPoreRadus_swigregister = _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister
4174 _GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
4175 
4176 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
4177  """Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
4178 
4179  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4180 
4181  def __init__(self, mean, k):
4182  """__init__(IMP::npctransport::PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
4183  this = _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k)
4184  try:
4185  self.this.append(this)
4186  except __builtin__.Exception:
4187  self.this = this
4188 
4189  def set_k(self, k):
4190  """set_k(PoreRadiusSingletonScore self, double k)"""
4191  return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
4192 
4193 
4194  def __str__(self):
4195  """__str__(PoreRadiusSingletonScore self) -> std::string"""
4196  return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
4197 
4198 
4199  def __repr__(self):
4200  """__repr__(PoreRadiusSingletonScore self) -> std::string"""
4201  return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
4202 
4203 
4204  @staticmethod
4205  def get_from(o):
4206  return _object_cast_to_PoreRadiusSingletonScore(o)
4207 
4208 PoreRadiusSingletonScore_swigregister = _IMP_npctransport.PoreRadiusSingletonScore_swigregister
4209 PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
4210 
4211 class ExcludeZRangeSingletonScore(IMP.SingletonScore):
4212  """Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
4213 
4214  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4215 
4216  def __init__(self, bottom, top, k):
4217  """__init__(IMP::npctransport::ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
4218  this = _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k)
4219  try:
4220  self.this.append(this)
4221  except __builtin__.Exception:
4222  self.this = this
4223 
4224  def get_bottom_z(self):
4225  """get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
4226  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
4227 
4228 
4229  def get_top_z(self):
4230  """get_top_z(ExcludeZRangeSingletonScore self) -> double"""
4231  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
4232 
4233 
4234  def get_k(self):
4235  """get_k(ExcludeZRangeSingletonScore self) -> double"""
4236  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
4237 
4238 
4239  def do_get_inputs(self, m, pis):
4240  """do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4241  return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
4242 
4243 
4244  def get_version_info(self):
4245  """get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
4246  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
4247 
4248 
4249  def __str__(self):
4250  """__str__(ExcludeZRangeSingletonScore self) -> std::string"""
4251  return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
4252 
4253 
4254  def __repr__(self):
4255  """__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
4256  return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
4257 
4258 
4259  @staticmethod
4260  def get_from(o):
4261  return _object_cast_to_ExcludeZRangeSingletonScore(o)
4262 
4263 ExcludeZRangeSingletonScore_swigregister = _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister
4264 ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
4265 
4266 class ZBiasSingletonScore(IMP.SingletonScore):
4267  """Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
4268 
4269  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4270 
4271  def __init__(self, *args):
4272  """
4273  __init__(IMP::npctransport::ZBiasSingletonScore self, double k, double max_r) -> ZBiasSingletonScore
4274  __init__(IMP::npctransport::ZBiasSingletonScore self, double k) -> ZBiasSingletonScore
4275  """
4276  this = _IMP_npctransport.new_ZBiasSingletonScore(*args)
4277  try:
4278  self.this.append(this)
4279  except __builtin__.Exception:
4280  self.this = this
4281 
4282  def get_k(self):
4283  """get_k(ZBiasSingletonScore self) -> double"""
4284  return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
4285 
4286 
4287  def set_k(self, k):
4288  """set_k(ZBiasSingletonScore self, double k)"""
4289  return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
4290 
4291 
4292  def do_get_inputs(self, m, pis):
4293  """do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4294  return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
4295 
4296 
4297  def get_version_info(self):
4298  """get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
4299  return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
4300 
4301 
4302  def __str__(self):
4303  """__str__(ZBiasSingletonScore self) -> std::string"""
4304  return _IMP_npctransport.ZBiasSingletonScore___str__(self)
4305 
4306 
4307  def __repr__(self):
4308  """__repr__(ZBiasSingletonScore self) -> std::string"""
4309  return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
4310 
4311 
4312  @staticmethod
4313  def get_from(o):
4314  return _object_cast_to_ZBiasSingletonScore(o)
4315 
4316 ZBiasSingletonScore_swigregister = _IMP_npctransport.ZBiasSingletonScore_swigregister
4317 ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
4318 
4319 class BodyStatisticsOptimizerState(IMP.OptimizerState):
4320  """Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
4321 
4322  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4323 
4324  def __init__(self, p, statistics_manager=None, periodicity=1):
4325  """
4326  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState
4327  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None) -> BodyStatisticsOptimizerState
4328  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p) -> BodyStatisticsOptimizerState
4329  """
4330  this = _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity)
4331  try:
4332  self.this.append(this)
4333  except __builtin__.Exception:
4334  self.this = this
4335 
4336  def get_correlation_time(self):
4337  """get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4338  return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4339 
4340 
4341  def get_diffusion_coefficient(self):
4342  """get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4343  return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4344 
4345 
4346  def update_particle_type_zr_distribution_map(self):
4347  """update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4348  return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4349 
4350 
4351  def do_update(self, call_num):
4352  """do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4353  return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4354 
4355 
4356  def get_version_info(self):
4357  """get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4358  return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4359 
4360 
4361  def __str__(self):
4362  """__str__(BodyStatisticsOptimizerState self) -> std::string"""
4363  return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4364 
4365 
4366  def __repr__(self):
4367  """__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4368  return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4369 
4370 
4371  @staticmethod
4372  def get_from(o):
4373  return _object_cast_to_BodyStatisticsOptimizerState(o)
4374 
4375 BodyStatisticsOptimizerState_swigregister = _IMP_npctransport.BodyStatisticsOptimizerState_swigregister
4376 BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4377 
4378 class ParticleTransportStatisticsOptimizerState(IMP.OptimizerState):
4379  """Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
4380 
4381  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4382 
4383  def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4384  """
4385  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0, WeakPointer< IMP::atom::Simulator > owner=0) -> ParticleTransportStatisticsOptimizerState
4386  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0) -> ParticleTransportStatisticsOptimizerState
4387  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z) -> ParticleTransportStatisticsOptimizerState
4388  """
4389  this = _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner)
4390  try:
4391  self.this.append(this)
4392  except __builtin__.Exception:
4393  self.this = this
4394 
4395  def set_owner(self, owner):
4396  """set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4397  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4398 
4399 
4400  def get_owner(self):
4401  """get_owner(ParticleTransportStatisticsOptimizerState self) -> WeakPointer< IMP::atom::Simulator >"""
4402  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4403 
4404 
4405  def get_n_transports_up(self):
4406  """get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4407  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4408 
4409 
4410  def get_n_transports_down(self):
4411  """get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4412  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4413 
4414 
4415  def get_total_n_transports(self):
4416  """get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4417  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4418 
4419 
4420  def get_transport_time_points_in_ns(self):
4421  """get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4422  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4423 
4424 
4425  def do_update(self, call_num):
4426  """do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4427  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4428 
4429 
4430  def get_version_info(self):
4431  """get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4432  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4433 
4434 
4435  def __str__(self):
4436  """__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4437  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4438 
4439 
4440  def __repr__(self):
4441  """__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4442  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4443 
4444 
4445  @staticmethod
4446  def get_from(o):
4447  return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4448 
4449 ParticleTransportStatisticsOptimizerState_swigregister = _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister
4450 ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4451 
4452 class ChainStatisticsOptimizerState(IMP.OptimizerState):
4453  """Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
4454 
4455  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4456 
4457  def __init__(self, ps, periodicity=1):
4458  """
4459  __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState
4460  __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps) -> ChainStatisticsOptimizerState
4461  """
4462  this = _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity)
4463  try:
4464  self.this.append(this)
4465  except __builtin__.Exception:
4466  self.this = this
4467 
4468  def get_correlation_time(self):
4469  """get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4470  return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4471 
4472 
4473  def get_local_diffusion_coefficients(self):
4474  """get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4475  return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4476 
4477 
4478  def get_diffusion_coefficient(self):
4479  """get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
4480  return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
4481 
4482 
4483  def get_mean_radius_of_gyration(self):
4484  """get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4485  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
4486 
4487 
4488  def get_mean_square_radius_of_gyration(self):
4489  """get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4490  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4491 
4492 
4493  def get_mean_end_to_end_distance(self):
4494  """get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4495  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4496 
4497 
4498  def get_mean_square_end_to_end_distance(self):
4499  """get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4500  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4501 
4502 
4503  def get_mean_bond_distance(self):
4504  """get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4505  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4506 
4507 
4508  def get_mean_square_bond_distance(self):
4509  """get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4510  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4511 
4512 
4513  def do_update(self, call_num):
4514  """do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4515  return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4516 
4517 
4518  def get_version_info(self):
4519  """get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4520  return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4521 
4522 
4523  def __str__(self):
4524  """__str__(ChainStatisticsOptimizerState self) -> std::string"""
4525  return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4526 
4527 
4528  def __repr__(self):
4529  """__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4530  return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4531 
4532 
4533  @staticmethod
4534  def get_from(o):
4535  return _object_cast_to_ChainStatisticsOptimizerState(o)
4536 
4537 ChainStatisticsOptimizerState_swigregister = _IMP_npctransport.ChainStatisticsOptimizerState_swigregister
4538 ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4539 
4540 class BipartitePairsStatisticsOptimizerState(IMP.OptimizerState):
4541  """Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4542 
4543  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4544 
4545  def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4546  """
4547  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0, double slack=1.0) -> BipartitePairsStatisticsOptimizerState
4548  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0) -> BipartitePairsStatisticsOptimizerState
4549  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII) -> BipartitePairsStatisticsOptimizerState
4550  """
4551  this = _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack)
4552  try:
4553  self.this.append(this)
4554  except __builtin__.Exception:
4555  self.this = this
4556 
4557  def get_interaction_type(self):
4558  """get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4559  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4560 
4561 
4562  def get_average_number_of_contacts(self):
4563  """get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4564  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4565 
4566 
4567  def get_average_off_per_contact_per_ns(self):
4568  """get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4569  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4570 
4571 
4572  def get_average_off_per_bound_I_per_ns(self):
4573  """get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4574  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4575 
4576 
4577  def get_average_off_per_bound_II_per_ns(self):
4578  """get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4579  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4580 
4581 
4582  def get_average_on_per_missing_contact_per_ns(self):
4583  """get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4584  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4585 
4586 
4587  def get_average_on_per_unbound_I_per_ns(self):
4588  """get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4589  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4590 
4591 
4592  def get_average_on_per_unbound_II_per_ns(self):
4593  """get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4594  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4595 
4596 
4597  def get_average_fraction_bound_particles_I(self):
4598  """get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4599  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4600 
4601 
4602  def get_average_fraction_bound_particles_II(self):
4603  """get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4604  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4605 
4606 
4607  def get_average_fraction_bound_particle_sites_I(self):
4608  """get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4609  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4610 
4611 
4612  def get_average_fraction_bound_particle_sites_II(self):
4613  """get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4614  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4615 
4616 
4617  def get_number_of_particles_1(self):
4618  """get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4619  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4620 
4621 
4622  def get_number_of_particles_2(self):
4623  """get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4624  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4625 
4626 
4627  def get_misc_stats_period_ns(self):
4628  """get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4629  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4630 
4631 
4632  def get_off_stats_period_ns(self):
4633  """get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4634  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4635 
4636 
4637  def get_off_I_stats_period_ns(self):
4638  """get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4639  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4640 
4641 
4642  def get_off_II_stats_period_ns(self):
4643  """get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4644  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4645 
4646 
4647  def get_on_stats_period_ns(self):
4648  """get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4649  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4650 
4651 
4652  def get_on_I_stats_period_ns(self):
4653  """get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4654  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4655 
4656 
4657  def get_on_II_stats_period_ns(self):
4658  """get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4659  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4660 
4661 
4662  def get_version_info(self):
4663  """get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4664  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4665 
4666 
4667  def __str__(self):
4668  """__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4669  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4670 
4671 
4672  def __repr__(self):
4673  """__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4674  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4675 
4676 
4677  @staticmethod
4678  def get_from(o):
4679  return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4680 
4681 BipartitePairsStatisticsOptimizerState_swigregister = _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister
4682 BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4683 
4684 
4685 def get_close_pairs_range(*args):
4686  """
4687  get_close_pairs_range(double max_range, double max_range_factor) -> double
4688  get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4689  """
4690  return _IMP_npctransport.get_close_pairs_range(*args)
4691 
4692 def get_time_step(*args):
4693  """
4694  get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0) -> double
4695  get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1) -> double
4696  get_time_step(double max_d_factor, double max_k, double min_radius, double min_range) -> double
4697  get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4698  get_time_step(::npctransport_proto::Assignment const & config) -> double
4699  """
4700  return _IMP_npctransport.get_time_step(*args)
4701 
4702 def get_frames_from_ns(ns, time_step):
4703  """get_frames_from_ns(double ns, double time_step) -> int"""
4704  return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4705 
4706 def get_number_of_frames(config, time_step):
4707  """get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4708  return _IMP_npctransport.get_number_of_frames(config, time_step)
4709 
4710 def get_dump_interval_in_frames(config, time_step):
4711  """get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4712  return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4713 
4714 def get_statistics_interval_in_frames(assign, time_step, default_value_ns=0.1):
4715  """
4716  get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int
4717  get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4718  """
4719  return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4720 
4721 def get_output_statistics_interval_in_frames(assign, time_step, default_value_ns=1.0):
4722  """
4723  get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int
4724  get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4725  """
4726  return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4727 
4728 def initialize_positions(*args):
4729  """
4730  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False, bool are_fgs_pre_initialized=False)
4731  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False)
4732  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0)
4733  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False)
4734  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints)
4735  initialize_positions(SimulationData sd)
4736  """
4737  return _IMP_npctransport.initialize_positions(*args)
4738 class Avro2PBReader(object):
4739  """Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4740 
4741  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4742 
4743  def __init__(self, *args):
4744  """
4745  __init__(IMP::npctransport::Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4746  __init__(IMP::npctransport::Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4747  """
4748  this = _IMP_npctransport.new_Avro2PBReader(*args)
4749  try:
4750  self.this.append(this)
4751  except __builtin__.Exception:
4752  self.this = this
4753  __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4754  __del__ = lambda self: None
4755 
4756  def read_next(self):
4757  """read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4758  return _IMP_npctransport.Avro2PBReader_read_next(self)
4759 
4760 
4761  def get_is_valid(self):
4762  """get_is_valid(Avro2PBReader self) -> bool"""
4763  return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4764 
4765 
4766  def get_cur_file_name(self):
4767  """get_cur_file_name(Avro2PBReader self) -> std::string"""
4768  return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4769 
4770 
4771  def show(self, *args):
4772  """
4773  show(Avro2PBReader self, _ostream out)
4774  show(Avro2PBReader self)
4775  """
4776  return _IMP_npctransport.Avro2PBReader_show(self, *args)
4777 
4778 
4779  def __str__(self):
4780  """__str__(Avro2PBReader self) -> std::string"""
4781  return _IMP_npctransport.Avro2PBReader___str__(self)
4782 
4783 
4784  def __repr__(self):
4785  """__repr__(Avro2PBReader self) -> std::string"""
4786  return _IMP_npctransport.Avro2PBReader___repr__(self)
4787 
4788 Avro2PBReader_swigregister = _IMP_npctransport.Avro2PBReader_swigregister
4789 Avro2PBReader_swigregister(Avro2PBReader)
4790 
4791 
4792 def get_optimizable_particles(particles):
4793  """get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4794  return _IMP_npctransport.get_optimizable_particles(particles)
4795 
4796 def get_non_optimizable_particles(particles):
4797  """get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4798  return _IMP_npctransport.get_non_optimizable_particles(particles)
4799 
4800 def get_particle_indexes(particles):
4801  """get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4802  return _IMP_npctransport.get_particle_indexes(particles)
4803 
4804 def get_protobuf_configuration_from_text(config_txt, config_pb):
4805  """get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4806  return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4807 
4809  """get_maximal_number_of_unordered_pairs(IMP::ParticlesTemp const & ps0, IMP::ParticlesTemp const & ps1) -> unsigned int"""
4810  return _IMP_npctransport.get_maximal_number_of_unordered_pairs(ps0, ps1)
4811 
4812 def get_spheres_from_vectors(vs, radius):
4813  """get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4814  return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4815 
4816 def get_spheres_centers(spheres):
4817  """get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4818  return _IMP_npctransport.get_spheres_centers(spheres)
4819 
4821  """copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4822  return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4823 
4825  """copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4826  return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4827 
4828 def copy_FGs_coordinates(src_sd, trg_sd):
4829  """copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4830  return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4831 
4832 try:
4833  from .npctransport_pb2 import *
4834  import google.protobuf
4835 except ImportError:
4836  print("no protobuf support in python")
4837 from ._configuration import *
4838 
4839 
4840 def get_module_version():
4841  """get_module_version() -> std::string const"""
4842  return _IMP_npctransport.get_module_version()
4843 
4844 def get_example_path(fname):
4845  """get_example_path(std::string fname) -> std::string"""
4846  return _IMP_npctransport.get_example_path(fname)
4847 
4848 def get_data_path(fname):
4849  """get_data_path(std::string fname) -> std::string"""
4850  return _IMP_npctransport.get_data_path(fname)
4851 
4852 from . import _version_check
4853 _version_check.check_version(get_module_version())
4854 __version__ = get_module_version()
4855 
4856 
4857 
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:37
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
FGChain * create_fg_chain(IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
Various classes to hold sets of particles.
int assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed)
The base class for geometry.
int get_output_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
Definition: typedefs.h:45
A base class for geometry from a set of particles.
double get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0)
Make CGAL functionality available to IMP.
void copy_FGs_coordinates(SimulationData const *src_sd, SimulationData *trg_sd)
copy coordinates of src_sd to trg_sd for FG repeats only
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
int get_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)
void get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
Simple Brownian dynamics simulator.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
Common base class for heavy weight IMP objects.
Definition: Object.h:106
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
int get_number_of_frames(const ::npctransport_proto::Assignment &config, double time_step)
Abstract class for scoring object(s) of type ParticleIndex.
int get_frames_from_ns(double ns, double time_step)
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
ParticlesTemp get_optimizable_particles(ParticlesTemp const &particles)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
int get_dump_interval_in_frames(const ::npctransport_proto::Assignment &config, double time_step)
atom::Hierarchies create_hierarchies_with_sites(RMF::FileConstHandle fh, Model *m)
unsigned int get_maximal_number_of_unordered_pairs(ParticlesTemp const &ps0, ParticlesTemp const &ps1)
Definition: util.h:172
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
void add_hierarchies_with_sites(RMF::FileHandle fh, const atom::Hierarchies &hs)
InteractionType make_unordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
Definition: typedefs.h:35
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
FGChain * get_fg_chain(atom::Hierarchy root)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for developing and analyzing benchmarks of IMP code.
InteractionType make_ordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
convenience method for creating and interaction type in swig
Definition: typedefs.h:26
Support for the RMF file format for storing hierarchical molecular data and markup.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
Display an IMP::core::XYZR particle as a ball.
Definition: XYZR.h:151
void add_test_sites(RMF::FileHandle fh, core::ParticleType t, double display_radius, algebra::Vector3Ds sites)
algebra::Sphere3Ds get_spheres_from_vectors(V3iter first, V3iter last, double radius)
convert vectors to spheres of passed radius
Definition: util.h:195