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IMP Reference Guide  2.14.0
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 2007-2020 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_NUMPY = _IMP_npctransport.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_npctransport._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_npctransport._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_npctransport.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_npctransport.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_npctransport.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
292 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
293 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
294 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
295 IMP_BENCHMARK_HAS_NUMPY = _IMP_npctransport.IMP_BENCHMARK_HAS_NUMPY
296 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
297 import IMP.benchmark
298 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
299 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
300 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
301 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
302 IMP_CGAL_HAS_NUMPY = _IMP_npctransport.IMP_CGAL_HAS_NUMPY
303 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
304 import IMP.cgal
305 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
306 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
307 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
308 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
309 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
310 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
311 IMP_ALGEBRA_HAS_NUMPY = _IMP_npctransport.IMP_ALGEBRA_HAS_NUMPY
312 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
313 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
314 import IMP.algebra
315 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
316 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
317 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
318 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
319 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
320 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
321 IMP_DISPLAY_HAS_NUMPY = _IMP_npctransport.IMP_DISPLAY_HAS_NUMPY
322 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
323 import IMP.display
324 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
325 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
326 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
327 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
328 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
329 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
330 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
331 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_NUMPY
332 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
333 import IMP.score_functor
334 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
335 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
336 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
337 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
338 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
339 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
340 IMP_STATISTICS_HAS_NUMPY = _IMP_npctransport.IMP_STATISTICS_HAS_NUMPY
341 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
342 import IMP.statistics
343 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
344 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
345 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
346 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
348 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
349 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
350 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
351 IMP_CORE_HAS_NUMPY = _IMP_npctransport.IMP_CORE_HAS_NUMPY
352 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
353 import IMP.core
354 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
355 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
356 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
357 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
358 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
359 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
360 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
362 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
363 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
364 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
365 IMP_CONTAINER_HAS_NUMPY = _IMP_npctransport.IMP_CONTAINER_HAS_NUMPY
366 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
367 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
368 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
369 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
370 import IMP.container
371 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
372 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
373 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
374 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
376 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
377 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
378 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
379 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
380 IMP_ATOM_HAS_NUMPY = _IMP_npctransport.IMP_ATOM_HAS_NUMPY
381 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
382 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
383 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
384 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
385 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
386 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
387 import IMP.atom
388 IMP_EM_HAS_IMP_CGAL = _IMP_npctransport.IMP_EM_HAS_IMP_CGAL
389 IMP_EM_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_EM_HAS_IMP_CONTAINER
390 IMP_EM_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_EM_HAS_IMP_DISPLAY
391 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_EM_HAS_IMP_SCORE_FUNCTOR
392 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_FILESYSTEM
393 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
394 IMP_EM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_EM_HAS_BOOST_RANDOM
395 IMP_EM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_EM_HAS_BOOST_REGEX
396 IMP_EM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_SYSTEM
397 IMP_EM_HAS_CGAL = _IMP_npctransport.IMP_EM_HAS_CGAL
398 IMP_EM_HAS_HDF5 = _IMP_npctransport.IMP_EM_HAS_HDF5
399 IMP_EM_HAS_NUMPY = _IMP_npctransport.IMP_EM_HAS_NUMPY
400 IMP_EM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_EM_HAS_PYTHON_IHM
401 IMPEM_SHOW_WARNINGS = _IMP_npctransport.IMPEM_SHOW_WARNINGS
402 import IMP.em
403 IMP_SAXS_HAS_IMP_CGAL = _IMP_npctransport.IMP_SAXS_HAS_IMP_CGAL
404 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_SAXS_HAS_IMP_CONTAINER
405 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_SAXS_HAS_IMP_DISPLAY
406 IMP_SAXS_HAS_IMP_KERNEL = _IMP_npctransport.IMP_SAXS_HAS_IMP_KERNEL
407 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
408 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_FILESYSTEM
409 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
410 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_RANDOM
411 IMP_SAXS_HAS_BOOST_REGEX = _IMP_npctransport.IMP_SAXS_HAS_BOOST_REGEX
412 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_SYSTEM
413 IMP_SAXS_HAS_CGAL = _IMP_npctransport.IMP_SAXS_HAS_CGAL
414 IMP_SAXS_HAS_HDF5 = _IMP_npctransport.IMP_SAXS_HAS_HDF5
415 IMP_SAXS_HAS_NUMPY = _IMP_npctransport.IMP_SAXS_HAS_NUMPY
416 IMP_SAXS_HAS_PYTHON_IHM = _IMP_npctransport.IMP_SAXS_HAS_PYTHON_IHM
417 IMPSAXS_SHOW_WARNINGS = _IMP_npctransport.IMPSAXS_SHOW_WARNINGS
418 import IMP.saxs
419 IMP_ISD_HAS_IMP_CGAL = _IMP_npctransport.IMP_ISD_HAS_IMP_CGAL
420 IMP_ISD_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_ISD_HAS_IMP_DISPLAY
421 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
422 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_FILESYSTEM
423 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
424 IMP_ISD_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ISD_HAS_BOOST_RANDOM
425 IMP_ISD_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ISD_HAS_BOOST_REGEX
426 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_SYSTEM
427 IMP_ISD_HAS_CGAL = _IMP_npctransport.IMP_ISD_HAS_CGAL
428 IMP_ISD_HAS_HDF5 = _IMP_npctransport.IMP_ISD_HAS_HDF5
429 IMP_ISD_HAS_NUMPY = _IMP_npctransport.IMP_ISD_HAS_NUMPY
430 IMP_ISD_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ISD_HAS_PYTHON_IHM
431 IMPISD_SHOW_WARNINGS = _IMP_npctransport.IMPISD_SHOW_WARNINGS
432 import IMP.isd
433 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
434 IMP_RMF_HAS_IMP_EM = _IMP_npctransport.IMP_RMF_HAS_IMP_EM
435 IMP_RMF_HAS_IMP_SAXS = _IMP_npctransport.IMP_RMF_HAS_IMP_SAXS
436 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
437 IMP_RMF_HAS_IMP_STATISTICS = _IMP_npctransport.IMP_RMF_HAS_IMP_STATISTICS
438 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
439 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
440 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
441 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
442 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
443 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
444 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
445 IMP_RMF_HAS_NUMPY = _IMP_npctransport.IMP_RMF_HAS_NUMPY
446 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
447 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
448 import IMP.rmf
449 import RMF
450 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
451 IMP_NPCTRANSPORT_HAS_IMP_EM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_EM
452 IMP_NPCTRANSPORT_HAS_IMP_ISD = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_ISD
453 IMP_NPCTRANSPORT_HAS_IMP_SAXS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_SAXS
454 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
455 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
456 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
457 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
458 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
459 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
460 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
461 IMP_NPCTRANSPORT_HAS_NUMPY = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_NUMPY
462 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
463 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
464 
465 _object_types.append("SitesPairScore")
466 
467 
468 def _object_cast_to_SitesPairScore(o):
469  """_object_cast_to_SitesPairScore(Object o) -> SitesPairScore"""
470  return _IMP_npctransport._object_cast_to_SitesPairScore(o)
471 
472 _object_types.append("Scoring")
473 
474 
475 def _object_cast_to_Scoring(o):
476  """_object_cast_to_Scoring(Object o) -> Scoring"""
477  return _IMP_npctransport._object_cast_to_Scoring(o)
478 
479 _object_types.append("BrownianDynamicsTAMDWithSlabSupport")
480 
481 
482 def _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o):
483  """_object_cast_to_BrownianDynamicsTAMDWithSlabSupport(Object o) -> BrownianDynamicsTAMDWithSlabSupport"""
484  return _IMP_npctransport._object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
485 
486 _object_types.append("Statistics")
487 
488 
489 def _object_cast_to_Statistics(o):
490  """_object_cast_to_Statistics(Object o) -> Statistics"""
491  return _IMP_npctransport._object_cast_to_Statistics(o)
492 
493 _object_types.append("SimulationData")
494 
495 
496 def _object_cast_to_SimulationData(o):
497  """_object_cast_to_SimulationData(Object o) -> SimulationData"""
498  return _IMP_npctransport._object_cast_to_SimulationData(o)
499 
500 _object_types.append("SitesGeometry")
501 
502 
503 def _object_cast_to_SitesGeometry(o):
504  """_object_cast_to_SitesGeometry(Object o) -> SitesGeometry"""
505  return _IMP_npctransport._object_cast_to_SitesGeometry(o)
506 
507 _object_types.append("TypedSitesGeometry")
508 
509 
510 def _object_cast_to_TypedSitesGeometry(o):
511  """_object_cast_to_TypedSitesGeometry(Object o) -> TypedSitesGeometry"""
512  return _IMP_npctransport._object_cast_to_TypedSitesGeometry(o)
513 
514 _object_types.append("SlabWithCylindricalPorePairScore")
515 
516 
517 def _object_cast_to_SlabWithCylindricalPorePairScore(o):
518  """_object_cast_to_SlabWithCylindricalPorePairScore(Object o) -> SlabWithCylindricalPorePairScore"""
519  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPorePairScore(o)
520 
521 _object_types.append("SlabWithToroidalPorePairScore")
522 
523 
524 def _object_cast_to_SlabWithToroidalPorePairScore(o):
525  """_object_cast_to_SlabWithToroidalPorePairScore(Object o) -> SlabWithToroidalPorePairScore"""
526  return _IMP_npctransport._object_cast_to_SlabWithToroidalPorePairScore(o)
527 
528 _object_types.append("PoreRadiusSingletonScore")
529 
530 
531 def _object_cast_to_PoreRadiusSingletonScore(o):
532  """_object_cast_to_PoreRadiusSingletonScore(Object o) -> PoreRadiusSingletonScore"""
533  return _IMP_npctransport._object_cast_to_PoreRadiusSingletonScore(o)
534 
535 _object_types.append("ExcludeZRangeSingletonScore")
536 
537 
538 def _object_cast_to_ExcludeZRangeSingletonScore(o):
539  """_object_cast_to_ExcludeZRangeSingletonScore(Object o) -> ExcludeZRangeSingletonScore"""
540  return _IMP_npctransport._object_cast_to_ExcludeZRangeSingletonScore(o)
541 
542 _object_types.append("ZBiasSingletonScore")
543 
544 
545 def _object_cast_to_ZBiasSingletonScore(o):
546  """_object_cast_to_ZBiasSingletonScore(Object o) -> ZBiasSingletonScore"""
547  return _IMP_npctransport._object_cast_to_ZBiasSingletonScore(o)
548 
549 _object_types.append("SlabWithCylindricalPoreWireGeometry")
550 
551 
552 def _object_cast_to_SlabWithCylindricalPoreWireGeometry(o):
553  """_object_cast_to_SlabWithCylindricalPoreWireGeometry(Object o) -> SlabWithCylindricalPoreWireGeometry"""
554  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
555 
556 _object_types.append("SlabWithCylindricalPoreSurfaceGeometry")
557 
558 
559 def _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o):
560  """_object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(Object o) -> SlabWithCylindricalPoreSurfaceGeometry"""
561  return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
562 
563 _object_types.append("SlabWithToroidalPoreWireGeometry")
564 
565 
566 def _object_cast_to_SlabWithToroidalPoreWireGeometry(o):
567  """_object_cast_to_SlabWithToroidalPoreWireGeometry(Object o) -> SlabWithToroidalPoreWireGeometry"""
568  return _IMP_npctransport._object_cast_to_SlabWithToroidalPoreWireGeometry(o)
569 
570 _object_types.append("LinearSoftSpherePairScore")
571 
572 
573 def _object_cast_to_LinearSoftSpherePairScore(o):
574  """_object_cast_to_LinearSoftSpherePairScore(Object o) -> LinearSoftSpherePairScore"""
575  return _IMP_npctransport._object_cast_to_LinearSoftSpherePairScore(o)
576 
577 _object_types.append("FunctorLinearSoftSpherePairScore")
578 
579 
580 def _object_cast_to_FunctorLinearSoftSpherePairScore(o):
581  """_object_cast_to_FunctorLinearSoftSpherePairScore(Object o) -> FunctorLinearSoftSpherePairScore"""
582  return _IMP_npctransport._object_cast_to_FunctorLinearSoftSpherePairScore(o)
583 
584 _object_types.append("LinearInteractionPairScore")
585 
586 
587 def _object_cast_to_LinearInteractionPairScore(o):
588  """_object_cast_to_LinearInteractionPairScore(Object o) -> LinearInteractionPairScore"""
589  return _IMP_npctransport._object_cast_to_LinearInteractionPairScore(o)
590 
591 _object_types.append("FunctorLinearInteractionPairScore")
592 
593 
594 def _object_cast_to_FunctorLinearInteractionPairScore(o):
595  """_object_cast_to_FunctorLinearInteractionPairScore(Object o) -> FunctorLinearInteractionPairScore"""
596  return _IMP_npctransport._object_cast_to_FunctorLinearInteractionPairScore(o)
597 
598 _object_types.append("LinearWellPairScore")
599 
600 
601 def _object_cast_to_LinearWellPairScore(o):
602  """_object_cast_to_LinearWellPairScore(Object o) -> LinearWellPairScore"""
603  return _IMP_npctransport._object_cast_to_LinearWellPairScore(o)
604 
605 _object_types.append("HarmonicSpringSingletonScore")
606 
607 
608 def _object_cast_to_HarmonicSpringSingletonScore(o):
609  """_object_cast_to_HarmonicSpringSingletonScore(Object o) -> HarmonicSpringSingletonScore"""
610  return _IMP_npctransport._object_cast_to_HarmonicSpringSingletonScore(o)
611 
612 _object_types.append("HierarchyWithSitesSaveLink")
613 
614 
615 def _object_cast_to_HierarchyWithSitesSaveLink(o):
616  """_object_cast_to_HierarchyWithSitesSaveLink(Object o) -> HierarchyWithSitesSaveLink"""
617  return _IMP_npctransport._object_cast_to_HierarchyWithSitesSaveLink(o)
618 
619 _object_types.append("HierarchyWithSitesLoadLink")
620 
621 
622 def _object_cast_to_HierarchyWithSitesLoadLink(o):
623  """_object_cast_to_HierarchyWithSitesLoadLink(Object o) -> HierarchyWithSitesLoadLink"""
624  return _IMP_npctransport._object_cast_to_HierarchyWithSitesLoadLink(o)
625 
626 _object_types.append("ChainStatisticsOptimizerState")
627 
628 
629 def _object_cast_to_ChainStatisticsOptimizerState(o):
630  """_object_cast_to_ChainStatisticsOptimizerState(Object o) -> ChainStatisticsOptimizerState"""
631  return _IMP_npctransport._object_cast_to_ChainStatisticsOptimizerState(o)
632 
633 _object_types.append("BodyStatisticsOptimizerState")
634 
635 
636 def _object_cast_to_BodyStatisticsOptimizerState(o):
637  """_object_cast_to_BodyStatisticsOptimizerState(Object o) -> BodyStatisticsOptimizerState"""
638  return _IMP_npctransport._object_cast_to_BodyStatisticsOptimizerState(o)
639 
640 _object_types.append("BipartitePairsStatisticsOptimizerState")
641 
642 
643 def _object_cast_to_BipartitePairsStatisticsOptimizerState(o):
644  """_object_cast_to_BipartitePairsStatisticsOptimizerState(Object o) -> BipartitePairsStatisticsOptimizerState"""
645  return _IMP_npctransport._object_cast_to_BipartitePairsStatisticsOptimizerState(o)
646 
647 _object_types.append("ParticleTransportStatisticsOptimizerState")
648 
649 
650 def _object_cast_to_ParticleTransportStatisticsOptimizerState(o):
651  """_object_cast_to_ParticleTransportStatisticsOptimizerState(Object o) -> ParticleTransportStatisticsOptimizerState"""
652  return _IMP_npctransport._object_cast_to_ParticleTransportStatisticsOptimizerState(o)
653 
654 _object_types.append("FGChain")
655 
656 
657 def _object_cast_to_FGChain(o):
658  """_object_cast_to_FGChain(Object o) -> FGChain"""
659  return _IMP_npctransport._object_cast_to_FGChain(o)
660 
661 _object_types.append("ParticleFactory")
662 
663 
664 def _object_cast_to_ParticleFactory(o):
665  """_object_cast_to_ParticleFactory(Object o) -> ParticleFactory"""
666  return _IMP_npctransport._object_cast_to_ParticleFactory(o)
667 
668 Avro2PBReaders=list
669 _plural_types.append("Avro2PBReaders")
670 _value_types.append("Avro2PBReader")
671 
672 
673 SitesPairScoreParametersList=list
674 _plural_types.append("SitesPairScoreParametersList")
675 _value_types.append("SitesPairScoreParameters")
676 
677 
678 def Transportings(l=[]):
679  return [Transporting(x) for x in l]
680 _plural_types.append("Transportings")
681 
682 
683 _value_types.append("Transporting")
684 
685 
686 def SlabWithPores(l=[]):
687  return [SlabWithPore(x) for x in l]
688 _plural_types.append("SlabWithPores")
689 
690 
691 _value_types.append("SlabWithPore")
692 
693 
694 def SlabWithCylindricalPores(l=[]):
695  return [SlabWithCylindricalPore(x) for x in l]
696 _plural_types.append("SlabWithCylindricalPores")
697 
698 
699 _value_types.append("SlabWithCylindricalPore")
700 
701 
702 def RelaxingSprings(l=[]):
703  return [RelaxingSpring(x) for x in l]
704 _plural_types.append("RelaxingSprings")
705 
706 
707 _value_types.append("RelaxingSpring")
708 
709 
710 def SlabWithToroidalPores(l=[]):
711  return [SlabWithToroidalPore(x) for x in l]
712 _plural_types.append("SlabWithToroidalPores")
713 
714 
715 _value_types.append("SlabWithToroidalPore")
716 
717 class _DoubleParameter(object):
718  """Proxy of C++ IMP::npctransport::Parameter<(double)> class."""
719 
720  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
721  __repr__ = _swig_repr
722 
723  def __init__(self, *args):
724  """
725  __init__(IMP::npctransport::Parameter<(double)> self) -> _DoubleParameter
726  __init__(IMP::npctransport::Parameter<(double)> self, double t) -> _DoubleParameter
727  """
728  this = _IMP_npctransport.new__DoubleParameter(*args)
729  try:
730  self.this.append(this)
731  except __builtin__.Exception:
732  self.this = this
733 
734  def get_value(self):
735  """get_value(_DoubleParameter self) -> double"""
736  return _IMP_npctransport._DoubleParameter_get_value(self)
737 
738 
739  def is_init(self):
740  """is_init(_DoubleParameter self) -> bool"""
741  return _IMP_npctransport._DoubleParameter_is_init(self)
742 
743  __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
744  __del__ = lambda self: None
745 _DoubleParameter_swigregister = _IMP_npctransport._DoubleParameter_swigregister
746 _DoubleParameter_swigregister(_DoubleParameter)
747 
748 class _IntParameter(object):
749  """Proxy of C++ IMP::npctransport::Parameter<(int)> class."""
750 
751  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
752  __repr__ = _swig_repr
753 
754  def __init__(self, *args):
755  """
756  __init__(IMP::npctransport::Parameter<(int)> self) -> _IntParameter
757  __init__(IMP::npctransport::Parameter<(int)> self, int t) -> _IntParameter
758  """
759  this = _IMP_npctransport.new__IntParameter(*args)
760  try:
761  self.this.append(this)
762  except __builtin__.Exception:
763  self.this = this
764 
765  def get_value(self):
766  """get_value(_IntParameter self) -> int"""
767  return _IMP_npctransport._IntParameter_get_value(self)
768 
769 
770  def is_init(self):
771  """is_init(_IntParameter self) -> bool"""
772  return _IMP_npctransport._IntParameter_is_init(self)
773 
774  __swig_destroy__ = _IMP_npctransport.delete__IntParameter
775  __del__ = lambda self: None
776 _IntParameter_swigregister = _IMP_npctransport._IntParameter_swigregister
777 _IntParameter_swigregister(_IntParameter)
778 
779 class _BoolParameter(object):
780  """Proxy of C++ IMP::npctransport::Parameter<(bool)> class."""
781 
782  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
783  __repr__ = _swig_repr
784 
785  def __init__(self, *args):
786  """
787  __init__(IMP::npctransport::Parameter<(bool)> self) -> _BoolParameter
788  __init__(IMP::npctransport::Parameter<(bool)> self, bool t) -> _BoolParameter
789  """
790  this = _IMP_npctransport.new__BoolParameter(*args)
791  try:
792  self.this.append(this)
793  except __builtin__.Exception:
794  self.this = this
795 
796  def get_value(self):
797  """get_value(_BoolParameter self) -> bool"""
798  return _IMP_npctransport._BoolParameter_get_value(self)
799 
800 
801  def is_init(self):
802  """is_init(_BoolParameter self) -> bool"""
803  return _IMP_npctransport._BoolParameter_is_init(self)
804 
805  __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
806  __del__ = lambda self: None
807 _BoolParameter_swigregister = _IMP_npctransport._BoolParameter_swigregister
808 _BoolParameter_swigregister(_BoolParameter)
809 
810 
812  """make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
813  return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
814 
816  """make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
817  return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
818 
820  """
821  make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
822  make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
823  """
824  return _IMP_npctransport.make_unordered_particle_index_pair(*args)
825 class LinearSoftSpherePairScore(IMP.PairScore):
826  """Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class."""
827 
828  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
829 
830  def __init__(self, *args):
831  """
832  __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k, std::string name) -> LinearSoftSpherePairScore
833  __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k) -> LinearSoftSpherePairScore
834  """
835  this = _IMP_npctransport.new_LinearSoftSpherePairScore(*args)
836  try:
837  self.this.append(this)
838  except __builtin__.Exception:
839  self.this = this
840 
841  def do_get_inputs(self, m, pis):
842  """do_get_inputs(LinearSoftSpherePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
843  return _IMP_npctransport.LinearSoftSpherePairScore_do_get_inputs(self, m, pis)
844 
845 
846  def get_k(self):
847  """get_k(LinearSoftSpherePairScore self) -> double"""
848  return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
849 
850 
851  def get_version_info(self):
852  """get_version_info(LinearSoftSpherePairScore self) -> VersionInfo"""
853  return _IMP_npctransport.LinearSoftSpherePairScore_get_version_info(self)
854 
855 
856  def __str__(self):
857  """__str__(LinearSoftSpherePairScore self) -> std::string"""
858  return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
859 
860 
861  def __repr__(self):
862  """__repr__(LinearSoftSpherePairScore self) -> std::string"""
863  return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
864 
865 
866  @staticmethod
867  def get_from(o):
868  return _object_cast_to_LinearSoftSpherePairScore(o)
869 
870 LinearSoftSpherePairScore_swigregister = _IMP_npctransport.LinearSoftSpherePairScore_swigregister
871 LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
872 
873 class LinearInteractionPairScore(IMP.PairScore):
874  """Proxy of C++ IMP::npctransport::LinearInteractionPairScore class."""
875 
876  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
877 
878  def __init__(self, *args):
879  """
880  __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr, std::string name) -> LinearInteractionPairScore
881  __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr) -> LinearInteractionPairScore
882  """
883  this = _IMP_npctransport.new_LinearInteractionPairScore(*args)
884  try:
885  self.this.append(this)
886  except __builtin__.Exception:
887  self.this = this
888 
889  def evaluate_if_good_index(self, *args):
890  """
891  evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPair const & p, DerivativeAccumulator da, double max) -> double
892  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
893  """
894  return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
895 
896 
897  def do_get_inputs(self, m, pis):
898  """do_get_inputs(LinearInteractionPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
899  return _IMP_npctransport.LinearInteractionPairScore_do_get_inputs(self, m, pis)
900 
901 
902  def get_range_attraction(self):
903  """get_range_attraction(LinearInteractionPairScore self) -> double"""
904  return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
905 
906 
907  def get_k_attraction(self):
908  """get_k_attraction(LinearInteractionPairScore self) -> double"""
909  return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
910 
911 
912  def set_k_attraction(self, k_attr):
913  """set_k_attraction(LinearInteractionPairScore self, double k_attr)"""
914  return _IMP_npctransport.LinearInteractionPairScore_set_k_attraction(self, k_attr)
915 
916 
917  def get_k_repulsion(self):
918  """get_k_repulsion(LinearInteractionPairScore self) -> double"""
919  return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
920 
921 
922  def set_k_repulsion(self, k_rep):
923  """set_k_repulsion(LinearInteractionPairScore self, double k_rep)"""
924  return _IMP_npctransport.LinearInteractionPairScore_set_k_repulsion(self, k_rep)
925 
926 
927  def get_version_info(self):
928  """get_version_info(LinearInteractionPairScore self) -> VersionInfo"""
929  return _IMP_npctransport.LinearInteractionPairScore_get_version_info(self)
930 
931 
932  def __str__(self):
933  """__str__(LinearInteractionPairScore self) -> std::string"""
934  return _IMP_npctransport.LinearInteractionPairScore___str__(self)
935 
936 
937  def __repr__(self):
938  """__repr__(LinearInteractionPairScore self) -> std::string"""
939  return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
940 
941 
942  @staticmethod
943  def get_from(o):
944  return _object_cast_to_LinearInteractionPairScore(o)
945 
946 LinearInteractionPairScore_swigregister = _IMP_npctransport.LinearInteractionPairScore_swigregister
947 LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
948 
949 class LinearWellPairScore(IMP.PairScore):
950  """Proxy of C++ IMP::npctransport::LinearWellPairScore 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::LinearWellPairScore self, double rest_length_factor, double k, std::string name) -> LinearWellPairScore
957  __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k) -> LinearWellPairScore
958  """
959  this = _IMP_npctransport.new_LinearWellPairScore(*args)
960  try:
961  self.this.append(this)
962  except __builtin__.Exception:
963  self.this = this
964 
965  def set_rest_length_factor(self, rest_length_factor):
966  """set_rest_length_factor(LinearWellPairScore self, double rest_length_factor)"""
967  return _IMP_npctransport.LinearWellPairScore_set_rest_length_factor(self, rest_length_factor)
968 
969 
970  def get_rest_length_factor(self):
971  """get_rest_length_factor(LinearWellPairScore self) -> double"""
972  return _IMP_npctransport.LinearWellPairScore_get_rest_length_factor(self)
973 
974 
975  def set_k(self, k):
976  """set_k(LinearWellPairScore self, double k)"""
977  return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
978 
979 
980  def get_k(self):
981  """get_k(LinearWellPairScore self) -> double"""
982  return _IMP_npctransport.LinearWellPairScore_get_k(self)
983 
984 
985  def do_get_inputs(self, m, pis):
986  """do_get_inputs(LinearWellPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
987  return _IMP_npctransport.LinearWellPairScore_do_get_inputs(self, m, pis)
988 
989 
990  def get_version_info(self):
991  """get_version_info(LinearWellPairScore self) -> VersionInfo"""
992  return _IMP_npctransport.LinearWellPairScore_get_version_info(self)
993 
994 
995  def __str__(self):
996  """__str__(LinearWellPairScore self) -> std::string"""
997  return _IMP_npctransport.LinearWellPairScore___str__(self)
998 
999 
1000  def __repr__(self):
1001  """__repr__(LinearWellPairScore self) -> std::string"""
1002  return _IMP_npctransport.LinearWellPairScore___repr__(self)
1003 
1004 
1005  @staticmethod
1006  def get_from(o):
1007  return _object_cast_to_LinearWellPairScore(o)
1008 
1009 LinearWellPairScore_swigregister = _IMP_npctransport.LinearWellPairScore_swigregister
1010 LinearWellPairScore_swigregister(LinearWellPairScore)
1011 
1012 class RelaxingSpring(IMP.Decorator):
1013  """Proxy of C++ IMP::npctransport::RelaxingSpring class."""
1014 
1015  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1016 
1017  def __init__(self, *args):
1018  """
1019  __init__(IMP::npctransport::RelaxingSpring self) -> RelaxingSpring
1020  __init__(IMP::npctransport::RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
1021  __init__(IMP::npctransport::RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
1022  """
1023  this = _IMP_npctransport.new_RelaxingSpring(*args)
1024  try:
1025  self.this.append(this)
1026  except __builtin__.Exception:
1027  self.this = this
1028 
1029  def show(self, *args):
1030  """
1031  show(RelaxingSpring self, _ostream out)
1032  show(RelaxingSpring self)
1033  """
1034  return _IMP_npctransport.RelaxingSpring_show(self, *args)
1035 
1036 
1037  def setup_particle(*args):
1038  """
1039  setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1040  setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1041  """
1042  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1043 
1044  setup_particle = staticmethod(setup_particle)
1045 
1046  def get_is_setup(*args):
1047  """
1048  get_is_setup(_ParticleAdaptor p) -> bool
1049  get_is_setup(Model m, ParticleIndex pi) -> bool
1050  """
1051  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1052 
1053  get_is_setup = staticmethod(get_is_setup)
1054 
1055  def get_bonded_particle_0_key():
1056  """get_bonded_particle_0_key() -> ParticleIndexKey"""
1057  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1058 
1059  get_bonded_particle_0_key = staticmethod(get_bonded_particle_0_key)
1060 
1061  def get_bonded_particle_1_key():
1062  """get_bonded_particle_1_key() -> ParticleIndexKey"""
1063  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1064 
1065  get_bonded_particle_1_key = staticmethod(get_bonded_particle_1_key)
1066 
1067  def get_equilibrium_rest_length_factor_key():
1068  """get_equilibrium_rest_length_factor_key() -> FloatKey"""
1069  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1070 
1071  get_equilibrium_rest_length_factor_key = staticmethod(get_equilibrium_rest_length_factor_key)
1072 
1073  def get_rest_length_key():
1074  """get_rest_length_key() -> FloatKey"""
1075  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1076 
1077  get_rest_length_key = staticmethod(get_rest_length_key)
1078 
1079  def get_rest_length_diffusion_coefficient_key():
1080  """get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1081  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1082 
1083  get_rest_length_diffusion_coefficient_key = staticmethod(get_rest_length_diffusion_coefficient_key)
1084 
1085  def get_bonded_particle_0(self):
1086  """get_bonded_particle_0(RelaxingSpring self) -> Particle"""
1087  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0(self)
1088 
1089 
1090  def get_bonded_particle_1(self):
1091  """get_bonded_particle_1(RelaxingSpring self) -> Particle"""
1092  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1(self)
1093 
1094 
1095  def get_bonded_particle_index_0(self):
1096  """get_bonded_particle_index_0(RelaxingSpring self) -> ParticleIndex"""
1097  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_0(self)
1098 
1099 
1100  def get_bonded_particle_index_1(self):
1101  """get_bonded_particle_index_1(RelaxingSpring self) -> ParticleIndex"""
1102  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_1(self)
1103 
1104 
1105  def get_equilibrium_rest_length_factor(self):
1106  """get_equilibrium_rest_length_factor(RelaxingSpring self) -> IMP::Float"""
1107  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor(self)
1108 
1109 
1110  def set_equilibrium_rest_length_factor(self, t):
1111  """set_equilibrium_rest_length_factor(RelaxingSpring self, IMP::Float t)"""
1112  return _IMP_npctransport.RelaxingSpring_set_equilibrium_rest_length_factor(self, t)
1113 
1114 
1115  def get_rest_length(self):
1116  """get_rest_length(RelaxingSpring self) -> IMP::Float"""
1117  return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1118 
1119 
1120  def set_rest_length(self, t):
1121  """set_rest_length(RelaxingSpring self, IMP::Float t)"""
1122  return _IMP_npctransport.RelaxingSpring_set_rest_length(self, t)
1123 
1124 
1125  def get_rest_length_diffusion_coefficient(self):
1126  """get_rest_length_diffusion_coefficient(RelaxingSpring self) -> IMP::Float"""
1127  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient(self)
1128 
1129 
1130  def set_rest_length_diffusion_coefficient(self, t):
1131  """set_rest_length_diffusion_coefficient(RelaxingSpring self, IMP::Float t)"""
1132  return _IMP_npctransport.RelaxingSpring_set_rest_length_diffusion_coefficient(self, t)
1133 
1134 
1135  def add_to_rest_length_derivative(self, d, da):
1136  """add_to_rest_length_derivative(RelaxingSpring self, double d, DerivativeAccumulator da)"""
1137  return _IMP_npctransport.RelaxingSpring_add_to_rest_length_derivative(self, d, da)
1138 
1139 
1140  def get_rest_length_derivative(self):
1141  """get_rest_length_derivative(RelaxingSpring self) -> double"""
1142  return _IMP_npctransport.RelaxingSpring_get_rest_length_derivative(self)
1143 
1144 
1145  def add_attribute(self, *args):
1146  """
1147  add_attribute(RelaxingSpring self, FloatKey k, IMP::Float v, bool opt)
1148  add_attribute(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1149  add_attribute(RelaxingSpring self, IntKey a0, IMP::Int a1)
1150  add_attribute(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1151  add_attribute(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1152  add_attribute(RelaxingSpring self, StringKey a0, IMP::String a1)
1153  add_attribute(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1154  add_attribute(RelaxingSpring self, ObjectKey a0, Object a1)
1155  """
1156  return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1157 
1158 
1159  def get_value(self, *args):
1160  """
1161  get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1162  get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1163  get_value(RelaxingSpring self, FloatsKey a0) -> IMP::Floats
1164  get_value(RelaxingSpring self, IntsKey a0) -> IMP::Ints
1165  get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1166  get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1167  get_value(RelaxingSpring self, ObjectKey a0) -> Object
1168  """
1169  return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1170 
1171 
1172  def set_value(self, *args):
1173  """
1174  set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1175  set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1176  set_value(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1177  set_value(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1178  set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1179  set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1180  set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1181  """
1182  return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1183 
1184 
1185  def remove_attribute(self, *args):
1186  """
1187  remove_attribute(RelaxingSpring self, FloatKey a0)
1188  remove_attribute(RelaxingSpring self, IntKey a0)
1189  remove_attribute(RelaxingSpring self, FloatsKey a0)
1190  remove_attribute(RelaxingSpring self, IntsKey a0)
1191  remove_attribute(RelaxingSpring self, StringKey a0)
1192  remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1193  remove_attribute(RelaxingSpring self, ObjectKey a0)
1194  """
1195  return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1196 
1197 
1198  def has_attribute(self, *args):
1199  """
1200  has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1201  has_attribute(RelaxingSpring self, IntKey a0) -> bool
1202  has_attribute(RelaxingSpring self, FloatsKey a0) -> bool
1203  has_attribute(RelaxingSpring self, IntsKey a0) -> bool
1204  has_attribute(RelaxingSpring self, StringKey a0) -> bool
1205  has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1206  has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1207  """
1208  return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1209 
1210 
1211  def get_derivative(self, a0):
1212  """get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1213  return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1214 
1215 
1216  def get_name(self):
1217  """get_name(RelaxingSpring self) -> std::string"""
1218  return _IMP_npctransport.RelaxingSpring_get_name(self)
1219 
1220 
1221  def clear_caches(self):
1222  """clear_caches(RelaxingSpring self)"""
1223  return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1224 
1225 
1226  def set_name(self, a0):
1227  """set_name(RelaxingSpring self, std::string a0)"""
1228  return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1229 
1230 
1231  def set_check_level(self, a0):
1232  """set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1233  return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1234 
1235 
1236  def add_to_derivative(self, a0, a1, a2):
1237  """add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1238  return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1239 
1240 
1241  def set_is_optimized(self, a0, a1):
1242  """set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1243  return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1244 
1245 
1246  def get_is_optimized(self, a0):
1247  """get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1248  return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1249 
1250 
1251  def get_check_level(self):
1252  """get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1253  return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1254 
1255 
1256  def __eq__(self, *args):
1257  """
1258  __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1259  __eq__(RelaxingSpring self, Particle d) -> bool
1260  """
1261  return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1262 
1263 
1264  def __ne__(self, *args):
1265  """
1266  __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1267  __ne__(RelaxingSpring self, Particle d) -> bool
1268  """
1269  return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1270 
1271 
1272  def __le__(self, *args):
1273  """
1274  __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1275  __le__(RelaxingSpring self, Particle d) -> bool
1276  """
1277  return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1278 
1279 
1280  def __lt__(self, *args):
1281  """
1282  __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1283  __lt__(RelaxingSpring self, Particle d) -> bool
1284  """
1285  return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1286 
1287 
1288  def __ge__(self, *args):
1289  """
1290  __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1291  __ge__(RelaxingSpring self, Particle d) -> bool
1292  """
1293  return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1294 
1295 
1296  def __gt__(self, *args):
1297  """
1298  __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1299  __gt__(RelaxingSpring self, Particle d) -> bool
1300  """
1301  return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1302 
1303 
1304  def __hash__(self):
1305  """__hash__(RelaxingSpring self) -> std::size_t"""
1306  return _IMP_npctransport.RelaxingSpring___hash__(self)
1307 
1308 
1309  def __str__(self):
1310  """__str__(RelaxingSpring self) -> std::string"""
1311  return _IMP_npctransport.RelaxingSpring___str__(self)
1312 
1313 
1314  def __repr__(self):
1315  """__repr__(RelaxingSpring self) -> std::string"""
1316  return _IMP_npctransport.RelaxingSpring___repr__(self)
1317 
1318  __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1319  __del__ = lambda self: None
1320 RelaxingSpring_swigregister = _IMP_npctransport.RelaxingSpring_swigregister
1321 RelaxingSpring_swigregister(RelaxingSpring)
1322 
1323 def RelaxingSpring_setup_particle(*args):
1324  """
1325  setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1326  RelaxingSpring_setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1327  """
1328  return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1329 
1330 def RelaxingSpring_get_is_setup(*args):
1331  """
1332  get_is_setup(_ParticleAdaptor p) -> bool
1333  RelaxingSpring_get_is_setup(Model m, ParticleIndex pi) -> bool
1334  """
1335  return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1336 
1337 def RelaxingSpring_get_bonded_particle_0_key():
1338  """RelaxingSpring_get_bonded_particle_0_key() -> ParticleIndexKey"""
1339  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1340 
1341 def RelaxingSpring_get_bonded_particle_1_key():
1342  """RelaxingSpring_get_bonded_particle_1_key() -> ParticleIndexKey"""
1343  return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1344 
1345 def RelaxingSpring_get_equilibrium_rest_length_factor_key():
1346  """RelaxingSpring_get_equilibrium_rest_length_factor_key() -> FloatKey"""
1347  return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1348 
1349 def RelaxingSpring_get_rest_length_key():
1350  """RelaxingSpring_get_rest_length_key() -> FloatKey"""
1351  return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1352 
1353 def RelaxingSpring_get_rest_length_diffusion_coefficient_key():
1354  """RelaxingSpring_get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1355  return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1356 
1357 class HarmonicSpringSingletonScore(IMP.SingletonScore):
1358  """Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1359 
1360  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1361 
1362  def __init__(self, *args):
1363  """
1364  __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2, std::string name) -> HarmonicSpringSingletonScore
1365  __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2) -> HarmonicSpringSingletonScore
1366  """
1367  this = _IMP_npctransport.new_HarmonicSpringSingletonScore(*args)
1368  try:
1369  self.this.append(this)
1370  except __builtin__.Exception:
1371  self.this = this
1372 
1373  def set_k1(self, k1):
1374  """set_k1(HarmonicSpringSingletonScore self, double k1)"""
1375  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1376 
1377 
1378  def get_k1(self):
1379  """get_k1(HarmonicSpringSingletonScore self) -> double"""
1380  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1381 
1382 
1383  def set_k2(self, k2):
1384  """set_k2(HarmonicSpringSingletonScore self, double k2)"""
1385  return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1386 
1387 
1388  def get_k2(self):
1389  """get_k2(HarmonicSpringSingletonScore self) -> double"""
1390  return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1391 
1392 
1393  def do_get_inputs(self, m, pis):
1394  """do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1395  return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1396 
1397 
1398  def get_version_info(self):
1399  """get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1400  return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1401 
1402 
1403  def __str__(self):
1404  """__str__(HarmonicSpringSingletonScore self) -> std::string"""
1405  return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1406 
1407 
1408  def __repr__(self):
1409  """__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1410  return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1411 
1412 
1413  @staticmethod
1414  def get_from(o):
1415  return _object_cast_to_HarmonicSpringSingletonScore(o)
1416 
1417 HarmonicSpringSingletonScore_swigregister = _IMP_npctransport.HarmonicSpringSingletonScore_swigregister
1418 HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1419 
1420 class LinearInteraction(object):
1421  """Proxy of C++ IMP::npctransport::LinearInteraction class."""
1422 
1423  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1424  __repr__ = _swig_repr
1425 
1426  def __init__(self, krep, attr_range, kattr):
1427  """__init__(IMP::npctransport::LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction"""
1428  this = _IMP_npctransport.new_LinearInteraction(krep, attr_range, kattr)
1429  try:
1430  self.this.append(this)
1431  except __builtin__.Exception:
1432  self.this = this
1433 
1434  def show(self, *args):
1435  """
1436  show(LinearInteraction self, _ostream out)
1437  show(LinearInteraction self)
1438  """
1439  return _IMP_npctransport.LinearInteraction_show(self, *args)
1440 
1441  __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1442  __del__ = lambda self: None
1443 LinearInteraction_swigregister = _IMP_npctransport.LinearInteraction_swigregister
1444 LinearInteraction_swigregister(LinearInteraction)
1445 
1446 class _DistancePairScoreForLinearSoftSphere(IMP.PairScore):
1447  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> class."""
1448 
1449  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1450  __repr__ = _swig_repr
1451 
1452  def __init__(self, *args):
1453  """
1454  __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
1455  __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
1456  """
1457  this = _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args)
1458  try:
1459  self.this.append(this)
1460  except __builtin__.Exception:
1461  self.this = this
1462 
1463  def do_get_inputs(self, m, pis):
1464  """do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1465  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1466 
1467 
1468  def get_score_functor(self):
1469  """get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1470  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1471 
1472 
1473  def get_version_info(self):
1474  """get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1475  return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1476 
1477 _DistancePairScoreForLinearSoftSphere_swigregister = _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister
1478 _DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1479 
1480 class _DistancePairScoreForLinearInteraction(IMP.PairScore):
1481  """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> class."""
1482 
1483  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1484  __repr__ = _swig_repr
1485 
1486  def __init__(self, *args):
1487  """
1488  __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
1489  __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0) -> _DistancePairScoreForLinearInteraction
1490  """
1491  this = _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args)
1492  try:
1493  self.this.append(this)
1494  except __builtin__.Exception:
1495  self.this = this
1496 
1497  def do_get_inputs(self, m, pis):
1498  """do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1499  return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1500 
1501 
1502  def get_score_functor(self):
1503  """get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1504  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1505 
1506 
1507  def get_version_info(self):
1508  """get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1509  return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1510 
1511 _DistancePairScoreForLinearInteraction_swigregister = _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister
1512 _DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1513 
1514 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1515  """Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1516 
1517  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1518 
1519  def __init__(self, *args):
1520  """
1521  __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k, std::string name) -> FunctorLinearSoftSpherePairScore
1522  __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k) -> FunctorLinearSoftSpherePairScore
1523  """
1524  this = _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args)
1525  try:
1526  self.this.append(this)
1527  except __builtin__.Exception:
1528  self.this = this
1529 
1530  def __str__(self):
1531  """__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1532  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1533 
1534 
1535  def __repr__(self):
1536  """__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1537  return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1538 
1539 
1540  @staticmethod
1541  def get_from(o):
1542  return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1543 
1544 FunctorLinearSoftSpherePairScore_swigregister = _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister
1545 FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1546 
1547 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1548  """Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1549 
1550  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1551 
1552  def __init__(self, *args):
1553  """
1554  __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name) -> FunctorLinearInteractionPairScore
1555  __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr) -> FunctorLinearInteractionPairScore
1556  """
1557  this = _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args)
1558  try:
1559  self.this.append(this)
1560  except __builtin__.Exception:
1561  self.this = this
1562 
1563  def __str__(self):
1564  """__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1565  return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1566 
1567 
1568  def __repr__(self):
1569  """__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1570  return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1571 
1572 
1573  @staticmethod
1574  def get_from(o):
1575  return _object_cast_to_FunctorLinearInteractionPairScore(o)
1576 
1577 FunctorLinearInteractionPairScore_swigregister = _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister
1578 FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1579 
1580 class BrownianDynamicsTAMDWithSlabSupport(IMP.atom.BrownianDynamicsTAMD):
1581  """Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1582 
1583  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1584 
1585  def __init__(self, *args):
1586  """
1587  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport
1588  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name) -> BrownianDynamicsTAMDWithSlabSupport
1589  __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m) -> BrownianDynamicsTAMDWithSlabSupport
1590  """
1591  this = _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args)
1592  try:
1593  self.this.append(this)
1594  except __builtin__.Exception:
1595  self.this = this
1596 
1597  def __str__(self):
1598  """__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1599  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1600 
1601 
1602  def __repr__(self):
1603  """__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1604  return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1605 
1606 
1607  @staticmethod
1608  def get_from(o):
1609  return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1610 
1611  __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1612  __del__ = lambda self: None
1613 BrownianDynamicsTAMDWithSlabSupport_swigregister = _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister
1614 BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1615 
1616 class SitesPairScoreParameters(object):
1617  """Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1618 
1619  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1620  r = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set)
1621  k = _swig_property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set)
1622  r2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set)
1623  kr = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set)
1624  kr2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set)
1625  cosSigma1_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set)
1626  cosSigma2_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set)
1627  is_orientational = _swig_property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set)
1628 
1629  def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1630  """
1631  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters
1632  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0) -> SitesPairScoreParameters
1633  __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient) -> SitesPairScoreParameters
1634  """
1635  this = _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg)
1636  try:
1637  self.this.append(this)
1638  except __builtin__.Exception:
1639  self.this = this
1640 
1641  def set_range(self, r):
1642  """set_range(SitesPairScoreParameters self, double r)"""
1643  return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1644 
1645 
1646  def set_force_coefficient(self, k):
1647  """set_force_coefficient(SitesPairScoreParameters self, double k)"""
1648  return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1649 
1650 
1651  def set_sigma1_max(self, sigma1_max_deg):
1652  """set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1653  return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1654 
1655 
1656  def set_sigma2_max(self, sigma2_max_deg):
1657  """set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1658  return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1659 
1660 
1661  def update_is_orientational(self):
1662  """update_is_orientational(SitesPairScoreParameters self)"""
1663  return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1664 
1665 
1666  def show(self, *args):
1667  """
1668  show(SitesPairScoreParameters self, _ostream out)
1669  show(SitesPairScoreParameters self)
1670  """
1671  return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1672 
1673 
1674  def __str__(self):
1675  """__str__(SitesPairScoreParameters self) -> std::string"""
1676  return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1677 
1678 
1679  def __repr__(self):
1680  """__repr__(SitesPairScoreParameters self) -> std::string"""
1681  return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1682 
1683  __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1684  __del__ = lambda self: None
1685 SitesPairScoreParameters_swigregister = _IMP_npctransport.SitesPairScoreParameters_swigregister
1686 SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1687 
1688 class SitesGeometry(IMP.core.XYZRGeometry):
1689  """Proxy of C++ IMP::npctransport::SitesGeometry class."""
1690 
1691  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1692 
1693  def __init__(self, p, sites):
1694  """__init__(IMP::npctransport::SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1695  this = _IMP_npctransport.new_SitesGeometry(p, sites)
1696  try:
1697  self.this.append(this)
1698  except __builtin__.Exception:
1699  self.this = this
1700 
1701  def __str__(self):
1702  """__str__(SitesGeometry self) -> std::string"""
1703  return _IMP_npctransport.SitesGeometry___str__(self)
1704 
1705 
1706  def __repr__(self):
1707  """__repr__(SitesGeometry self) -> std::string"""
1708  return _IMP_npctransport.SitesGeometry___repr__(self)
1709 
1710 
1711  @staticmethod
1712  def get_from(o):
1713  return _object_cast_to_SitesGeometry(o)
1714 
1715 SitesGeometry_swigregister = _IMP_npctransport.SitesGeometry_swigregister
1716 SitesGeometry_swigregister(SitesGeometry)
1717 
1718 class TypedSitesGeometry(IMP.display.SingletonsGeometry):
1719  """Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1720 
1721  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1722 
1723  def __init__(self, sc):
1724  """__init__(IMP::npctransport::TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1725  this = _IMP_npctransport.new_TypedSitesGeometry(sc)
1726  try:
1727  self.this.append(this)
1728  except __builtin__.Exception:
1729  self.this = this
1730 
1731  def set_sites(self, t, s):
1732  """set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1733  return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1734 
1735 
1736  def get_version_info(self):
1737  """get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1738  return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1739 
1740 
1741  def __str__(self):
1742  """__str__(TypedSitesGeometry self) -> std::string"""
1743  return _IMP_npctransport.TypedSitesGeometry___str__(self)
1744 
1745 
1746  def __repr__(self):
1747  """__repr__(TypedSitesGeometry self) -> std::string"""
1748  return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1749 
1750 
1751  @staticmethod
1752  def get_from(o):
1753  return _object_cast_to_TypedSitesGeometry(o)
1754 
1755 TypedSitesGeometry_swigregister = _IMP_npctransport.TypedSitesGeometry_swigregister
1756 TypedSitesGeometry_swigregister(TypedSitesGeometry)
1757 
1758 class SitesPairScore(LinearInteractionPairScore):
1759  """Proxy of C++ IMP::npctransport::SitesPairScore class."""
1760 
1761  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1762 
1763  def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1764  """__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"""
1765  this = _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1)
1766  try:
1767  self.this.append(this)
1768  except __builtin__.Exception:
1769  self.this = this
1770 
1771  def get_sites_range(self):
1772  """get_sites_range(SitesPairScore self) -> double"""
1773  return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1774 
1775 
1776  def get_sites_k(self):
1777  """get_sites_k(SitesPairScore self) -> double"""
1778  return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1779 
1780 
1781  def get_parameters(self):
1782  """get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1783  return _IMP_npctransport.SitesPairScore_get_parameters(self)
1784 
1785 
1786  def set_sites(self, sites0, sites1):
1787  """set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1788  return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1789 
1790 
1791  def set_sites0(self, sites0):
1792  """set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1793  return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1794 
1795 
1796  def set_sites1(self, sites1):
1797  """set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1798  return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1799 
1800 
1801  def __str__(self):
1802  """__str__(SitesPairScore self) -> std::string"""
1803  return _IMP_npctransport.SitesPairScore___str__(self)
1804 
1805 
1806  def __repr__(self):
1807  """__repr__(SitesPairScore self) -> std::string"""
1808  return _IMP_npctransport.SitesPairScore___repr__(self)
1809 
1810 
1811  @staticmethod
1812  def get_from(o):
1813  return _object_cast_to_SitesPairScore(o)
1814 
1815 SitesPairScore_swigregister = _IMP_npctransport.SitesPairScore_swigregister
1816 SitesPairScore_swigregister(SitesPairScore)
1817 
1818 class FGChain(IMP.Object):
1819  """Proxy of C++ IMP::npctransport::FGChain class."""
1820 
1821  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1822 
1823  def __init__(self, *args):
1824  """
1825  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name) -> FGChain
1826  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0) -> FGChain
1827  __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0) -> FGChain
1828  __init__(IMP::npctransport::FGChain self, Particle root) -> FGChain
1829  """
1830  this = _IMP_npctransport.new_FGChain(*args)
1831  try:
1832  self.this.append(this)
1833  except __builtin__.Exception:
1834  self.this = this
1835 
1836  def get_root(self):
1837  """get_root(FGChain self) -> Hierarchy"""
1838  return _IMP_npctransport.FGChain_get_root(self)
1839 
1840 
1841  def get_beads(self):
1842  """get_beads(FGChain self) -> IMP::ParticlesTemp"""
1843  return _IMP_npctransport.FGChain_get_beads(self)
1844 
1845 
1846  def get_bead(self, i):
1847  """get_bead(FGChain self, unsigned int i) -> Particle"""
1848  return _IMP_npctransport.FGChain_get_bead(self, i)
1849 
1850 
1851  def get_bead_index(self, i):
1852  """get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1853  return _IMP_npctransport.FGChain_get_bead_index(self, i)
1854 
1855 
1856  def get_number_of_beads(self):
1857  """get_number_of_beads(FGChain self) -> unsigned int"""
1858  return _IMP_npctransport.FGChain_get_number_of_beads(self)
1859 
1860 
1861  def get_chain_restraints(self, scoring_manager):
1862  """get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1863  return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1864 
1865 
1866  def set_rest_length_factor(self, rlf):
1867  """set_rest_length_factor(FGChain self, double rlf)"""
1868  return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1869 
1870 
1871  def set_backbone_k(self, k):
1872  """set_backbone_k(FGChain self, double k)"""
1873  return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1874 
1875 
1876  def get_rest_length_factor(self):
1877  """get_rest_length_factor(FGChain self) -> double"""
1878  return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1879 
1880 
1881  def get_backbone_k(self):
1882  """get_backbone_k(FGChain self) -> double"""
1883  return _IMP_npctransport.FGChain_get_backbone_k(self)
1884 
1885 
1886  def get_version_info(self):
1887  """get_version_info(FGChain self) -> VersionInfo"""
1888  return _IMP_npctransport.FGChain_get_version_info(self)
1889 
1890 
1891  def __str__(self):
1892  """__str__(FGChain self) -> std::string"""
1893  return _IMP_npctransport.FGChain___str__(self)
1894 
1895 
1896  def __repr__(self):
1897  """__repr__(FGChain self) -> std::string"""
1898  return _IMP_npctransport.FGChain___repr__(self)
1899 
1900 
1901  @staticmethod
1902  def get_from(o):
1903  return _object_cast_to_FGChain(o)
1904 
1905 FGChain_swigregister = _IMP_npctransport.FGChain_swigregister
1906 FGChain_swigregister(FGChain)
1907 
1908 
1909 def create_fg_chain(sd, parent, fg_data, c):
1910  """create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1911  return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1912 
1913 def get_fg_chain(*args):
1914  """
1915  get_fg_chain(Hierarchy root) -> FGChain
1916  get_fg_chain(Particle p_root) -> FGChain
1917  """
1918  return _IMP_npctransport.get_fg_chain(*args)
1919 class Scoring(IMP.Object):
1920  """Proxy of C++ IMP::npctransport::Scoring class."""
1921 
1922  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1923 
1924  def __init__(self, owner_sd, data):
1925  """__init__(IMP::npctransport::Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1926  this = _IMP_npctransport.new_Scoring(owner_sd, data)
1927  try:
1928  self.this.append(this)
1929  except __builtin__.Exception:
1930  self.this = this
1931 
1932  def get_scoring_function(self, force_update=False):
1933  """
1934  get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction
1935  get_scoring_function(Scoring self) -> ScoringFunction
1936  """
1937  return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1938 
1939 
1940  def get_scoring_function_restraints(self, force_update=False):
1941  """
1942  get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints
1943  get_scoring_function_restraints(Scoring self) -> IMP::Restraints
1944  """
1945  return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1946 
1947 
1948  def get_custom_scoring_function(self, *args):
1949  """
1950  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
1951  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1952  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
1953  get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1954  """
1955  return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1956 
1957 
1958  def get_close_beads_container(self, update=False):
1959  """
1960  get_close_beads_container(Scoring self, bool update=False) -> PairContainer
1961  get_close_beads_container(Scoring self) -> PairContainer
1962  """
1963  return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1964 
1965 
1966  def get_predicates_pair_restraint(self, update=False):
1967  """
1968  get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint
1969  get_predicates_pair_restraint(Scoring self) -> PredicatePairsRestraint
1970  """
1971  return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1972 
1973 
1974  def get_bounding_volume_restraint(self, update=False):
1975  """
1976  get_bounding_volume_restraint(Scoring self, bool update=False) -> Restraint
1977  get_bounding_volume_restraint(Scoring self) -> Restraint
1978  """
1979  return _IMP_npctransport.Scoring_get_bounding_volume_restraint(self, update)
1980 
1981 
1982  def get_slab_restraint(self, update=False):
1983  """
1984  get_slab_restraint(Scoring self, bool update=False) -> Restraint
1985  get_slab_restraint(Scoring self) -> Restraint
1986  """
1987  return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1988 
1989 
1990  def add_interaction(self, idata):
1991  """add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1992  return _IMP_npctransport.Scoring_add_interaction(self, idata)
1993 
1994 
1995  def create_close_beads_container(self, *args):
1996  """
1997  create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1998  create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1999  """
2000  return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
2001 
2002 
2003  def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
2004  """
2005  create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint
2006  create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs) -> PredicatePairsRestraint
2007  """
2008  return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
2009 
2010 
2011  def create_bounding_volume_restraint(self, beads):
2012  """create_bounding_volume_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
2013  return _IMP_npctransport.Scoring_create_bounding_volume_restraint(self, beads)
2014 
2015 
2016  def create_slab_restraint(self, beads):
2017  """create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
2018  return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
2019 
2020 
2021  def get_model(self):
2022  """get_model(Scoring self) -> Model"""
2023  return _IMP_npctransport.Scoring_get_model(self)
2024 
2025 
2026  def get_sd(self):
2027  """get_sd(Scoring self) -> SimulationData"""
2028  return _IMP_npctransport.Scoring_get_sd(self)
2029 
2030 
2031  def get_has_bounding_box(self):
2032  """get_has_bounding_box(Scoring self) -> bool"""
2033  return _IMP_npctransport.Scoring_get_has_bounding_box(self)
2034 
2035 
2036  def get_has_bounding_sphere(self):
2037  """get_has_bounding_sphere(Scoring self) -> bool"""
2038  return _IMP_npctransport.Scoring_get_has_bounding_sphere(self)
2039 
2040 
2041  def get_has_bounding_volume(self):
2042  """get_has_bounding_volume(Scoring self) -> bool"""
2043  return _IMP_npctransport.Scoring_get_has_bounding_volume(self)
2044 
2045 
2046  def get_default_backbone_k(self):
2047  """get_default_backbone_k(Scoring self) -> double"""
2048  return _IMP_npctransport.Scoring_get_default_backbone_k(self)
2049 
2050 
2051  def get_is_backbone_harmonic(self):
2052  """get_is_backbone_harmonic(Scoring self) -> bool"""
2053  return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
2054 
2055 
2056  def get_excluded_volume_k(self):
2057  """get_excluded_volume_k(Scoring self) -> double"""
2058  return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
2059 
2060 
2061  def get_interaction_k(self):
2062  """get_interaction_k(Scoring self) -> double"""
2063  return _IMP_npctransport.Scoring_get_interaction_k(self)
2064 
2065 
2066  def get_predicate_pair_score(self, *args):
2067  """
2068  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
2069  get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
2070  """
2071  return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
2072 
2073 
2074  def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
2075  """
2076  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double
2077  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True) -> double
2078  get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2) -> double
2079  """
2080  return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
2081 
2082 
2083  def get_ordered_type_pair_predicate(self):
2084  """get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
2085  return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
2086 
2087 
2088  def add_chain_restraints(self, chain):
2089  """add_chain_restraints(Scoring self, FGChain chain)"""
2090  return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
2091 
2092 
2093  def get_chain_restraints_on(self, beads):
2094  """get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
2095  return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
2096 
2097 
2098  def get_all_chain_restraints(self):
2099  """get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
2100  return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
2101 
2102 
2103  def remove_particle_type(self, pt):
2104  """remove_particle_type(Scoring self, ParticleType pt)"""
2105  return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
2106 
2107 
2108  def add_z_bias_restraint(self, *args):
2109  """
2110  add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
2111  add_z_bias_restraint(Scoring self, Particle p, double k)
2112  """
2113  return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
2114 
2115 
2116  def get_z_bias_restraints(self):
2117  """get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
2118  return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
2119 
2120 
2121  def create_z_bias_restraint(self, ps, k):
2122  """create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
2123  return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
2124 
2125 
2126  def add_custom_restraint(self, r):
2127  """add_custom_restraint(Scoring self, Restraint r)"""
2128  return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
2129 
2130 
2131  def add_custom_restraints(self, R):
2132  """add_custom_restraints(Scoring self, IMP::Restraints R)"""
2133  return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
2134 
2135 
2136  def clear_custom_restraints(self):
2137  """clear_custom_restraints(Scoring self)"""
2138  return _IMP_npctransport.Scoring_clear_custom_restraints(self)
2139 
2140 
2141  def get_custom_restraints(self):
2142  """get_custom_restraints(Scoring self) -> IMP::Restraints"""
2143  return _IMP_npctransport.Scoring_get_custom_restraints(self)
2144 
2145 
2146  def add_restrained_anchor_bead(self, p):
2147  """add_restrained_anchor_bead(Scoring self, Particle p)"""
2148  return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
2149 
2150 
2151  def get_pore_radius_restraint(self):
2152  """get_pore_radius_restraint(Scoring self) -> Restraint"""
2153  return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
2154 
2155 
2156  def get_range(self):
2157  """get_range(Scoring self) -> double"""
2158  return _IMP_npctransport.Scoring_get_range(self)
2159 
2160 
2161  def set_interaction_range_factor(self, type, value):
2162  """set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
2163  return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
2164 
2165 
2166  def set_interaction_k_factor(self, type, value):
2167  """set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
2168  return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
2169 
2170 
2171  def get_version_info(self):
2172  """get_version_info(Scoring self) -> VersionInfo"""
2173  return _IMP_npctransport.Scoring_get_version_info(self)
2174 
2175 
2176  def __str__(self):
2177  """__str__(Scoring self) -> std::string"""
2178  return _IMP_npctransport.Scoring___str__(self)
2179 
2180 
2181  def __repr__(self):
2182  """__repr__(Scoring self) -> std::string"""
2183  return _IMP_npctransport.Scoring___repr__(self)
2184 
2185 
2186  @staticmethod
2187  def get_from(o):
2188  return _object_cast_to_Scoring(o)
2189 
2190 Scoring_swigregister = _IMP_npctransport.Scoring_swigregister
2191 Scoring_swigregister(Scoring)
2192 
2193 class timer(object):
2194  """Proxy of C++ boost::timer class."""
2195 
2196  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2197  __repr__ = _swig_repr
2198 
2199  def __init__(self):
2200  """__init__(boost::timer self) -> timer"""
2201  this = _IMP_npctransport.new_timer()
2202  try:
2203  self.this.append(this)
2204  except __builtin__.Exception:
2205  self.this = this
2206  __swig_destroy__ = _IMP_npctransport.delete_timer
2207  __del__ = lambda self: None
2208 timer_swigregister = _IMP_npctransport.timer_swigregister
2209 timer_swigregister(timer)
2210 
2211 class Statistics(IMP.Object):
2212  """Proxy of C++ IMP::npctransport::Statistics class."""
2213 
2214  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2215 
2216  def remove_particle_type(self, pt):
2217  """remove_particle_type(Statistics self, ParticleType pt)"""
2218  return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2219 
2220 
2221  def __init__(self, sd, statistics_interval_frames, output_file_name):
2222  """__init__(IMP::npctransport::Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2223  this = _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name)
2224  try:
2225  self.this.append(this)
2226  except __builtin__.Exception:
2227  self.this = this
2228 
2229  def add_fg_chain_stats(self, fg_chain):
2230  """add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2231  return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2232 
2233 
2234  def add_floater_stats(self, p):
2235  """add_floater_stats(Statistics self, Particle p)"""
2236  return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2237 
2238 
2239  def add_interaction_stats(self, type0, type1):
2240  """add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2241  return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2242 
2243 
2244  def add_optimizer_states(self, o=None):
2245  """
2246  add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates
2247  add_optimizer_states(Statistics self) -> IMP::OptimizerStates
2248  """
2249  return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2250 
2251 
2252  def update_particle_type_zr_distribution_map(self, p):
2253  """update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2254  return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2255 
2256 
2257  def update_particle_type_xyz_distribution_map(self, p):
2258  """update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2259  return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2260 
2261 
2262  def update(self, timer, nf_new=1):
2263  """
2264  update(Statistics self, timer timer, unsigned int nf_new=1)
2265  update(Statistics self, timer timer)
2266  """
2267  return _IMP_npctransport.Statistics_update(self, timer, nf_new)
2268 
2269 
2270  def reset_statistics_optimizer_states(self):
2271  """reset_statistics_optimizer_states(Statistics self)"""
2272  return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2273 
2274 
2275  def set_interrupted(self, tf):
2276  """set_interrupted(Statistics self, bool tf)"""
2277  return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2278 
2279 
2280  def get_model(self):
2281  """get_model(Statistics self) -> Model"""
2282  return _IMP_npctransport.Statistics_get_model(self)
2283 
2284 
2285  def get_sd(self):
2286  """get_sd(Statistics self) -> SimulationData"""
2287  return _IMP_npctransport.Statistics_get_sd(self)
2288 
2289 
2290  def get_is_activated(self):
2291  """get_is_activated(Statistics self) -> bool"""
2292  return _IMP_npctransport.Statistics_get_is_activated(self)
2293 
2294 
2295  def get_output_file_name(self):
2296  """get_output_file_name(Statistics self) -> std::string"""
2297  return _IMP_npctransport.Statistics_get_output_file_name(self)
2298 
2299 
2300  def get_version_info(self):
2301  """get_version_info(Statistics self) -> VersionInfo"""
2302  return _IMP_npctransport.Statistics_get_version_info(self)
2303 
2304 
2305  def __str__(self):
2306  """__str__(Statistics self) -> std::string"""
2307  return _IMP_npctransport.Statistics___str__(self)
2308 
2309 
2310  def __repr__(self):
2311  """__repr__(Statistics self) -> std::string"""
2312  return _IMP_npctransport.Statistics___repr__(self)
2313 
2314 
2315  @staticmethod
2316  def get_from(o):
2317  return _object_cast_to_Statistics(o)
2318 
2319 Statistics_swigregister = _IMP_npctransport.Statistics_swigregister
2320 Statistics_swigregister(Statistics)
2321 
2322 
2323 def create_boost_timer():
2324  """create_boost_timer() -> timer"""
2325  return _IMP_npctransport.create_boost_timer()
2326 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2327 class SimulationData(IMP.Object):
2328  """Proxy of C++ IMP::npctransport::SimulationData class."""
2329 
2330  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2331 
2332  def get_output_npctransport_version(self):
2333  """get_output_npctransport_version(SimulationData self) -> double"""
2334  return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2335 
2336 
2337  def get_range(self):
2338  """get_range(SimulationData self) -> double"""
2339  return _IMP_npctransport.SimulationData_get_range(self)
2340 
2341 
2342  def get_output_statistics_interval_frames(self):
2343  """get_output_statistics_interval_frames(SimulationData self) -> int"""
2344  return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2345 
2346 
2347  def get_is_exclude_floaters_from_slab_initially(self):
2348  """get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2349  return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2350 
2351 
2352  def get_are_floaters_on_one_slab_side(self):
2353  """get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2354  return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2355 
2356 
2357  def get_is_xyz_hist_stats(self):
2358  """get_is_xyz_hist_stats(SimulationData self) -> bool"""
2359  return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2360 
2361 
2362  def get_angular_d_factor(self):
2363  """get_angular_d_factor(SimulationData self) -> double"""
2364  return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2365 
2366 
2367  def __init__(self, *args):
2368  """
2369  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name, std::string new_output_file) -> SimulationData
2370  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name) -> SimulationData
2371  __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick) -> SimulationData
2372  """
2373  this = _IMP_npctransport.new_SimulationData(*args)
2374  try:
2375  self.this.append(this)
2376  except __builtin__.Exception:
2377  self.this = this
2378 
2379  def get_model(self):
2380  """get_model(SimulationData self) -> Model"""
2381  return _IMP_npctransport.SimulationData_get_model(self)
2382 
2383 
2384  def get_scoring(self):
2385  """get_scoring(SimulationData self) -> Scoring"""
2386  return _IMP_npctransport.SimulationData_get_scoring(self)
2387 
2388 
2389  def get_statistics(self):
2390  """get_statistics(SimulationData self) -> Statistics"""
2391  return _IMP_npctransport.SimulationData_get_statistics(self)
2392 
2393 
2394  def get_bd(self, recreate=False):
2395  """
2396  get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics
2397  get_bd(SimulationData self) -> BrownianDynamics
2398  """
2399  return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2400 
2401 
2402  def activate_statistics(self):
2403  """activate_statistics(SimulationData self)"""
2404  return _IMP_npctransport.SimulationData_activate_statistics(self)
2405 
2406 
2407  def get_statistics_fraction(self):
2408  """get_statistics_fraction(SimulationData self) -> double"""
2409  return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2410 
2411 
2412  def get_is_fg_bead(self, *args):
2413  """
2414  get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2415  get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2416  """
2417  return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2418 
2419 
2420  def get_is_fg_chain(self, *args):
2421  """
2422  get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2423  get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2424  """
2425  return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2426 
2427 
2428  def get_fg_bead_types(self):
2429  """get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2430  return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2431 
2432 
2433  def get_fg_chain_types(self):
2434  """get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2435  return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2436 
2437 
2438  def get_floater_types(self):
2439  """get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2440  return _IMP_npctransport.SimulationData_get_floater_types(self)
2441 
2442 
2443  def get_obstacle_types(self):
2444  """get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2445  return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2446 
2447 
2448  def get_fg_chain_roots(self):
2449  """get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2450  return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2451 
2452 
2453  def get_fg_chains(self):
2454  """get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2455  return _IMP_npctransport.SimulationData_get_fg_chains(self)
2456 
2457 
2458  def get_obstacle_particles(self):
2459  """get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2460  return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2461 
2462 
2463  def get_beads(self):
2464  """get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2465  return _IMP_npctransport.SimulationData_get_beads(self)
2466 
2467 
2468  def get_optimizable_beads(self):
2469  """get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2470  return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2471 
2472 
2473  def get_non_optimizable_beads(self):
2474  """get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2475  return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2476 
2477 
2478  def get_is_backbone_harmonic(self):
2479  """get_is_backbone_harmonic(SimulationData self) -> bool"""
2480  return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2481 
2482 
2483  def get_backbone_tau_ns(self):
2484  """get_backbone_tau_ns(SimulationData self) -> double"""
2485  return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2486 
2487 
2488  def get_temperature_k(self):
2489  """get_temperature_k(SimulationData self) -> double"""
2490  return _IMP_npctransport.SimulationData_get_temperature_k(self)
2491 
2492 
2493  def get_initial_simulation_time_ns(self):
2494  """get_initial_simulation_time_ns(SimulationData self) -> double"""
2495  return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2496 
2497 
2498  def get_site_centers(self, t0):
2499  """get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2500  return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2501 
2502 
2503  def get_sites(self, t0):
2504  """get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2505  return _IMP_npctransport.SimulationData_get_sites(self, t0)
2506 
2507 
2508  def set_sites(self, *args):
2509  """
2510  set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2511  set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2512  """
2513  return _IMP_npctransport.SimulationData_set_sites(self, *args)
2514 
2515 
2516  def get_site_display_radius(self, arg2):
2517  """get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2518  return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2519 
2520 
2521  def get_maximum_number_of_minutes(self):
2522  """get_maximum_number_of_minutes(SimulationData self) -> double"""
2523  return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2524 
2525 
2526  def remove_particle_type(self, pt):
2527  """remove_particle_type(SimulationData self, ParticleType pt)"""
2528  return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2529 
2530 
2531  def remove_fgs_with_prefix(self, s_fg_type):
2532  """remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2533  return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2534 
2535 
2536  def get_bounding_box(self):
2537  """get_bounding_box(SimulationData self) -> BoundingBox3D"""
2538  return _IMP_npctransport.SimulationData_get_bounding_box(self)
2539 
2540 
2541  def get_bounding_sphere(self):
2542  """get_bounding_sphere(SimulationData self) -> Sphere3D"""
2543  return _IMP_npctransport.SimulationData_get_bounding_sphere(self)
2544 
2545 
2546  def get_bounding_box_size(self):
2547  """get_bounding_box_size(SimulationData self) -> double"""
2548  return _IMP_npctransport.SimulationData_get_bounding_box_size(self)
2549 
2550 
2551  def set_bounding_box_size(self, box_size):
2552  """set_bounding_box_size(SimulationData self, double box_size)"""
2553  return _IMP_npctransport.SimulationData_set_bounding_box_size(self, box_size)
2554 
2555 
2556  def get_bounding_sphere_radius(self):
2557  """get_bounding_sphere_radius(SimulationData self) -> double"""
2558  return _IMP_npctransport.SimulationData_get_bounding_sphere_radius(self)
2559 
2560 
2561  def set_bounding_sphere_radius(self, sphere_radius):
2562  """set_bounding_sphere_radius(SimulationData self, double sphere_radius)"""
2563  return _IMP_npctransport.SimulationData_set_bounding_sphere_radius(self, sphere_radius)
2564 
2565 
2566  def get_bounding_volume(self):
2567  """get_bounding_volume(SimulationData self) -> double"""
2568  return _IMP_npctransport.SimulationData_get_bounding_volume(self)
2569 
2570 
2571  def set_bounding_volume(self, volume_A3):
2572  """set_bounding_volume(SimulationData self, double volume_A3)"""
2573  return _IMP_npctransport.SimulationData_set_bounding_volume(self, volume_A3)
2574 
2575 
2576  def get_has_slab(self):
2577  """get_has_slab(SimulationData self) -> bool"""
2578  return _IMP_npctransport.SimulationData_get_has_slab(self)
2579 
2580 
2581  def get_is_slab_with_cylindrical_pore(self):
2582  """get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2583  return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2584 
2585 
2586  def get_is_slab_with_toroidal_pore(self):
2587  """get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2588  return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2589 
2590 
2591  def get_slab_particle(self):
2592  """get_slab_particle(SimulationData self) -> Particle"""
2593  return _IMP_npctransport.SimulationData_get_slab_particle(self)
2594 
2595 
2596  def get_cylinder(self):
2597  """get_cylinder(SimulationData self) -> Cylinder3D"""
2598  return _IMP_npctransport.SimulationData_get_cylinder(self)
2599 
2600 
2601  def get_has_bounding_box(self):
2602  """get_has_bounding_box(SimulationData self) -> bool"""
2603  return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2604 
2605 
2606  def get_has_bounding_sphere(self):
2607  """get_has_bounding_sphere(SimulationData self) -> bool"""
2608  return _IMP_npctransport.SimulationData_get_has_bounding_sphere(self)
2609 
2610 
2611  def get_has_bounding_volume(self):
2612  """get_has_bounding_volume(SimulationData self) -> bool"""
2613  return _IMP_npctransport.SimulationData_get_has_bounding_volume(self)
2614 
2615 
2616  def initialize_positions_from_rmf(self, fh, frame_number=-1):
2617  """
2618  initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)
2619  initialize_positions_from_rmf(SimulationData self, FileConstHandle fh)
2620  """
2621  return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2622 
2623 
2624  def link_rmf_file_handle(self, fh, is_restraints=True):
2625  """
2626  link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)
2627  link_rmf_file_handle(SimulationData self, FileHandle fh)
2628  """
2629  return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2630 
2631 
2632  def get_rmf_sos_writer(self):
2633  """get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2634  return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2635 
2636 
2637  def reset_rmf(self):
2638  """reset_rmf(SimulationData self)"""
2639  return _IMP_npctransport.SimulationData_reset_rmf(self)
2640 
2641 
2642  def switch_suspend_rmf(self, suspend):
2643  """switch_suspend_rmf(SimulationData self, bool suspend)"""
2644  return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2645 
2646 
2647  def write_geometry(self, out):
2648  """write_geometry(SimulationData self, std::string out)"""
2649  return _IMP_npctransport.SimulationData_write_geometry(self, out)
2650 
2651 
2652  def dump_geometry(self):
2653  """dump_geometry(SimulationData self)"""
2654  return _IMP_npctransport.SimulationData_dump_geometry(self)
2655 
2656 
2657  def get_root_of_type(self, type):
2658  """get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2659  return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2660 
2661 
2662  def get_number_of_frames(self):
2663  """get_number_of_frames(SimulationData self) -> unsigned int"""
2664  return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2665 
2666 
2667  def get_number_of_trials(self):
2668  """get_number_of_trials(SimulationData self) -> unsigned int"""
2669  return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2670 
2671 
2672  def get_root(self):
2673  """get_root(SimulationData self) -> Hierarchy"""
2674  return _IMP_npctransport.SimulationData_get_root(self)
2675 
2676 
2677  def get_slab_thickness(self):
2678  """get_slab_thickness(SimulationData self) -> double"""
2679  return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2680 
2681 
2682  def get_tunnel_radius(self):
2683  """get_tunnel_radius(SimulationData self) -> double"""
2684  return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2685 
2686 
2687  def get_pore_radius(self):
2688  """get_pore_radius(SimulationData self) -> double"""
2689  return _IMP_npctransport.SimulationData_get_pore_radius(self)
2690 
2691 
2692  def get_tunnel_radius_k(self):
2693  """get_tunnel_radius_k(SimulationData self) -> double"""
2694  return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2695 
2696 
2697  def get_pore_radius_k(self):
2698  """get_pore_radius_k(SimulationData self) -> double"""
2699  return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2700 
2701 
2702  def get_is_pore_radius_dynamic(self):
2703  """get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2704  return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2705 
2706 
2707  def get_pore_anchored_beads_k(self):
2708  """get_pore_anchored_beads_k(SimulationData self) -> double"""
2709  return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2710 
2711 
2712  def get_static_geometry(self):
2713  """get_static_geometry(SimulationData self) -> Geometry"""
2714  return _IMP_npctransport.SimulationData_get_static_geometry(self)
2715 
2716 
2717  def get_rmf_dump_interval_frames(self):
2718  """get_rmf_dump_interval_frames(SimulationData self) -> int"""
2719  return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2720 
2721 
2722  def get_rmf_file_name(self):
2723  """get_rmf_file_name(SimulationData self) -> std::string"""
2724  return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2725 
2726 
2727  def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2728  """
2729  set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)
2730  set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True)
2731  set_rmf_file(SimulationData self, std::string const & new_name)
2732  """
2733  return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2734 
2735 
2736  def get_version_info(self):
2737  """get_version_info(SimulationData self) -> VersionInfo"""
2738  return _IMP_npctransport.SimulationData_get_version_info(self)
2739 
2740 
2741  def __str__(self):
2742  """__str__(SimulationData self) -> std::string"""
2743  return _IMP_npctransport.SimulationData___str__(self)
2744 
2745 
2746  def __repr__(self):
2747  """__repr__(SimulationData self) -> std::string"""
2748  return _IMP_npctransport.SimulationData___repr__(self)
2749 
2750 
2751  @staticmethod
2752  def get_from(o):
2753  return _object_cast_to_SimulationData(o)
2754 
2755 SimulationData_swigregister = _IMP_npctransport.SimulationData_swigregister
2756 SimulationData_swigregister(SimulationData)
2757 
2758 
2759 def get_simulation_data_key():
2760  """get_simulation_data_key() -> IMP::WeakObjectKey"""
2761  return _IMP_npctransport.get_simulation_data_key()
2762 
2763 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2764  """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)"""
2765  return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2766 class ParticleFactory(IMP.Object):
2767  """Proxy of C++ IMP::npctransport::ParticleFactory class."""
2768 
2769  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2770  sd_ = _swig_property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set)
2771  radius_ = _swig_property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set)
2772  D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set)
2773  angular_D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set)
2774  color_ = _swig_property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set)
2775  type_ = _swig_property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set)
2776 
2777  def __init__(self, *args):
2778  """
2779  __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name) -> ParticleFactory
2780  __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type) -> ParticleFactory
2781  """
2782  this = _IMP_npctransport.new_ParticleFactory(*args)
2783  try:
2784  self.this.append(this)
2785  except __builtin__.Exception:
2786  self.this = this
2787 
2788  def create(self, *args):
2789  """
2790  create(ParticleFactory self, std::string name) -> Particle
2791  create(ParticleFactory self) -> Particle
2792  """
2793  return _IMP_npctransport.ParticleFactory_create(self, *args)
2794 
2795 
2796  def get_model(self):
2797  """get_model(ParticleFactory self) -> Model"""
2798  return _IMP_npctransport.ParticleFactory_get_model(self)
2799 
2800 
2801  def get_simulation_data(self):
2802  """get_simulation_data(ParticleFactory self) -> SimulationData"""
2803  return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2804 
2805 
2806  def get_radius(self):
2807  """get_radius(ParticleFactory self) -> double"""
2808  return _IMP_npctransport.ParticleFactory_get_radius(self)
2809 
2810 
2811  def get_version_info(self):
2812  """get_version_info(ParticleFactory self) -> VersionInfo"""
2813  return _IMP_npctransport.ParticleFactory_get_version_info(self)
2814 
2815 
2816  def __str__(self):
2817  """__str__(ParticleFactory self) -> std::string"""
2818  return _IMP_npctransport.ParticleFactory___str__(self)
2819 
2820 
2821  def __repr__(self):
2822  """__repr__(ParticleFactory self) -> std::string"""
2823  return _IMP_npctransport.ParticleFactory___repr__(self)
2824 
2825 
2826  @staticmethod
2827  def get_from(o):
2828  return _object_cast_to_ParticleFactory(o)
2829 
2830 ParticleFactory_swigregister = _IMP_npctransport.ParticleFactory_swigregister
2831 ParticleFactory_swigregister(ParticleFactory)
2832 
2833 class HierarchyWithSitesLoadLink(IMP.rmf.HierarchyLoadLink):
2834  """Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2835 
2836  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2837 
2838  def __init__(self, fh):
2839  """__init__(IMP::npctransport::HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2840  this = _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh)
2841  try:
2842  self.this.append(this)
2843  except __builtin__.Exception:
2844  self.this = this
2845 
2846  def get_name():
2847  """get_name() -> char const *"""
2848  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2849 
2850  get_name = staticmethod(get_name)
2851 
2852  def __str__(self):
2853  """__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2854  return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2855 
2856 
2857  def __repr__(self):
2858  """__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2859  return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2860 
2861 
2862  @staticmethod
2863  def get_from(o):
2864  return _object_cast_to_HierarchyWithSitesLoadLink(o)
2865 
2866  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2867  __del__ = lambda self: None
2868 HierarchyWithSitesLoadLink_swigregister = _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister
2869 HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2870 
2871 def HierarchyWithSitesLoadLink_get_name():
2872  """HierarchyWithSitesLoadLink_get_name() -> char const *"""
2873  return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2874 
2875 class HierarchyWithSitesSaveLink(IMP.rmf.HierarchySaveLink):
2876  """Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2877 
2878  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2879 
2880  def __init__(self, fh):
2881  """__init__(IMP::npctransport::HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2882  this = _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh)
2883  try:
2884  self.this.append(this)
2885  except __builtin__.Exception:
2886  self.this = this
2887 
2888  def get_name():
2889  """get_name() -> char const *"""
2890  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2891 
2892  get_name = staticmethod(get_name)
2893 
2894  def __str__(self):
2895  """__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2896  return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2897 
2898 
2899  def __repr__(self):
2900  """__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2901  return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2902 
2903 
2904  @staticmethod
2905  def get_from(o):
2906  return _object_cast_to_HierarchyWithSitesSaveLink(o)
2907 
2908  __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2909  __del__ = lambda self: None
2910 HierarchyWithSitesSaveLink_swigregister = _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister
2911 HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2912 
2913 def HierarchyWithSitesSaveLink_get_name():
2914  """HierarchyWithSitesSaveLink_get_name() -> char const *"""
2915  return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2916 
2917 
2918 def add_test_sites(*args):
2919  """
2920  add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2921  add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2922  """
2923  return _IMP_npctransport.add_test_sites(*args)
2924 
2925 def add_hierarchies_with_sites(*args):
2926  """
2927  add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2928  add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2929  """
2930  return _IMP_npctransport.add_hierarchies_with_sites(*args)
2931 
2932 def add_hierarchy_with_sites(fh, hs):
2933  """add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2934  return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2935 
2937  """create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2938  return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2939 
2940 def link_hierarchies_with_sites(fh, hs):
2941  """link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2942  return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2943 class Transporting(IMP.Decorator):
2944  """Proxy of C++ IMP::npctransport::Transporting class."""
2945 
2946  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2947 
2948  def __init__(self, *args):
2949  """
2950  __init__(IMP::npctransport::Transporting self) -> Transporting
2951  __init__(IMP::npctransport::Transporting self, Model m, ParticleIndex id) -> Transporting
2952  __init__(IMP::npctransport::Transporting self, _ParticleAdaptor d) -> Transporting
2953  """
2954  this = _IMP_npctransport.new_Transporting(*args)
2955  try:
2956  self.this.append(this)
2957  except __builtin__.Exception:
2958  self.this = this
2959 
2960  def show(self, *args):
2961  """
2962  show(Transporting self, _ostream out)
2963  show(Transporting self)
2964  """
2965  return _IMP_npctransport.Transporting_show(self, *args)
2966 
2967 
2968  def setup_particle(*args):
2969  """
2970  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2971  setup_particle(Model m, ParticleIndex pi) -> Transporting
2972  setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
2973  setup_particle(_ParticleAdaptor decorator) -> Transporting
2974  """
2975  return _IMP_npctransport.Transporting_setup_particle(*args)
2976 
2977  setup_particle = staticmethod(setup_particle)
2978 
2979  def get_is_setup(*args):
2980  """
2981  get_is_setup(_ParticleAdaptor p) -> bool
2982  get_is_setup(Model m, ParticleIndex pi) -> bool
2983  """
2984  return _IMP_npctransport.Transporting_get_is_setup(*args)
2985 
2986  get_is_setup = staticmethod(get_is_setup)
2987 
2988  def set_is_last_entry_from_top(self, is_last_entry_from_top):
2989  """set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2990  return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2991 
2992 
2993  def get_is_last_entry_from_top(self):
2994  """get_is_last_entry_from_top(Transporting self) -> bool"""
2995  return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2996 
2997 
2998  def get_is_last_entry_from_top_key():
2999  """get_is_last_entry_from_top_key() -> IntKey"""
3000  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3001 
3002  get_is_last_entry_from_top_key = staticmethod(get_is_last_entry_from_top_key)
3003 
3004  def set_last_tracked_z(self, last_tracked_z):
3005  """set_last_tracked_z(Transporting self, double last_tracked_z)"""
3006  return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
3007 
3008 
3009  def get_last_tracked_z(self):
3010  """get_last_tracked_z(Transporting self) -> double"""
3011  return _IMP_npctransport.Transporting_get_last_tracked_z(self)
3012 
3013 
3014  def get_last_tracked_z_key():
3015  """get_last_tracked_z_key() -> FloatKey"""
3016  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3017 
3018  get_last_tracked_z_key = staticmethod(get_last_tracked_z_key)
3019 
3020  def set_n_entries_bottom(self, n):
3021  """set_n_entries_bottom(Transporting self, int n)"""
3022  return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
3023 
3024 
3025  def get_n_entries_bottom(self):
3026  """get_n_entries_bottom(Transporting self) -> int"""
3027  return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
3028 
3029 
3030  def get_n_entries_bottom_key():
3031  """get_n_entries_bottom_key() -> IntKey"""
3032  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3033 
3034  get_n_entries_bottom_key = staticmethod(get_n_entries_bottom_key)
3035 
3036  def set_n_entries_top(self, n):
3037  """set_n_entries_top(Transporting self, int n)"""
3038  return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
3039 
3040 
3041  def get_n_entries_top(self):
3042  """get_n_entries_top(Transporting self) -> int"""
3043  return _IMP_npctransport.Transporting_get_n_entries_top(self)
3044 
3045 
3046  def get_n_entries_top_key():
3047  """get_n_entries_top_key() -> IntKey"""
3048  return _IMP_npctransport.Transporting_get_n_entries_top_key()
3049 
3050  get_n_entries_top_key = staticmethod(get_n_entries_top_key)
3051 
3052  def add_attribute(self, *args):
3053  """
3054  add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
3055  add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
3056  add_attribute(Transporting self, IntKey a0, IMP::Int a1)
3057  add_attribute(Transporting self, FloatsKey a0, IMP::Floats a1)
3058  add_attribute(Transporting self, IntsKey a0, IMP::Ints a1)
3059  add_attribute(Transporting self, StringKey a0, IMP::String a1)
3060  add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
3061  add_attribute(Transporting self, ObjectKey a0, Object a1)
3062  """
3063  return _IMP_npctransport.Transporting_add_attribute(self, *args)
3064 
3065 
3066  def get_value(self, *args):
3067  """
3068  get_value(Transporting self, FloatKey a0) -> IMP::Float
3069  get_value(Transporting self, IntKey a0) -> IMP::Int
3070  get_value(Transporting self, FloatsKey a0) -> IMP::Floats
3071  get_value(Transporting self, IntsKey a0) -> IMP::Ints
3072  get_value(Transporting self, StringKey a0) -> IMP::String
3073  get_value(Transporting self, ParticleIndexKey a0) -> Particle
3074  get_value(Transporting self, ObjectKey a0) -> Object
3075  """
3076  return _IMP_npctransport.Transporting_get_value(self, *args)
3077 
3078 
3079  def set_value(self, *args):
3080  """
3081  set_value(Transporting self, FloatKey a0, IMP::Float a1)
3082  set_value(Transporting self, IntKey a0, IMP::Int a1)
3083  set_value(Transporting self, FloatsKey a0, IMP::Floats a1)
3084  set_value(Transporting self, IntsKey a0, IMP::Ints a1)
3085  set_value(Transporting self, StringKey a0, IMP::String a1)
3086  set_value(Transporting self, ParticleIndexKey a0, Particle a1)
3087  set_value(Transporting self, ObjectKey a0, Object a1)
3088  """
3089  return _IMP_npctransport.Transporting_set_value(self, *args)
3090 
3091 
3092  def remove_attribute(self, *args):
3093  """
3094  remove_attribute(Transporting self, FloatKey a0)
3095  remove_attribute(Transporting self, IntKey a0)
3096  remove_attribute(Transporting self, FloatsKey a0)
3097  remove_attribute(Transporting self, IntsKey a0)
3098  remove_attribute(Transporting self, StringKey a0)
3099  remove_attribute(Transporting self, ParticleIndexKey a0)
3100  remove_attribute(Transporting self, ObjectKey a0)
3101  """
3102  return _IMP_npctransport.Transporting_remove_attribute(self, *args)
3103 
3104 
3105  def has_attribute(self, *args):
3106  """
3107  has_attribute(Transporting self, FloatKey a0) -> bool
3108  has_attribute(Transporting self, IntKey a0) -> bool
3109  has_attribute(Transporting self, FloatsKey a0) -> bool
3110  has_attribute(Transporting self, IntsKey a0) -> bool
3111  has_attribute(Transporting self, StringKey a0) -> bool
3112  has_attribute(Transporting self, ParticleIndexKey a0) -> bool
3113  has_attribute(Transporting self, ObjectKey a0) -> bool
3114  """
3115  return _IMP_npctransport.Transporting_has_attribute(self, *args)
3116 
3117 
3118  def get_derivative(self, a0):
3119  """get_derivative(Transporting self, FloatKey a0) -> double"""
3120  return _IMP_npctransport.Transporting_get_derivative(self, a0)
3121 
3122 
3123  def get_name(self):
3124  """get_name(Transporting self) -> std::string"""
3125  return _IMP_npctransport.Transporting_get_name(self)
3126 
3127 
3128  def clear_caches(self):
3129  """clear_caches(Transporting self)"""
3130  return _IMP_npctransport.Transporting_clear_caches(self)
3131 
3132 
3133  def set_name(self, a0):
3134  """set_name(Transporting self, std::string a0)"""
3135  return _IMP_npctransport.Transporting_set_name(self, a0)
3136 
3137 
3138  def set_check_level(self, a0):
3139  """set_check_level(Transporting self, IMP::CheckLevel a0)"""
3140  return _IMP_npctransport.Transporting_set_check_level(self, a0)
3141 
3142 
3143  def add_to_derivative(self, a0, a1, a2):
3144  """add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3145  return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
3146 
3147 
3148  def set_is_optimized(self, a0, a1):
3149  """set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
3150  return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
3151 
3152 
3153  def get_is_optimized(self, a0):
3154  """get_is_optimized(Transporting self, FloatKey a0) -> bool"""
3155  return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
3156 
3157 
3158  def get_check_level(self):
3159  """get_check_level(Transporting self) -> IMP::CheckLevel"""
3160  return _IMP_npctransport.Transporting_get_check_level(self)
3161 
3162 
3163  def __eq__(self, *args):
3164  """
3165  __eq__(Transporting self, Transporting o) -> bool
3166  __eq__(Transporting self, Particle d) -> bool
3167  """
3168  return _IMP_npctransport.Transporting___eq__(self, *args)
3169 
3170 
3171  def __ne__(self, *args):
3172  """
3173  __ne__(Transporting self, Transporting o) -> bool
3174  __ne__(Transporting self, Particle d) -> bool
3175  """
3176  return _IMP_npctransport.Transporting___ne__(self, *args)
3177 
3178 
3179  def __le__(self, *args):
3180  """
3181  __le__(Transporting self, Transporting o) -> bool
3182  __le__(Transporting self, Particle d) -> bool
3183  """
3184  return _IMP_npctransport.Transporting___le__(self, *args)
3185 
3186 
3187  def __lt__(self, *args):
3188  """
3189  __lt__(Transporting self, Transporting o) -> bool
3190  __lt__(Transporting self, Particle d) -> bool
3191  """
3192  return _IMP_npctransport.Transporting___lt__(self, *args)
3193 
3194 
3195  def __ge__(self, *args):
3196  """
3197  __ge__(Transporting self, Transporting o) -> bool
3198  __ge__(Transporting self, Particle d) -> bool
3199  """
3200  return _IMP_npctransport.Transporting___ge__(self, *args)
3201 
3202 
3203  def __gt__(self, *args):
3204  """
3205  __gt__(Transporting self, Transporting o) -> bool
3206  __gt__(Transporting self, Particle d) -> bool
3207  """
3208  return _IMP_npctransport.Transporting___gt__(self, *args)
3209 
3210 
3211  def __hash__(self):
3212  """__hash__(Transporting self) -> std::size_t"""
3213  return _IMP_npctransport.Transporting___hash__(self)
3214 
3215 
3216  def __str__(self):
3217  """__str__(Transporting self) -> std::string"""
3218  return _IMP_npctransport.Transporting___str__(self)
3219 
3220 
3221  def __repr__(self):
3222  """__repr__(Transporting self) -> std::string"""
3223  return _IMP_npctransport.Transporting___repr__(self)
3224 
3225  __swig_destroy__ = _IMP_npctransport.delete_Transporting
3226  __del__ = lambda self: None
3227 Transporting_swigregister = _IMP_npctransport.Transporting_swigregister
3228 Transporting_swigregister(Transporting)
3229 
3230 def Transporting_setup_particle(*args):
3231  """
3232  setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
3233  setup_particle(Model m, ParticleIndex pi) -> Transporting
3234  setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
3235  Transporting_setup_particle(_ParticleAdaptor decorator) -> Transporting
3236  """
3237  return _IMP_npctransport.Transporting_setup_particle(*args)
3238 
3239 def Transporting_get_is_setup(*args):
3240  """
3241  get_is_setup(_ParticleAdaptor p) -> bool
3242  Transporting_get_is_setup(Model m, ParticleIndex pi) -> bool
3243  """
3244  return _IMP_npctransport.Transporting_get_is_setup(*args)
3245 
3246 def Transporting_get_is_last_entry_from_top_key():
3247  """Transporting_get_is_last_entry_from_top_key() -> IntKey"""
3248  return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3249 
3250 def Transporting_get_last_tracked_z_key():
3251  """Transporting_get_last_tracked_z_key() -> FloatKey"""
3252  return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3253 
3254 def Transporting_get_n_entries_bottom_key():
3255  """Transporting_get_n_entries_bottom_key() -> IntKey"""
3256  return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3257 
3258 def Transporting_get_n_entries_top_key():
3259  """Transporting_get_n_entries_top_key() -> IntKey"""
3260  return _IMP_npctransport.Transporting_get_n_entries_top_key()
3261 
3262 
3263 def show_ranges(fname):
3264  """show_ranges(std::string fname)"""
3265  return _IMP_npctransport.show_ranges(fname)
3266 
3267 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
3268  """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"""
3269  return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
3270 
3271 def get_number_of_work_units(configuration_file):
3272  """get_number_of_work_units(std::string configuration_file) -> int"""
3273  return _IMP_npctransport.get_number_of_work_units(configuration_file)
3274 class SlabWithPore(IMP.Decorator):
3275  """Proxy of C++ IMP::npctransport::SlabWithPore class."""
3276 
3277  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3278 
3279  def __init__(self, *args):
3280  """
3281  __init__(IMP::npctransport::SlabWithPore self) -> SlabWithPore
3282  __init__(IMP::npctransport::SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
3283  __init__(IMP::npctransport::SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
3284  """
3285  this = _IMP_npctransport.new_SlabWithPore(*args)
3286  try:
3287  self.this.append(this)
3288  except __builtin__.Exception:
3289  self.this = this
3290 
3291  def show(self, *args):
3292  """
3293  show(SlabWithPore self, _ostream out)
3294  show(SlabWithPore self)
3295  """
3296  return _IMP_npctransport.SlabWithPore_show(self, *args)
3297 
3298 
3299  def setup_particle(*args):
3300  """
3301  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3302  setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3303  """
3304  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3305 
3306  setup_particle = staticmethod(setup_particle)
3307 
3308  def get_is_setup(*args):
3309  """
3310  get_is_setup(_ParticleAdaptor p) -> bool
3311  get_is_setup(Model m, ParticleIndex pi) -> bool
3312  """
3313  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3314 
3315  get_is_setup = staticmethod(get_is_setup)
3316 
3317  def set_thickness(self, thickness):
3318  """set_thickness(SlabWithPore self, double thickness)"""
3319  return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
3320 
3321 
3322  def get_thickness(self):
3323  """get_thickness(SlabWithPore self) -> IMP::Float"""
3324  return _IMP_npctransport.SlabWithPore_get_thickness(self)
3325 
3326 
3327  def get_pore_radius(self):
3328  """get_pore_radius(SlabWithPore self) -> IMP::Float"""
3329  return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
3330 
3331 
3332  def set_pore_radius(self, r):
3333  """set_pore_radius(SlabWithPore self, double r)"""
3334  return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
3335 
3336 
3337  def add_to_pore_radius_derivative(self, v, d):
3338  """add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
3339  return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
3340 
3341 
3342  def get_pore_radius_is_optimized(self):
3343  """get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
3344  return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
3345 
3346 
3347  def set_pore_radius_is_optimized(self, tf):
3348  """set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
3349  return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
3350 
3351 
3352  def get_thickness_key():
3353  """get_thickness_key() -> FloatKey"""
3354  return _IMP_npctransport.SlabWithPore_get_thickness_key()
3355 
3356  get_thickness_key = staticmethod(get_thickness_key)
3357 
3358  def get_pore_radius_key():
3359  """get_pore_radius_key() -> FloatKey"""
3360  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3361 
3362  get_pore_radius_key = staticmethod(get_pore_radius_key)
3363 
3364  def add_attribute(self, *args):
3365  """
3366  add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
3367  add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
3368  add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
3369  add_attribute(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3370  add_attribute(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3371  add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
3372  add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3373  add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
3374  """
3375  return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
3376 
3377 
3378  def get_value(self, *args):
3379  """
3380  get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
3381  get_value(SlabWithPore self, IntKey a0) -> IMP::Int
3382  get_value(SlabWithPore self, FloatsKey a0) -> IMP::Floats
3383  get_value(SlabWithPore self, IntsKey a0) -> IMP::Ints
3384  get_value(SlabWithPore self, StringKey a0) -> IMP::String
3385  get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3386  get_value(SlabWithPore self, ObjectKey a0) -> Object
3387  """
3388  return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3389 
3390 
3391  def set_value(self, *args):
3392  """
3393  set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3394  set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3395  set_value(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3396  set_value(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3397  set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3398  set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3399  set_value(SlabWithPore self, ObjectKey a0, Object a1)
3400  """
3401  return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3402 
3403 
3404  def remove_attribute(self, *args):
3405  """
3406  remove_attribute(SlabWithPore self, FloatKey a0)
3407  remove_attribute(SlabWithPore self, IntKey a0)
3408  remove_attribute(SlabWithPore self, FloatsKey a0)
3409  remove_attribute(SlabWithPore self, IntsKey a0)
3410  remove_attribute(SlabWithPore self, StringKey a0)
3411  remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3412  remove_attribute(SlabWithPore self, ObjectKey a0)
3413  """
3414  return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3415 
3416 
3417  def has_attribute(self, *args):
3418  """
3419  has_attribute(SlabWithPore self, FloatKey a0) -> bool
3420  has_attribute(SlabWithPore self, IntKey a0) -> bool
3421  has_attribute(SlabWithPore self, FloatsKey a0) -> bool
3422  has_attribute(SlabWithPore self, IntsKey a0) -> bool
3423  has_attribute(SlabWithPore self, StringKey a0) -> bool
3424  has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3425  has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3426  """
3427  return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3428 
3429 
3430  def get_derivative(self, a0):
3431  """get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3432  return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3433 
3434 
3435  def get_name(self):
3436  """get_name(SlabWithPore self) -> std::string"""
3437  return _IMP_npctransport.SlabWithPore_get_name(self)
3438 
3439 
3440  def clear_caches(self):
3441  """clear_caches(SlabWithPore self)"""
3442  return _IMP_npctransport.SlabWithPore_clear_caches(self)
3443 
3444 
3445  def set_name(self, a0):
3446  """set_name(SlabWithPore self, std::string a0)"""
3447  return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3448 
3449 
3450  def set_check_level(self, a0):
3451  """set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3452  return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3453 
3454 
3455  def add_to_derivative(self, a0, a1, a2):
3456  """add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3457  return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3458 
3459 
3460  def set_is_optimized(self, a0, a1):
3461  """set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3462  return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3463 
3464 
3465  def get_is_optimized(self, a0):
3466  """get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3467  return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3468 
3469 
3470  def get_check_level(self):
3471  """get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3472  return _IMP_npctransport.SlabWithPore_get_check_level(self)
3473 
3474 
3475  def __eq__(self, *args):
3476  """
3477  __eq__(SlabWithPore self, SlabWithPore o) -> bool
3478  __eq__(SlabWithPore self, Particle d) -> bool
3479  """
3480  return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3481 
3482 
3483  def __ne__(self, *args):
3484  """
3485  __ne__(SlabWithPore self, SlabWithPore o) -> bool
3486  __ne__(SlabWithPore self, Particle d) -> bool
3487  """
3488  return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3489 
3490 
3491  def __le__(self, *args):
3492  """
3493  __le__(SlabWithPore self, SlabWithPore o) -> bool
3494  __le__(SlabWithPore self, Particle d) -> bool
3495  """
3496  return _IMP_npctransport.SlabWithPore___le__(self, *args)
3497 
3498 
3499  def __lt__(self, *args):
3500  """
3501  __lt__(SlabWithPore self, SlabWithPore o) -> bool
3502  __lt__(SlabWithPore self, Particle d) -> bool
3503  """
3504  return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3505 
3506 
3507  def __ge__(self, *args):
3508  """
3509  __ge__(SlabWithPore self, SlabWithPore o) -> bool
3510  __ge__(SlabWithPore self, Particle d) -> bool
3511  """
3512  return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3513 
3514 
3515  def __gt__(self, *args):
3516  """
3517  __gt__(SlabWithPore self, SlabWithPore o) -> bool
3518  __gt__(SlabWithPore self, Particle d) -> bool
3519  """
3520  return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3521 
3522 
3523  def __hash__(self):
3524  """__hash__(SlabWithPore self) -> std::size_t"""
3525  return _IMP_npctransport.SlabWithPore___hash__(self)
3526 
3527 
3528  def __str__(self):
3529  """__str__(SlabWithPore self) -> std::string"""
3530  return _IMP_npctransport.SlabWithPore___str__(self)
3531 
3532 
3533  def __repr__(self):
3534  """__repr__(SlabWithPore self) -> std::string"""
3535  return _IMP_npctransport.SlabWithPore___repr__(self)
3536 
3537  __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3538  __del__ = lambda self: None
3539 SlabWithPore_swigregister = _IMP_npctransport.SlabWithPore_swigregister
3540 SlabWithPore_swigregister(SlabWithPore)
3541 
3542 def SlabWithPore_setup_particle(*args):
3543  """
3544  setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3545  SlabWithPore_setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3546  """
3547  return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3548 
3549 def SlabWithPore_get_is_setup(*args):
3550  """
3551  get_is_setup(_ParticleAdaptor p) -> bool
3552  SlabWithPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3553  """
3554  return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3555 
3556 def SlabWithPore_get_thickness_key():
3557  """SlabWithPore_get_thickness_key() -> FloatKey"""
3558  return _IMP_npctransport.SlabWithPore_get_thickness_key()
3559 
3560 def SlabWithPore_get_pore_radius_key():
3561  """SlabWithPore_get_pore_radius_key() -> FloatKey"""
3562  return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3563 
3564 class SlabWithCylindricalPore(SlabWithPore):
3565  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3566 
3567  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3568 
3569  def __init__(self, *args):
3570  """
3571  __init__(IMP::npctransport::SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3572  __init__(IMP::npctransport::SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3573  __init__(IMP::npctransport::SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3574  """
3575  this = _IMP_npctransport.new_SlabWithCylindricalPore(*args)
3576  try:
3577  self.this.append(this)
3578  except __builtin__.Exception:
3579  self.this = this
3580 
3581  def show(self, *args):
3582  """
3583  show(SlabWithCylindricalPore self, _ostream out)
3584  show(SlabWithCylindricalPore self)
3585  """
3586  return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3587 
3588 
3589  def setup_particle(*args):
3590  """
3591  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3592  setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3593  """
3594  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3595 
3596  setup_particle = staticmethod(setup_particle)
3597 
3598  def get_is_setup(*args):
3599  """
3600  get_is_setup(_ParticleAdaptor p) -> bool
3601  get_is_setup(Model m, ParticleIndex pi) -> bool
3602  """
3603  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3604 
3605  get_is_setup = staticmethod(get_is_setup)
3606 
3607  def get_cylindrical_pore_key():
3608  """get_cylindrical_pore_key() -> IntKey"""
3609  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3610 
3611  get_cylindrical_pore_key = staticmethod(get_cylindrical_pore_key)
3612 
3613  def add_attribute(self, *args):
3614  """
3615  add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3616  add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3617  add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3618  add_attribute(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3619  add_attribute(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3620  add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3621  add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3622  add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3623  """
3624  return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3625 
3626 
3627  def get_value(self, *args):
3628  """
3629  get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3630  get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3631  get_value(SlabWithCylindricalPore self, FloatsKey a0) -> IMP::Floats
3632  get_value(SlabWithCylindricalPore self, IntsKey a0) -> IMP::Ints
3633  get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3634  get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3635  get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3636  """
3637  return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3638 
3639 
3640  def set_value(self, *args):
3641  """
3642  set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3643  set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3644  set_value(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3645  set_value(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3646  set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3647  set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3648  set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3649  """
3650  return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3651 
3652 
3653  def remove_attribute(self, *args):
3654  """
3655  remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3656  remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3657  remove_attribute(SlabWithCylindricalPore self, FloatsKey a0)
3658  remove_attribute(SlabWithCylindricalPore self, IntsKey a0)
3659  remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3660  remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3661  remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3662  """
3663  return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3664 
3665 
3666  def has_attribute(self, *args):
3667  """
3668  has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3669  has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3670  has_attribute(SlabWithCylindricalPore self, FloatsKey a0) -> bool
3671  has_attribute(SlabWithCylindricalPore self, IntsKey a0) -> bool
3672  has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3673  has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3674  has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3675  """
3676  return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3677 
3678 
3679  def get_derivative(self, a0):
3680  """get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3681  return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3682 
3683 
3684  def get_name(self):
3685  """get_name(SlabWithCylindricalPore self) -> std::string"""
3686  return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3687 
3688 
3689  def clear_caches(self):
3690  """clear_caches(SlabWithCylindricalPore self)"""
3691  return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3692 
3693 
3694  def set_name(self, a0):
3695  """set_name(SlabWithCylindricalPore self, std::string a0)"""
3696  return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3697 
3698 
3699  def set_check_level(self, a0):
3700  """set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3701  return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3702 
3703 
3704  def add_to_derivative(self, a0, a1, a2):
3705  """add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3706  return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3707 
3708 
3709  def set_is_optimized(self, a0, a1):
3710  """set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3711  return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3712 
3713 
3714  def get_is_optimized(self, a0):
3715  """get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3716  return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3717 
3718 
3719  def get_check_level(self):
3720  """get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3721  return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3722 
3723 
3724  def __eq__(self, *args):
3725  """
3726  __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3727  __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3728  """
3729  return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3730 
3731 
3732  def __ne__(self, *args):
3733  """
3734  __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3735  __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3736  """
3737  return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3738 
3739 
3740  def __le__(self, *args):
3741  """
3742  __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3743  __le__(SlabWithCylindricalPore self, Particle d) -> bool
3744  """
3745  return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3746 
3747 
3748  def __lt__(self, *args):
3749  """
3750  __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3751  __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3752  """
3753  return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3754 
3755 
3756  def __ge__(self, *args):
3757  """
3758  __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3759  __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3760  """
3761  return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3762 
3763 
3764  def __gt__(self, *args):
3765  """
3766  __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3767  __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3768  """
3769  return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3770 
3771 
3772  def __hash__(self):
3773  """__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3774  return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3775 
3776 
3777  def __str__(self):
3778  """__str__(SlabWithCylindricalPore self) -> std::string"""
3779  return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3780 
3781 
3782  def __repr__(self):
3783  """__repr__(SlabWithCylindricalPore self) -> std::string"""
3784  return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3785 
3786  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3787  __del__ = lambda self: None
3788 SlabWithCylindricalPore_swigregister = _IMP_npctransport.SlabWithCylindricalPore_swigregister
3789 SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3790 
3791 def SlabWithCylindricalPore_setup_particle(*args):
3792  """
3793  setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3794  SlabWithCylindricalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3795  """
3796  return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3797 
3798 def SlabWithCylindricalPore_get_is_setup(*args):
3799  """
3800  get_is_setup(_ParticleAdaptor p) -> bool
3801  SlabWithCylindricalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3802  """
3803  return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3804 
3805 def SlabWithCylindricalPore_get_cylindrical_pore_key():
3806  """SlabWithCylindricalPore_get_cylindrical_pore_key() -> IntKey"""
3807  return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3808 
3809 class SlabWithToroidalPore(SlabWithPore):
3810  """Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3811 
3812  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3813 
3814  def __init__(self, *args):
3815  """
3816  __init__(IMP::npctransport::SlabWithToroidalPore self) -> SlabWithToroidalPore
3817  __init__(IMP::npctransport::SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3818  __init__(IMP::npctransport::SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3819  """
3820  this = _IMP_npctransport.new_SlabWithToroidalPore(*args)
3821  try:
3822  self.this.append(this)
3823  except __builtin__.Exception:
3824  self.this = this
3825 
3826  def show(self, *args):
3827  """
3828  show(SlabWithToroidalPore self, _ostream out)
3829  show(SlabWithToroidalPore self)
3830  """
3831  return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3832 
3833 
3834  def setup_particle(*args):
3835  """
3836  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3837  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
3838  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3839  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3840  """
3841  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3842 
3843  setup_particle = staticmethod(setup_particle)
3844 
3845  def get_is_setup(*args):
3846  """
3847  get_is_setup(_ParticleAdaptor p) -> bool
3848  get_is_setup(Model m, ParticleIndex pi) -> bool
3849  """
3850  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3851 
3852  get_is_setup = staticmethod(get_is_setup)
3853 
3854  def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3855  """set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3856  return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3857 
3858 
3859  def get_minor_radius_h2v_aspect_ratio(self):
3860  """get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3861  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3862 
3863 
3864  def get_vertical_minor_radius(self):
3865  """get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3866  return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3867 
3868 
3869  def set_vertical_minor_radius(self, rv):
3870  """set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3871  return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3872 
3873 
3874  def get_horizontal_minor_radius(self):
3875  """get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3876  return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3877 
3878 
3879  def set_horizontal_minor_radius(self, rh):
3880  """set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3881  return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3882 
3883 
3884  def get_minor_radius_h2v_aspect_ratio_key():
3885  """get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3886  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3887 
3888  get_minor_radius_h2v_aspect_ratio_key = staticmethod(get_minor_radius_h2v_aspect_ratio_key)
3889 
3890  def get_toroidal_pore_key():
3891  """get_toroidal_pore_key() -> IntKey"""
3892  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3893 
3894  get_toroidal_pore_key = staticmethod(get_toroidal_pore_key)
3895 
3896  def add_attribute(self, *args):
3897  """
3898  add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3899  add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3900  add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3901  add_attribute(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3902  add_attribute(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3903  add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3904  add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3905  add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3906  """
3907  return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3908 
3909 
3910  def get_value(self, *args):
3911  """
3912  get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3913  get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3914  get_value(SlabWithToroidalPore self, FloatsKey a0) -> IMP::Floats
3915  get_value(SlabWithToroidalPore self, IntsKey a0) -> IMP::Ints
3916  get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3917  get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3918  get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3919  """
3920  return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3921 
3922 
3923  def set_value(self, *args):
3924  """
3925  set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3926  set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3927  set_value(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3928  set_value(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3929  set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3930  set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3931  set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3932  """
3933  return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3934 
3935 
3936  def remove_attribute(self, *args):
3937  """
3938  remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3939  remove_attribute(SlabWithToroidalPore self, IntKey a0)
3940  remove_attribute(SlabWithToroidalPore self, FloatsKey a0)
3941  remove_attribute(SlabWithToroidalPore self, IntsKey a0)
3942  remove_attribute(SlabWithToroidalPore self, StringKey a0)
3943  remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3944  remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3945  """
3946  return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3947 
3948 
3949  def has_attribute(self, *args):
3950  """
3951  has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3952  has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3953  has_attribute(SlabWithToroidalPore self, FloatsKey a0) -> bool
3954  has_attribute(SlabWithToroidalPore self, IntsKey a0) -> bool
3955  has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3956  has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3957  has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3958  """
3959  return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3960 
3961 
3962  def get_derivative(self, a0):
3963  """get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3964  return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3965 
3966 
3967  def get_name(self):
3968  """get_name(SlabWithToroidalPore self) -> std::string"""
3969  return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3970 
3971 
3972  def clear_caches(self):
3973  """clear_caches(SlabWithToroidalPore self)"""
3974  return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3975 
3976 
3977  def set_name(self, a0):
3978  """set_name(SlabWithToroidalPore self, std::string a0)"""
3979  return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3980 
3981 
3982  def set_check_level(self, a0):
3983  """set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3984  return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3985 
3986 
3987  def add_to_derivative(self, a0, a1, a2):
3988  """add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3989  return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3990 
3991 
3992  def set_is_optimized(self, a0, a1):
3993  """set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3994  return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3995 
3996 
3997  def get_is_optimized(self, a0):
3998  """get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3999  return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
4000 
4001 
4002  def get_check_level(self):
4003  """get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
4004  return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
4005 
4006 
4007  def __eq__(self, *args):
4008  """
4009  __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4010  __eq__(SlabWithToroidalPore self, Particle d) -> bool
4011  """
4012  return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
4013 
4014 
4015  def __ne__(self, *args):
4016  """
4017  __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4018  __ne__(SlabWithToroidalPore self, Particle d) -> bool
4019  """
4020  return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
4021 
4022 
4023  def __le__(self, *args):
4024  """
4025  __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4026  __le__(SlabWithToroidalPore self, Particle d) -> bool
4027  """
4028  return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
4029 
4030 
4031  def __lt__(self, *args):
4032  """
4033  __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4034  __lt__(SlabWithToroidalPore self, Particle d) -> bool
4035  """
4036  return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
4037 
4038 
4039  def __ge__(self, *args):
4040  """
4041  __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4042  __ge__(SlabWithToroidalPore self, Particle d) -> bool
4043  """
4044  return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
4045 
4046 
4047  def __gt__(self, *args):
4048  """
4049  __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4050  __gt__(SlabWithToroidalPore self, Particle d) -> bool
4051  """
4052  return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
4053 
4054 
4055  def __hash__(self):
4056  """__hash__(SlabWithToroidalPore self) -> std::size_t"""
4057  return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
4058 
4059 
4060  def __str__(self):
4061  """__str__(SlabWithToroidalPore self) -> std::string"""
4062  return _IMP_npctransport.SlabWithToroidalPore___str__(self)
4063 
4064 
4065  def __repr__(self):
4066  """__repr__(SlabWithToroidalPore self) -> std::string"""
4067  return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
4068 
4069  __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
4070  __del__ = lambda self: None
4071 SlabWithToroidalPore_swigregister = _IMP_npctransport.SlabWithToroidalPore_swigregister
4072 SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
4073 
4074 def SlabWithToroidalPore_setup_particle(*args):
4075  """
4076  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
4077  setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
4078  setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4079  SlabWithToroidalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4080  """
4081  return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
4082 
4083 def SlabWithToroidalPore_get_is_setup(*args):
4084  """
4085  get_is_setup(_ParticleAdaptor p) -> bool
4086  SlabWithToroidalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
4087  """
4088  return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
4089 
4090 def SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key():
4091  """SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
4092  return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
4093 
4094 def SlabWithToroidalPore_get_toroidal_pore_key():
4095  """SlabWithToroidalPore_get_toroidal_pore_key() -> IntKey"""
4096  return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
4097 
4098 
4099 def __lshift__(*args):
4100  """
4101  __lshift__(_ostream out, RelaxingSpring n) -> _ostream
4102  __lshift__(_ostream out, Transporting n) -> _ostream
4103  __lshift__(_ostream out, SlabWithPore n) -> _ostream
4104  __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
4105  __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
4106  """
4107  return _IMP_npctransport.__lshift__(*args)
4108 class SlabWithCylindricalPorePairScore(IMP.PairScore):
4109  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
4110 
4111  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4112 
4113  def __init__(self, k):
4114  """__init__(IMP::npctransport::SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
4115  this = _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k)
4116  try:
4117  self.this.append(this)
4118  except __builtin__.Exception:
4119  self.this = this
4120 
4121  def get_displacement_direction(self, slab, v):
4122  """get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
4123  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
4124 
4125 
4126  def get_displacement_magnitude(self, slab, v):
4127  """get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
4128  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
4129 
4130 
4131  def do_get_inputs(self, m, pis):
4132  """do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4133  return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
4134 
4135 
4136  def get_version_info(self):
4137  """get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
4138  return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
4139 
4140 
4141  def __str__(self):
4142  """__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
4143  return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
4144 
4145 
4146  def __repr__(self):
4147  """__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
4148  return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
4149 
4150 
4151  @staticmethod
4152  def get_from(o):
4153  return _object_cast_to_SlabWithCylindricalPorePairScore(o)
4154 
4155 SlabWithCylindricalPorePairScore_swigregister = _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister
4156 SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
4157 
4158 class SlabWithToroidalPorePairScore(IMP.PairScore):
4159  """Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
4160 
4161  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4162 
4163  def __init__(self, k):
4164  """__init__(IMP::npctransport::SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
4165  this = _IMP_npctransport.new_SlabWithToroidalPorePairScore(k)
4166  try:
4167  self.this.append(this)
4168  except __builtin__.Exception:
4169  self.this = this
4170 
4171  def do_get_inputs(self, m, pis):
4172  """do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4173  return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
4174 
4175 
4176  def get_version_info(self):
4177  """get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
4178  return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
4179 
4180 
4181  def __str__(self):
4182  """__str__(SlabWithToroidalPorePairScore self) -> std::string"""
4183  return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
4184 
4185 
4186  def __repr__(self):
4187  """__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
4188  return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
4189 
4190 
4191  @staticmethod
4192  def get_from(o):
4193  return _object_cast_to_SlabWithToroidalPorePairScore(o)
4194 
4195 SlabWithToroidalPorePairScore_swigregister = _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister
4196 SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
4197 
4198 class SlabWithCylindricalPoreWireGeometry(IMP.display.Geometry):
4199  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
4200 
4201  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4202 
4203  def __init__(self, height, radius, length):
4204  """__init__(IMP::npctransport::SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
4205  this = _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length)
4206  try:
4207  self.this.append(this)
4208  except __builtin__.Exception:
4209  self.this = this
4210 
4211  def get_version_info(self):
4212  """get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
4213  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
4214 
4215 
4216  def __str__(self):
4217  """__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4218  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
4219 
4220 
4221  def __repr__(self):
4222  """__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4223  return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
4224 
4225 
4226  @staticmethod
4227  def get_from(o):
4228  return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
4229 
4230 SlabWithCylindricalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister
4231 SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
4232 
4233 class SlabWithCylindricalPoreSurfaceGeometry(IMP.display.SurfaceMeshGeometry):
4234  """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
4235 
4236  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4237 
4238  def __init__(self, height, radius, length):
4239  """__init__(IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
4240  this = _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length)
4241  try:
4242  self.this.append(this)
4243  except __builtin__.Exception:
4244  self.this = this
4245 
4246  def __str__(self):
4247  """__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4248  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
4249 
4250 
4251  def __repr__(self):
4252  """__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4253  return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
4254 
4255 
4256  @staticmethod
4257  def get_from(o):
4258  return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
4259 
4260  __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
4261  __del__ = lambda self: None
4262 SlabWithCylindricalPoreSurfaceGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister
4263 SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
4264 
4265 class SlabWithToroidalPoreWireGeometry(IMP.display.Geometry):
4266  """Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
4267 
4268  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4269 
4270  def __init__(self, *args):
4271  """
4272  __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
4273  __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
4274  """
4275  this = _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args)
4276  try:
4277  self.this.append(this)
4278  except __builtin__.Exception:
4279  self.this = this
4280 
4281  def get_version_info(self):
4282  """get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
4283  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
4284 
4285 
4286  def __str__(self):
4287  """__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4288  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
4289 
4290 
4291  def __repr__(self):
4292  """__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4293  return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
4294 
4295 
4296  @staticmethod
4297  def get_from(o):
4298  return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
4299 
4300 SlabWithToroidalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister
4301 SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
4302 
4303 class _GenericAttributeSingletonScoreForPoreRadus(IMP.SingletonScore):
4304  """Proxy of C++ IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> class."""
4305 
4306  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4307  __repr__ = _swig_repr
4308 
4309  def __init__(self, f, k):
4310  """__init__(IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
4311  this = _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k)
4312  try:
4313  self.this.append(this)
4314  except __builtin__.Exception:
4315  self.this = this
4316 
4317  def do_get_inputs(self, m, pis):
4318  """do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4319  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
4320 
4321 
4322  def get_unary_function(self):
4323  """get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
4324  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
4325 
4326 
4327  def get_version_info(self):
4328  """get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
4329  return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
4330 
4331 _GenericAttributeSingletonScoreForPoreRadus_swigregister = _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister
4332 _GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
4333 
4334 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
4335  """Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
4336 
4337  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4338 
4339  def __init__(self, mean, k):
4340  """__init__(IMP::npctransport::PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
4341  this = _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k)
4342  try:
4343  self.this.append(this)
4344  except __builtin__.Exception:
4345  self.this = this
4346 
4347  def set_k(self, k):
4348  """set_k(PoreRadiusSingletonScore self, double k)"""
4349  return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
4350 
4351 
4352  def __str__(self):
4353  """__str__(PoreRadiusSingletonScore self) -> std::string"""
4354  return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
4355 
4356 
4357  def __repr__(self):
4358  """__repr__(PoreRadiusSingletonScore self) -> std::string"""
4359  return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
4360 
4361 
4362  @staticmethod
4363  def get_from(o):
4364  return _object_cast_to_PoreRadiusSingletonScore(o)
4365 
4366 PoreRadiusSingletonScore_swigregister = _IMP_npctransport.PoreRadiusSingletonScore_swigregister
4367 PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
4368 
4369 class ExcludeZRangeSingletonScore(IMP.SingletonScore):
4370  """Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
4371 
4372  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4373 
4374  def __init__(self, bottom, top, k):
4375  """__init__(IMP::npctransport::ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
4376  this = _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k)
4377  try:
4378  self.this.append(this)
4379  except __builtin__.Exception:
4380  self.this = this
4381 
4382  def get_bottom_z(self):
4383  """get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
4384  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
4385 
4386 
4387  def get_top_z(self):
4388  """get_top_z(ExcludeZRangeSingletonScore self) -> double"""
4389  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
4390 
4391 
4392  def get_k(self):
4393  """get_k(ExcludeZRangeSingletonScore self) -> double"""
4394  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
4395 
4396 
4397  def do_get_inputs(self, m, pis):
4398  """do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4399  return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
4400 
4401 
4402  def get_version_info(self):
4403  """get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
4404  return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
4405 
4406 
4407  def __str__(self):
4408  """__str__(ExcludeZRangeSingletonScore self) -> std::string"""
4409  return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
4410 
4411 
4412  def __repr__(self):
4413  """__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
4414  return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
4415 
4416 
4417  @staticmethod
4418  def get_from(o):
4419  return _object_cast_to_ExcludeZRangeSingletonScore(o)
4420 
4421 ExcludeZRangeSingletonScore_swigregister = _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister
4422 ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
4423 
4424 class ZBiasSingletonScore(IMP.SingletonScore):
4425  """Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
4426 
4427  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4428 
4429  def __init__(self, *args):
4430  """
4431  __init__(IMP::npctransport::ZBiasSingletonScore self, double k, double max_r) -> ZBiasSingletonScore
4432  __init__(IMP::npctransport::ZBiasSingletonScore self, double k) -> ZBiasSingletonScore
4433  """
4434  this = _IMP_npctransport.new_ZBiasSingletonScore(*args)
4435  try:
4436  self.this.append(this)
4437  except __builtin__.Exception:
4438  self.this = this
4439 
4440  def get_k(self):
4441  """get_k(ZBiasSingletonScore self) -> double"""
4442  return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
4443 
4444 
4445  def set_k(self, k):
4446  """set_k(ZBiasSingletonScore self, double k)"""
4447  return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
4448 
4449 
4450  def do_get_inputs(self, m, pis):
4451  """do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4452  return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
4453 
4454 
4455  def get_version_info(self):
4456  """get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
4457  return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
4458 
4459 
4460  def __str__(self):
4461  """__str__(ZBiasSingletonScore self) -> std::string"""
4462  return _IMP_npctransport.ZBiasSingletonScore___str__(self)
4463 
4464 
4465  def __repr__(self):
4466  """__repr__(ZBiasSingletonScore self) -> std::string"""
4467  return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
4468 
4469 
4470  @staticmethod
4471  def get_from(o):
4472  return _object_cast_to_ZBiasSingletonScore(o)
4473 
4474 ZBiasSingletonScore_swigregister = _IMP_npctransport.ZBiasSingletonScore_swigregister
4475 ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
4476 
4477 class BodyStatisticsOptimizerState(IMP.OptimizerState):
4478  """Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
4479 
4480  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4481 
4482  def __init__(self, p, statistics_manager=None, periodicity=1):
4483  """
4484  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState
4485  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None) -> BodyStatisticsOptimizerState
4486  __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p) -> BodyStatisticsOptimizerState
4487  """
4488  this = _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity)
4489  try:
4490  self.this.append(this)
4491  except __builtin__.Exception:
4492  self.this = this
4493 
4494  def get_correlation_time(self):
4495  """get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4496  return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4497 
4498 
4499  def get_diffusion_coefficient(self):
4500  """get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4501  return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4502 
4503 
4504  def update_particle_type_zr_distribution_map(self):
4505  """update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4506  return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4507 
4508 
4509  def do_update(self, call_num):
4510  """do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4511  return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4512 
4513 
4514  def get_version_info(self):
4515  """get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4516  return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4517 
4518 
4519  def __str__(self):
4520  """__str__(BodyStatisticsOptimizerState self) -> std::string"""
4521  return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4522 
4523 
4524  def __repr__(self):
4525  """__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4526  return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4527 
4528 
4529  @staticmethod
4530  def get_from(o):
4531  return _object_cast_to_BodyStatisticsOptimizerState(o)
4532 
4533 BodyStatisticsOptimizerState_swigregister = _IMP_npctransport.BodyStatisticsOptimizerState_swigregister
4534 BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4535 
4536 class ParticleTransportStatisticsOptimizerState(IMP.OptimizerState):
4537  """Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
4538 
4539  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4540 
4541  def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4542  """
4543  __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
4544  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0) -> ParticleTransportStatisticsOptimizerState
4545  __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z) -> ParticleTransportStatisticsOptimizerState
4546  """
4547  this = _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner)
4548  try:
4549  self.this.append(this)
4550  except __builtin__.Exception:
4551  self.this = this
4552 
4553  def set_owner(self, owner):
4554  """set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4555  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4556 
4557 
4558  def get_owner(self):
4559  """get_owner(ParticleTransportStatisticsOptimizerState self) -> WeakPointer< IMP::atom::Simulator >"""
4560  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4561 
4562 
4563  def get_n_transports_up(self):
4564  """get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4565  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4566 
4567 
4568  def get_n_transports_down(self):
4569  """get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4570  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4571 
4572 
4573  def get_total_n_transports(self):
4574  """get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4575  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4576 
4577 
4578  def get_transport_time_points_in_ns(self):
4579  """get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4580  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4581 
4582 
4583  def do_update(self, call_num):
4584  """do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4585  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4586 
4587 
4588  def get_version_info(self):
4589  """get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4590  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4591 
4592 
4593  def __str__(self):
4594  """__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4595  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4596 
4597 
4598  def __repr__(self):
4599  """__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4600  return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4601 
4602 
4603  @staticmethod
4604  def get_from(o):
4605  return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4606 
4607 ParticleTransportStatisticsOptimizerState_swigregister = _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister
4608 ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4609 
4610 class ChainStatisticsOptimizerState(IMP.OptimizerState):
4611  """Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
4612 
4613  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4614 
4615  def __init__(self, ps, periodicity=1):
4616  """
4617  __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState
4618  __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps) -> ChainStatisticsOptimizerState
4619  """
4620  this = _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity)
4621  try:
4622  self.this.append(this)
4623  except __builtin__.Exception:
4624  self.this = this
4625 
4626  def get_correlation_time(self):
4627  """get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4628  return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4629 
4630 
4631  def get_local_diffusion_coefficients(self):
4632  """get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4633  return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4634 
4635 
4636  def get_diffusion_coefficient(self):
4637  """get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
4638  return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
4639 
4640 
4641  def get_mean_radius_of_gyration(self):
4642  """get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4643  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
4644 
4645 
4646  def get_mean_square_radius_of_gyration(self):
4647  """get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4648  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4649 
4650 
4651  def get_mean_end_to_end_distance(self):
4652  """get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4653  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4654 
4655 
4656  def get_mean_square_end_to_end_distance(self):
4657  """get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4658  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4659 
4660 
4661  def get_mean_bond_distance(self):
4662  """get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4663  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4664 
4665 
4666  def get_mean_square_bond_distance(self):
4667  """get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4668  return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4669 
4670 
4671  def do_update(self, call_num):
4672  """do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4673  return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4674 
4675 
4676  def get_version_info(self):
4677  """get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4678  return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4679 
4680 
4681  def __str__(self):
4682  """__str__(ChainStatisticsOptimizerState self) -> std::string"""
4683  return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4684 
4685 
4686  def __repr__(self):
4687  """__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4688  return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4689 
4690 
4691  @staticmethod
4692  def get_from(o):
4693  return _object_cast_to_ChainStatisticsOptimizerState(o)
4694 
4695 ChainStatisticsOptimizerState_swigregister = _IMP_npctransport.ChainStatisticsOptimizerState_swigregister
4696 ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4697 
4698 class BipartitePairsStatisticsOptimizerState(IMP.OptimizerState):
4699  """Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4700 
4701  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4702 
4703  def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4704  """
4705  __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
4706  __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
4707  __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII) -> BipartitePairsStatisticsOptimizerState
4708  """
4709  this = _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack)
4710  try:
4711  self.this.append(this)
4712  except __builtin__.Exception:
4713  self.this = this
4714 
4715  def get_interaction_type(self):
4716  """get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4717  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4718 
4719 
4720  def get_average_number_of_contacts(self):
4721  """get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4722  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4723 
4724 
4725  def get_average_off_per_contact_per_ns(self):
4726  """get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4727  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4728 
4729 
4730  def get_average_off_per_bound_I_per_ns(self):
4731  """get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4732  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4733 
4734 
4735  def get_average_off_per_bound_II_per_ns(self):
4736  """get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4737  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4738 
4739 
4740  def get_average_on_per_missing_contact_per_ns(self):
4741  """get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4742  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4743 
4744 
4745  def get_average_on_per_unbound_I_per_ns(self):
4746  """get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4747  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4748 
4749 
4750  def get_average_on_per_unbound_II_per_ns(self):
4751  """get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4752  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4753 
4754 
4755  def get_average_fraction_bound_particles_I(self):
4756  """get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4757  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4758 
4759 
4760  def get_average_fraction_bound_particles_II(self):
4761  """get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4762  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4763 
4764 
4765  def get_average_fraction_bound_particle_sites_I(self):
4766  """get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4767  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4768 
4769 
4770  def get_average_fraction_bound_particle_sites_II(self):
4771  """get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4772  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4773 
4774 
4775  def get_average_fraction_nonspecific_interactions_I(self):
4776  """get_average_fraction_nonspecific_interactions_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4777  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_I(self)
4778 
4779 
4780  def get_average_fraction_nonspecific_interactions_II(self):
4781  """get_average_fraction_nonspecific_interactions_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4782  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_II(self)
4783 
4784 
4785  def get_number_of_particles_1(self):
4786  """get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4787  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4788 
4789 
4790  def get_number_of_particles_2(self):
4791  """get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4792  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4793 
4794 
4795  def get_misc_stats_period_ns(self):
4796  """get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4797  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4798 
4799 
4800  def get_off_stats_period_ns(self):
4801  """get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4802  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4803 
4804 
4805  def get_off_I_stats_period_ns(self):
4806  """get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4807  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4808 
4809 
4810  def get_off_II_stats_period_ns(self):
4811  """get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4812  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4813 
4814 
4815  def get_on_stats_period_ns(self):
4816  """get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4817  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4818 
4819 
4820  def get_on_I_stats_period_ns(self):
4821  """get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4822  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4823 
4824 
4825  def get_on_II_stats_period_ns(self):
4826  """get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4827  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4828 
4829 
4830  def get_version_info(self):
4831  """get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4832  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4833 
4834 
4835  def __str__(self):
4836  """__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4837  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4838 
4839 
4840  def __repr__(self):
4841  """__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4842  return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4843 
4844 
4845  @staticmethod
4846  def get_from(o):
4847  return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4848 
4849 BipartitePairsStatisticsOptimizerState_swigregister = _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister
4850 BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4851 
4852 
4853 def get_close_pairs_range(*args):
4854  """
4855  get_close_pairs_range(double max_range, double max_range_factor) -> double
4856  get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4857  """
4858  return _IMP_npctransport.get_close_pairs_range(*args)
4859 
4860 def get_time_step(*args):
4861  """
4862  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
4863  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
4864  get_time_step(double max_d_factor, double max_k, double min_radius, double min_range) -> double
4865  get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4866  get_time_step(::npctransport_proto::Assignment const & config) -> double
4867  """
4868  return _IMP_npctransport.get_time_step(*args)
4869 
4870 def get_frames_from_ns(ns, time_step):
4871  """get_frames_from_ns(double ns, double time_step) -> int"""
4872  return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4873 
4874 def get_number_of_frames(config, time_step):
4875  """get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4876  return _IMP_npctransport.get_number_of_frames(config, time_step)
4877 
4878 def get_dump_interval_in_frames(config, time_step):
4879  """get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4880  return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4881 
4882 def get_statistics_interval_in_frames(assign, time_step, default_value_ns=0.1):
4883  """
4884  get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int
4885  get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4886  """
4887  return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4888 
4889 def get_output_statistics_interval_in_frames(assign, time_step, default_value_ns=1.0):
4890  """
4891  get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int
4892  get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4893  """
4894  return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4895 
4896 def initialize_positions(*args):
4897  """
4898  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)
4899  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False)
4900  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0)
4901  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False)
4902  initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints)
4903  initialize_positions(SimulationData sd)
4904  """
4905  return _IMP_npctransport.initialize_positions(*args)
4906 class Avro2PBReader(object):
4907  """Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4908 
4909  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
4910 
4911  def __init__(self, *args):
4912  """
4913  __init__(IMP::npctransport::Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4914  __init__(IMP::npctransport::Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4915  """
4916  this = _IMP_npctransport.new_Avro2PBReader(*args)
4917  try:
4918  self.this.append(this)
4919  except __builtin__.Exception:
4920  self.this = this
4921  __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4922  __del__ = lambda self: None
4923 
4924  def read_next(self):
4925  """read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4926  return _IMP_npctransport.Avro2PBReader_read_next(self)
4927 
4928 
4929  def get_is_valid(self):
4930  """get_is_valid(Avro2PBReader self) -> bool"""
4931  return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4932 
4933 
4934  def get_cur_file_name(self):
4935  """get_cur_file_name(Avro2PBReader self) -> std::string"""
4936  return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4937 
4938 
4939  def show(self, *args):
4940  """
4941  show(Avro2PBReader self, _ostream out)
4942  show(Avro2PBReader self)
4943  """
4944  return _IMP_npctransport.Avro2PBReader_show(self, *args)
4945 
4946 
4947  def __str__(self):
4948  """__str__(Avro2PBReader self) -> std::string"""
4949  return _IMP_npctransport.Avro2PBReader___str__(self)
4950 
4951 
4952  def __repr__(self):
4953  """__repr__(Avro2PBReader self) -> std::string"""
4954  return _IMP_npctransport.Avro2PBReader___repr__(self)
4955 
4956 Avro2PBReader_swigregister = _IMP_npctransport.Avro2PBReader_swigregister
4957 Avro2PBReader_swigregister(Avro2PBReader)
4958 
4959 
4960 def get_optimizable_particles(particles):
4961  """get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4962  return _IMP_npctransport.get_optimizable_particles(particles)
4963 
4964 def get_non_optimizable_particles(particles):
4965  """get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4966  return _IMP_npctransport.get_non_optimizable_particles(particles)
4967 
4968 def get_particle_indexes(particles):
4969  """get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4970  return _IMP_npctransport.get_particle_indexes(particles)
4971 
4972 def get_protobuf_configuration_from_text(config_txt, config_pb):
4973  """get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4974  return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4975 
4976 def get_spheres_from_vectors(vs, radius):
4977  """get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4978  return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4979 
4980 def get_spheres_centers(spheres):
4981  """get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4982  return _IMP_npctransport.get_spheres_centers(spheres)
4983 
4985  """copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4986  return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4987 
4989  """copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4990  return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4991 
4992 def copy_FGs_coordinates(src_sd, trg_sd):
4993  """copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4994  return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4995 
4996 try:
4997  from .npctransport_pb2 import *
4998  import google.protobuf
4999 except ImportError:
5000  print("no protobuf support in python")
5001 from ._configuration import *
5002 
5003 
5004 def get_module_version():
5005  """get_module_version() -> std::string const"""
5006  return _IMP_npctransport.get_module_version()
5007 
5008 def get_example_path(fname):
5009  """get_example_path(std::string fname) -> std::string"""
5010  return _IMP_npctransport.get_example_path(fname)
5011 
5012 def get_data_path(fname):
5013  """get_data_path(std::string fname) -> std::string"""
5014  return _IMP_npctransport.get_data_path(fname)
5015 
5016 from . import _version_check
5017 _version_check.check_version(get_module_version())
5018 __version__ = get_module_version()
5019 
5020 
5021 
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_module_version()
Return the version of this module, as a string.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
int get_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)
void get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
Simple Brownian dynamics simulator.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
Common base class for heavy weight IMP objects.
Definition: Object.h: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)
Basic utilities for handling cryo-electron microscopy 3D density maps.
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h: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)
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
void add_hierarchies_with_sites(RMF::FileHandle fh, const atom::Hierarchies &hs)
InteractionType make_unordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
Definition: typedefs.h:35
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
FGChain * get_fg_chain(atom::Hierarchy root)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for developing and analyzing benchmarks of IMP code.
InteractionType make_ordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
convenience method for creating and interaction type in swig
Definition: typedefs.h:26
Support for the RMF file format for storing hierarchical molecular data and markup.
Support for small angle X-ray scattering (SAXS) data.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h: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)
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
algebra::Sphere3Ds get_spheres_from_vectors(V3iter first, V3iter last, double radius)
convert vectors to spheres of passed radius
Definition: util.h:169