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IMP Reference Guide  develop.e1fe35f,2019/09/16
The Integrative Modeling Platform
pmi/__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 2007-2019 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_pmi')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_pmi')
25  _IMP_pmi = 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_pmi', [dirname(__file__)])
34  except ImportError:
35  import _IMP_pmi
36  return _IMP_pmi
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_pmi', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_pmi = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_pmi
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_PMI_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_PMI_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_pmi.delete_IMP_PMI_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_PMI_SwigPyIterator self) -> PyObject *"""
126  return _IMP_pmi.IMP_PMI_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator
132  incr(IMP_PMI_SwigPyIterator self) -> IMP_PMI_SwigPyIterator
133  """
134  return _IMP_pmi.IMP_PMI_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_PMI_SwigPyIterator self, size_t n=1) -> IMP_PMI_SwigPyIterator
140  decr(IMP_PMI_SwigPyIterator self) -> IMP_PMI_SwigPyIterator
141  """
142  return _IMP_pmi.IMP_PMI_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_pmi.IMP_PMI_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
152  return _IMP_pmi.IMP_PMI_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_PMI_SwigPyIterator self) -> IMP_PMI_SwigPyIterator"""
157  return _IMP_pmi.IMP_PMI_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_PMI_SwigPyIterator self) -> PyObject *"""
162  return _IMP_pmi.IMP_PMI_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_PMI_SwigPyIterator self) -> PyObject *"""
167  return _IMP_pmi.IMP_PMI_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_PMI_SwigPyIterator self) -> PyObject *"""
172  return _IMP_pmi.IMP_PMI_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
177  return _IMP_pmi.IMP_PMI_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
182  return _IMP_pmi.IMP_PMI_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> bool"""
187  return _IMP_pmi.IMP_PMI_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
192  return _IMP_pmi.IMP_PMI_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
197  return _IMP_pmi.IMP_PMI_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator"""
202  return _IMP_pmi.IMP_PMI_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_PMI_SwigPyIterator self, ptrdiff_t n) -> IMP_PMI_SwigPyIterator
208  __sub__(IMP_PMI_SwigPyIterator self, IMP_PMI_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_pmi.IMP_PMI_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_PMI_SwigPyIterator_swigregister = _IMP_pmi.IMP_PMI_SwigPyIterator_swigregister
215 IMP_PMI_SwigPyIterator_swigregister(IMP_PMI_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_pmi.IMP_DEBUG
224 IMP_RELEASE = _IMP_pmi.IMP_RELEASE
225 IMP_SILENT = _IMP_pmi.IMP_SILENT
226 IMP_PROGRESS = _IMP_pmi.IMP_PROGRESS
227 IMP_TERSE = _IMP_pmi.IMP_TERSE
228 IMP_VERBOSE = _IMP_pmi.IMP_VERBOSE
229 IMP_MEMORY = _IMP_pmi.IMP_MEMORY
230 IMP_NONE = _IMP_pmi.IMP_NONE
231 IMP_USAGE = _IMP_pmi.IMP_USAGE
232 IMP_INTERNAL = _IMP_pmi.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_pmi.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_pmi.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_pmi.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_pmi.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_pmi.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_pmi.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_pmi.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_pmi.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_pmi._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_pmi._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_pmi.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_pmi.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_pmi.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_pmi.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_pmi.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_pmi.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_MMCIF_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_MMCIF_HAS_BOOST_FILESYSTEM
299 IMP_MMCIF_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_MMCIF_HAS_BOOST_PROGRAMOPTIONS
300 IMP_MMCIF_HAS_BOOST_RANDOM = _IMP_pmi.IMP_MMCIF_HAS_BOOST_RANDOM
301 IMP_MMCIF_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_MMCIF_HAS_BOOST_SYSTEM
302 IMP_MMCIF_HAS_NUMPY = _IMP_pmi.IMP_MMCIF_HAS_NUMPY
303 IMPMMCIF_SHOW_WARNINGS = _IMP_pmi.IMPMMCIF_SHOW_WARNINGS
304 import IMP.mmcif
305 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_IMP_CGAL
306 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
307 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
308 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_RANDOM
309 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ALGEBRA_HAS_BOOST_SYSTEM
310 IMP_ALGEBRA_HAS_CGAL = _IMP_pmi.IMP_ALGEBRA_HAS_CGAL
311 IMP_ALGEBRA_HAS_NUMPY = _IMP_pmi.IMP_ALGEBRA_HAS_NUMPY
312 IMP_ALGEBRA_HAS_ANN = _IMP_pmi.IMP_ALGEBRA_HAS_ANN
313 IMPALGEBRA_SHOW_WARNINGS = _IMP_pmi.IMPALGEBRA_SHOW_WARNINGS
314 import IMP.algebra
315 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_IMP_CGAL
316 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
317 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
318 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_RANDOM
319 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_DISPLAY_HAS_BOOST_SYSTEM
320 IMP_DISPLAY_HAS_CGAL = _IMP_pmi.IMP_DISPLAY_HAS_CGAL
321 IMP_DISPLAY_HAS_NUMPY = _IMP_pmi.IMP_DISPLAY_HAS_NUMPY
322 IMPDISPLAY_SHOW_WARNINGS = _IMP_pmi.IMPDISPLAY_SHOW_WARNINGS
323 import IMP.display
324 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
325 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
326 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
327 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
328 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
329 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_CGAL
330 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_HDF5
331 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_pmi.IMP_SCORE_FUNCTOR_HAS_NUMPY
332 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_pmi.IMPSCOREFUNCTOR_SHOW_WARNINGS
333 import IMP.score_functor
334 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_IMP_CGAL
335 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
336 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
337 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_RANDOM
338 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_STATISTICS_HAS_BOOST_SYSTEM
339 IMP_STATISTICS_HAS_CGAL = _IMP_pmi.IMP_STATISTICS_HAS_CGAL
340 IMP_STATISTICS_HAS_NUMPY = _IMP_pmi.IMP_STATISTICS_HAS_NUMPY
341 IMPSTATISTICS_SHOW_WARNINGS = _IMP_pmi.IMPSTATISTICS_SHOW_WARNINGS
342 import IMP.statistics
343 IMP_CORE_HAS_IMP_CGAL = _IMP_pmi.IMP_CORE_HAS_IMP_CGAL
344 IMP_CORE_HAS_IMP_KERNEL = _IMP_pmi.IMP_CORE_HAS_IMP_KERNEL
345 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_FILESYSTEM
346 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CORE_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CORE_HAS_BOOST_RANDOM
348 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CORE_HAS_BOOST_SYSTEM
349 IMP_CORE_HAS_CGAL = _IMP_pmi.IMP_CORE_HAS_CGAL
350 IMP_CORE_HAS_HDF5 = _IMP_pmi.IMP_CORE_HAS_HDF5
351 IMP_CORE_HAS_NUMPY = _IMP_pmi.IMP_CORE_HAS_NUMPY
352 IMPCORE_SHOW_WARNINGS = _IMP_pmi.IMPCORE_SHOW_WARNINGS
353 import IMP.core
354 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_CONTAINER_HAS_IMP_ALGEBRA
355 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_CGAL
356 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_pmi.IMP_CONTAINER_HAS_IMP_DISPLAY
357 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_pmi.IMP_CONTAINER_HAS_IMP_KERNEL
358 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
359 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
360 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_RANDOM
362 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_CONTAINER_HAS_BOOST_SYSTEM
363 IMP_CONTAINER_HAS_CGAL = _IMP_pmi.IMP_CONTAINER_HAS_CGAL
364 IMP_CONTAINER_HAS_HDF5 = _IMP_pmi.IMP_CONTAINER_HAS_HDF5
365 IMP_CONTAINER_HAS_NUMPY = _IMP_pmi.IMP_CONTAINER_HAS_NUMPY
366 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_pmi.IMP_CONTAINER_HAS_PYTHON_IHM
367 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_pmi.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
368 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_pmi.IMP_CONTAINER_HAS_ROBIN_MAP
369 IMPCONTAINER_SHOW_WARNINGS = _IMP_pmi.IMPCONTAINER_SHOW_WARNINGS
370 import IMP.container
371 IMP_ATOM_HAS_IMP_CGAL = _IMP_pmi.IMP_ATOM_HAS_IMP_CGAL
372 IMP_ATOM_HAS_IMP_KERNEL = _IMP_pmi.IMP_ATOM_HAS_IMP_KERNEL
373 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
374 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ATOM_HAS_BOOST_RANDOM
376 IMP_ATOM_HAS_BOOST_REGEX = _IMP_pmi.IMP_ATOM_HAS_BOOST_REGEX
377 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ATOM_HAS_BOOST_SYSTEM
378 IMP_ATOM_HAS_CGAL = _IMP_pmi.IMP_ATOM_HAS_CGAL
379 IMP_ATOM_HAS_HDF5 = _IMP_pmi.IMP_ATOM_HAS_HDF5
380 IMP_ATOM_HAS_NUMPY = _IMP_pmi.IMP_ATOM_HAS_NUMPY
381 IMP_ATOM_HAS_PYTHON_IHM = _IMP_pmi.IMP_ATOM_HAS_PYTHON_IHM
382 IMPATOM_SHOW_WARNINGS = _IMP_pmi.IMPATOM_SHOW_WARNINGS
383 IMP_ATOM_TYPE_INDEX = _IMP_pmi.IMP_ATOM_TYPE_INDEX
384 IMP_RESIDUE_TYPE_INDEX = _IMP_pmi.IMP_RESIDUE_TYPE_INDEX
385 IMP_HIERARCHY_TYPE_INDEX = _IMP_pmi.IMP_HIERARCHY_TYPE_INDEX
386 IMP_CHAIN_TYPE_INDEX = _IMP_pmi.IMP_CHAIN_TYPE_INDEX
387 import IMP.atom
388 IMP_EM_HAS_IMP_CGAL = _IMP_pmi.IMP_EM_HAS_IMP_CGAL
389 IMP_EM_HAS_IMP_CONTAINER = _IMP_pmi.IMP_EM_HAS_IMP_CONTAINER
390 IMP_EM_HAS_IMP_DISPLAY = _IMP_pmi.IMP_EM_HAS_IMP_DISPLAY
391 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_EM_HAS_IMP_SCORE_FUNCTOR
392 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_FILESYSTEM
393 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
394 IMP_EM_HAS_BOOST_RANDOM = _IMP_pmi.IMP_EM_HAS_BOOST_RANDOM
395 IMP_EM_HAS_BOOST_REGEX = _IMP_pmi.IMP_EM_HAS_BOOST_REGEX
396 IMP_EM_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_EM_HAS_BOOST_SYSTEM
397 IMP_EM_HAS_CGAL = _IMP_pmi.IMP_EM_HAS_CGAL
398 IMP_EM_HAS_HDF5 = _IMP_pmi.IMP_EM_HAS_HDF5
399 IMP_EM_HAS_NUMPY = _IMP_pmi.IMP_EM_HAS_NUMPY
400 IMP_EM_HAS_PYTHON_IHM = _IMP_pmi.IMP_EM_HAS_PYTHON_IHM
401 IMPEM_SHOW_WARNINGS = _IMP_pmi.IMPEM_SHOW_WARNINGS
402 import IMP.em
403 IMP_SAXS_HAS_IMP_CGAL = _IMP_pmi.IMP_SAXS_HAS_IMP_CGAL
404 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_pmi.IMP_SAXS_HAS_IMP_CONTAINER
405 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_pmi.IMP_SAXS_HAS_IMP_DISPLAY
406 IMP_SAXS_HAS_IMP_KERNEL = _IMP_pmi.IMP_SAXS_HAS_IMP_KERNEL
407 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
408 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_FILESYSTEM
409 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
410 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_pmi.IMP_SAXS_HAS_BOOST_RANDOM
411 IMP_SAXS_HAS_BOOST_REGEX = _IMP_pmi.IMP_SAXS_HAS_BOOST_REGEX
412 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_SAXS_HAS_BOOST_SYSTEM
413 IMP_SAXS_HAS_CGAL = _IMP_pmi.IMP_SAXS_HAS_CGAL
414 IMP_SAXS_HAS_HDF5 = _IMP_pmi.IMP_SAXS_HAS_HDF5
415 IMP_SAXS_HAS_NUMPY = _IMP_pmi.IMP_SAXS_HAS_NUMPY
416 IMP_SAXS_HAS_PYTHON_IHM = _IMP_pmi.IMP_SAXS_HAS_PYTHON_IHM
417 IMPSAXS_SHOW_WARNINGS = _IMP_pmi.IMPSAXS_SHOW_WARNINGS
418 import IMP.saxs
419 IMP_ISD_HAS_IMP_CGAL = _IMP_pmi.IMP_ISD_HAS_IMP_CGAL
420 IMP_ISD_HAS_IMP_DISPLAY = _IMP_pmi.IMP_ISD_HAS_IMP_DISPLAY
421 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
422 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_FILESYSTEM
423 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
424 IMP_ISD_HAS_BOOST_RANDOM = _IMP_pmi.IMP_ISD_HAS_BOOST_RANDOM
425 IMP_ISD_HAS_BOOST_REGEX = _IMP_pmi.IMP_ISD_HAS_BOOST_REGEX
426 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_ISD_HAS_BOOST_SYSTEM
427 IMP_ISD_HAS_CGAL = _IMP_pmi.IMP_ISD_HAS_CGAL
428 IMP_ISD_HAS_HDF5 = _IMP_pmi.IMP_ISD_HAS_HDF5
429 IMP_ISD_HAS_NUMPY = _IMP_pmi.IMP_ISD_HAS_NUMPY
430 IMP_ISD_HAS_PYTHON_IHM = _IMP_pmi.IMP_ISD_HAS_PYTHON_IHM
431 IMPISD_SHOW_WARNINGS = _IMP_pmi.IMPISD_SHOW_WARNINGS
432 import IMP.isd
433 IMP_PMI_HAS_IMP_ALGEBRA = _IMP_pmi.IMP_PMI_HAS_IMP_ALGEBRA
434 IMP_PMI_HAS_IMP_ATOM = _IMP_pmi.IMP_PMI_HAS_IMP_ATOM
435 IMP_PMI_HAS_IMP_CGAL = _IMP_pmi.IMP_PMI_HAS_IMP_CGAL
436 IMP_PMI_HAS_IMP_DISPLAY = _IMP_pmi.IMP_PMI_HAS_IMP_DISPLAY
437 IMP_PMI_HAS_IMP_EM = _IMP_pmi.IMP_PMI_HAS_IMP_EM
438 IMP_PMI_HAS_IMP_KERNEL = _IMP_pmi.IMP_PMI_HAS_IMP_KERNEL
439 IMP_PMI_HAS_IMP_SAXS = _IMP_pmi.IMP_PMI_HAS_IMP_SAXS
440 IMP_PMI_HAS_IMP_SCORE_FUNCTOR = _IMP_pmi.IMP_PMI_HAS_IMP_SCORE_FUNCTOR
441 IMP_PMI_HAS_IMP_STATISTICS = _IMP_pmi.IMP_PMI_HAS_IMP_STATISTICS
442 IMP_PMI_HAS_BOOST_FILESYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_FILESYSTEM
443 IMP_PMI_HAS_BOOST_PROGRAMOPTIONS = _IMP_pmi.IMP_PMI_HAS_BOOST_PROGRAMOPTIONS
444 IMP_PMI_HAS_BOOST_RANDOM = _IMP_pmi.IMP_PMI_HAS_BOOST_RANDOM
445 IMP_PMI_HAS_BOOST_REGEX = _IMP_pmi.IMP_PMI_HAS_BOOST_REGEX
446 IMP_PMI_HAS_BOOST_SYSTEM = _IMP_pmi.IMP_PMI_HAS_BOOST_SYSTEM
447 IMP_PMI_HAS_CGAL = _IMP_pmi.IMP_PMI_HAS_CGAL
448 IMP_PMI_HAS_HDF5 = _IMP_pmi.IMP_PMI_HAS_HDF5
449 IMP_PMI_HAS_NUMPY = _IMP_pmi.IMP_PMI_HAS_NUMPY
450 IMP_PMI_HAS_PYTHON_IHM = _IMP_pmi.IMP_PMI_HAS_PYTHON_IHM
451 IMPPMI_SHOW_WARNINGS = _IMP_pmi.IMPPMI_SHOW_WARNINGS
452 
453 _object_types.append("CompositeRestraint")
454 
455 
456 def _object_cast_to_CompositeRestraint(o):
457  """_object_cast_to_CompositeRestraint(Object o) -> CompositeRestraint"""
458  return _IMP_pmi._object_cast_to_CompositeRestraint(o)
459 
460 def Uncertainties(l=[]):
461  return [Uncertainty(x) for x in l]
462 _plural_types.append("Uncertainties")
463 
464 
465 _value_types.append("Uncertainty")
466 
467 
468 def Resolutions(l=[]):
469  return [Resolution(x) for x in l]
470 _plural_types.append("Resolutions")
471 
472 
473 _value_types.append("Resolution")
474 
475 
476 def Symmetrics(l=[]):
477  return [Symmetric(x) for x in l]
478 _plural_types.append("Symmetrics")
479 
480 
481 _value_types.append("Symmetric")
482 
483 
484 _object_types.append("SigmoidRestraintSphere")
485 
486 
487 def _object_cast_to_SigmoidRestraintSphere(o):
488  """_object_cast_to_SigmoidRestraintSphere(Object o) -> SigmoidRestraintSphere"""
489  return _IMP_pmi._object_cast_to_SigmoidRestraintSphere(o)
490 
491 _object_types.append("TransformMover")
492 
493 
494 def _object_cast_to_TransformMover(o):
495  """_object_cast_to_TransformMover(Object o) -> TransformMover"""
496  return _IMP_pmi._object_cast_to_TransformMover(o)
497 
498 _object_types.append("MembraneRestraint")
499 
500 
501 def _object_cast_to_MembraneRestraint(o):
502  """_object_cast_to_MembraneRestraint(Object o) -> MembraneRestraint"""
503  return _IMP_pmi._object_cast_to_MembraneRestraint(o)
504 
505 _object_types.append("InternalCoordinatesConstraint")
506 
507 
508 def _object_cast_to_InternalCoordinatesConstraint(o):
509  """_object_cast_to_InternalCoordinatesConstraint(Object o) -> InternalCoordinatesConstraint"""
510  return _IMP_pmi._object_cast_to_InternalCoordinatesConstraint(o)
511 
512 class StructureWarning(UserWarning):
513  """Warning related to handling of structures"""
514  pass
515 
516 
517 class ParameterWarning(UserWarning):
518  """Warning for probably incorrect input parameters"""
519  pass
520 
521 
522 class MissingFileWarning(UserWarning):
523  """Warning for an expected, but missing, file"""
524  pass
525 
526 
527 def deprecated_pmi1_object(version, help_message):
528  """Mark a PMI1 class as deprecated. Point to its replacement or IMP.pmi1"""
529  return IMP.deprecated_object(version,
530  "This is a PMI1 class. New applications of PMI should use PMI2 "
531  "classes. In this case, %s. If you need to use PMI1 classes, "
532  "for example to maintain a published protocol, use the legacy "
533  "IMP.pmi1 module instead of IMP.pmi." % help_message)
534 
535 class MembraneRestraint(IMP.isd.ISDRestraint):
536  """Proxy of C++ IMP::pmi::MembraneRestraint class."""
537 
538  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
539 
540  def __init__(self, m, z_nuisance, thickness, softness, plateau, linear):
541  """__init__(IMP::pmi::MembraneRestraint self, Model m, ParticleIndex z_nuisance, double thickness, double softness, double plateau, double linear) -> MembraneRestraint"""
542  this = _IMP_pmi.new_MembraneRestraint(m, z_nuisance, thickness, softness, plateau, linear)
543  try:
544  self.this.append(this)
545  except __builtin__.Exception:
546  self.this = this
547 
548  def add_particles_below(self, particles):
549  """add_particles_below(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
550  return _IMP_pmi.MembraneRestraint_add_particles_below(self, particles)
551 
552 
553  def add_particles_above(self, particles):
554  """add_particles_above(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
555  return _IMP_pmi.MembraneRestraint_add_particles_above(self, particles)
556 
557 
558  def add_particles_inside(self, particles):
559  """add_particles_inside(MembraneRestraint self, IMP::ParticleIndexes const & particles)"""
560  return _IMP_pmi.MembraneRestraint_add_particles_inside(self, particles)
561 
562 
563  def get_score(self, prob):
564  """get_score(MembraneRestraint self, double prob) -> double"""
565  return _IMP_pmi.MembraneRestraint_get_score(self, prob)
566 
567 
568  def get_probability_above(self, z, z_slope_center_upper):
569  """get_probability_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
570  return _IMP_pmi.MembraneRestraint_get_probability_above(self, z, z_slope_center_upper)
571 
572 
573  def get_score_above(self, z, z_slope_center_upper):
574  """get_score_above(MembraneRestraint self, double z, double z_slope_center_upper) -> double"""
575  return _IMP_pmi.MembraneRestraint_get_score_above(self, z, z_slope_center_upper)
576 
577 
578  def get_probability_below(self, z, z_slope_center_lower):
579  """get_probability_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
580  return _IMP_pmi.MembraneRestraint_get_probability_below(self, z, z_slope_center_lower)
581 
582 
583  def get_score_below(self, z, z_slope_center_lower):
584  """get_score_below(MembraneRestraint self, double z, double z_slope_center_lower) -> double"""
585  return _IMP_pmi.MembraneRestraint_get_score_below(self, z, z_slope_center_lower)
586 
587 
588  def get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper):
589  """get_score_inside(MembraneRestraint self, double z, double z_slope_center_lower, double z_slope_center_upper) -> double"""
590  return _IMP_pmi.MembraneRestraint_get_score_inside(self, z, z_slope_center_lower, z_slope_center_upper)
591 
592 
593  def __str__(self):
594  """__str__(MembraneRestraint self) -> std::string"""
595  return _IMP_pmi.MembraneRestraint___str__(self)
596 
597 
598  def __repr__(self):
599  """__repr__(MembraneRestraint self) -> std::string"""
600  return _IMP_pmi.MembraneRestraint___repr__(self)
601 
602 
603  @staticmethod
604  def get_from(o):
605  return _object_cast_to_MembraneRestraint(o)
606 
607 MembraneRestraint_swigregister = _IMP_pmi.MembraneRestraint_swigregister
608 MembraneRestraint_swigregister(MembraneRestraint)
609 
610 class CompositeRestraint(IMP.Restraint):
611  """Proxy of C++ IMP::pmi::CompositeRestraint class."""
612 
613  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
614 
615  def __init__(self, *args):
616  """
617  __init__(IMP::pmi::CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau, std::string name) -> CompositeRestraint
618  __init__(IMP::pmi::CompositeRestraint self, Model m, _ParticleIndexesAdaptor handle_particle_indexes, double coffd, double l, bool tabprob, double plateau) -> CompositeRestraint
619  """
620  this = _IMP_pmi.new_CompositeRestraint(*args)
621  try:
622  self.this.append(this)
623  except __builtin__.Exception:
624  self.this = this
625 
626  def add_composite_particle(self, pi):
627  """add_composite_particle(CompositeRestraint self, _ParticleIndexesAdaptor pi)"""
628  return _IMP_pmi.CompositeRestraint_add_composite_particle(self, pi)
629 
630 
631  def get_number_of_elements(self):
632  """get_number_of_elements(CompositeRestraint self) -> unsigned int"""
633  return _IMP_pmi.CompositeRestraint_get_number_of_elements(self)
634 
635 
636  def do_get_inputs(self):
637  """do_get_inputs(CompositeRestraint self) -> IMP::ModelObjectsTemp"""
638  return _IMP_pmi.CompositeRestraint_do_get_inputs(self)
639 
640 
641  def get_version_info(self):
642  """get_version_info(CompositeRestraint self) -> VersionInfo"""
643  return _IMP_pmi.CompositeRestraint_get_version_info(self)
644 
645 
646  def get_probability(self):
647  """get_probability(CompositeRestraint self) -> double"""
648  return _IMP_pmi.CompositeRestraint_get_probability(self)
649 
650 
651  def __str__(self):
652  """__str__(CompositeRestraint self) -> std::string"""
653  return _IMP_pmi.CompositeRestraint___str__(self)
654 
655 
656  def __repr__(self):
657  """__repr__(CompositeRestraint self) -> std::string"""
658  return _IMP_pmi.CompositeRestraint___repr__(self)
659 
660 
661  @staticmethod
662  def get_from(o):
663  return _object_cast_to_CompositeRestraint(o)
664 
665 CompositeRestraint_swigregister = _IMP_pmi.CompositeRestraint_swigregister
666 CompositeRestraint_swigregister(CompositeRestraint)
667 
668 class Uncertainty(IMP.Decorator):
669  """Proxy of C++ IMP::pmi::Uncertainty class."""
670 
671  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
672 
673  def get_uncertainty(self):
674  """get_uncertainty(Uncertainty self) -> IMP::Float"""
675  return _IMP_pmi.Uncertainty_get_uncertainty(self)
676 
677 
678  def set_uncertainty(self, d):
679  """set_uncertainty(Uncertainty self, IMP::Float d)"""
680  return _IMP_pmi.Uncertainty_set_uncertainty(self, d)
681 
682 
683  def __init__(self, *args):
684  """
685  __init__(IMP::pmi::Uncertainty self) -> Uncertainty
686  __init__(IMP::pmi::Uncertainty self, Model m, ParticleIndex id) -> Uncertainty
687  __init__(IMP::pmi::Uncertainty self, _ParticleAdaptor d) -> Uncertainty
688  """
689  this = _IMP_pmi.new_Uncertainty(*args)
690  try:
691  self.this.append(this)
692  except __builtin__.Exception:
693  self.this = this
694 
695  def get_is_setup(*args):
696  """
697  get_is_setup(Model m, ParticleIndex pi) -> bool
698  get_is_setup(_ParticleAdaptor p) -> bool
699  """
700  return _IMP_pmi.Uncertainty_get_is_setup(*args)
701 
702  get_is_setup = staticmethod(get_is_setup)
703 
704  def show(self, *args):
705  """
706  show(Uncertainty self, _ostream out)
707  show(Uncertainty self)
708  """
709  return _IMP_pmi.Uncertainty_show(self, *args)
710 
711 
712  def setup_particle(*args):
713  """
714  setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
715  setup_particle(_ParticleAdaptor decorator, IMP::Float uncertainty) -> Uncertainty
716  """
717  return _IMP_pmi.Uncertainty_setup_particle(*args)
718 
719  setup_particle = staticmethod(setup_particle)
720 
721  def get_uncertainty_key():
722  """get_uncertainty_key() -> FloatKey"""
723  return _IMP_pmi.Uncertainty_get_uncertainty_key()
724 
725  get_uncertainty_key = staticmethod(get_uncertainty_key)
726 
727  def add_attribute(self, *args):
728  """
729  add_attribute(Uncertainty self, FloatKey k, IMP::Float v, bool opt)
730  add_attribute(Uncertainty self, FloatKey a0, IMP::Float a1)
731  add_attribute(Uncertainty self, IntKey a0, IMP::Int a1)
732  add_attribute(Uncertainty self, StringKey a0, IMP::String a1)
733  add_attribute(Uncertainty self, ParticleIndexKey a0, Particle a1)
734  add_attribute(Uncertainty self, ObjectKey a0, Object a1)
735  """
736  return _IMP_pmi.Uncertainty_add_attribute(self, *args)
737 
738 
739  def get_value(self, *args):
740  """
741  get_value(Uncertainty self, FloatKey a0) -> IMP::Float
742  get_value(Uncertainty self, IntKey a0) -> IMP::Int
743  get_value(Uncertainty self, StringKey a0) -> IMP::String
744  get_value(Uncertainty self, ParticleIndexKey a0) -> Particle
745  get_value(Uncertainty self, ObjectKey a0) -> Object
746  """
747  return _IMP_pmi.Uncertainty_get_value(self, *args)
748 
749 
750  def set_value(self, *args):
751  """
752  set_value(Uncertainty self, FloatKey a0, IMP::Float a1)
753  set_value(Uncertainty self, IntKey a0, IMP::Int a1)
754  set_value(Uncertainty self, StringKey a0, IMP::String a1)
755  set_value(Uncertainty self, ParticleIndexKey a0, Particle a1)
756  set_value(Uncertainty self, ObjectKey a0, Object a1)
757  """
758  return _IMP_pmi.Uncertainty_set_value(self, *args)
759 
760 
761  def remove_attribute(self, *args):
762  """
763  remove_attribute(Uncertainty self, FloatKey a0)
764  remove_attribute(Uncertainty self, IntKey a0)
765  remove_attribute(Uncertainty self, StringKey a0)
766  remove_attribute(Uncertainty self, ParticleIndexKey a0)
767  remove_attribute(Uncertainty self, ObjectKey a0)
768  """
769  return _IMP_pmi.Uncertainty_remove_attribute(self, *args)
770 
771 
772  def has_attribute(self, *args):
773  """
774  has_attribute(Uncertainty self, FloatKey a0) -> bool
775  has_attribute(Uncertainty self, IntKey a0) -> bool
776  has_attribute(Uncertainty self, StringKey a0) -> bool
777  has_attribute(Uncertainty self, ParticleIndexKey a0) -> bool
778  has_attribute(Uncertainty self, ObjectKey a0) -> bool
779  """
780  return _IMP_pmi.Uncertainty_has_attribute(self, *args)
781 
782 
783  def get_derivative(self, a0):
784  """get_derivative(Uncertainty self, FloatKey a0) -> double"""
785  return _IMP_pmi.Uncertainty_get_derivative(self, a0)
786 
787 
788  def get_name(self):
789  """get_name(Uncertainty self) -> std::string"""
790  return _IMP_pmi.Uncertainty_get_name(self)
791 
792 
793  def clear_caches(self):
794  """clear_caches(Uncertainty self)"""
795  return _IMP_pmi.Uncertainty_clear_caches(self)
796 
797 
798  def set_name(self, a0):
799  """set_name(Uncertainty self, std::string a0)"""
800  return _IMP_pmi.Uncertainty_set_name(self, a0)
801 
802 
803  def set_check_level(self, a0):
804  """set_check_level(Uncertainty self, IMP::CheckLevel a0)"""
805  return _IMP_pmi.Uncertainty_set_check_level(self, a0)
806 
807 
808  def add_to_derivative(self, a0, a1, a2):
809  """add_to_derivative(Uncertainty self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
810  return _IMP_pmi.Uncertainty_add_to_derivative(self, a0, a1, a2)
811 
812 
813  def set_is_optimized(self, a0, a1):
814  """set_is_optimized(Uncertainty self, FloatKey a0, bool a1)"""
815  return _IMP_pmi.Uncertainty_set_is_optimized(self, a0, a1)
816 
817 
818  def get_is_optimized(self, a0):
819  """get_is_optimized(Uncertainty self, FloatKey a0) -> bool"""
820  return _IMP_pmi.Uncertainty_get_is_optimized(self, a0)
821 
822 
823  def get_check_level(self):
824  """get_check_level(Uncertainty self) -> IMP::CheckLevel"""
825  return _IMP_pmi.Uncertainty_get_check_level(self)
826 
827 
828  def __eq__(self, *args):
829  """
830  __eq__(Uncertainty self, Uncertainty o) -> bool
831  __eq__(Uncertainty self, Particle d) -> bool
832  """
833  return _IMP_pmi.Uncertainty___eq__(self, *args)
834 
835 
836  def __ne__(self, *args):
837  """
838  __ne__(Uncertainty self, Uncertainty o) -> bool
839  __ne__(Uncertainty self, Particle d) -> bool
840  """
841  return _IMP_pmi.Uncertainty___ne__(self, *args)
842 
843 
844  def __le__(self, *args):
845  """
846  __le__(Uncertainty self, Uncertainty o) -> bool
847  __le__(Uncertainty self, Particle d) -> bool
848  """
849  return _IMP_pmi.Uncertainty___le__(self, *args)
850 
851 
852  def __lt__(self, *args):
853  """
854  __lt__(Uncertainty self, Uncertainty o) -> bool
855  __lt__(Uncertainty self, Particle d) -> bool
856  """
857  return _IMP_pmi.Uncertainty___lt__(self, *args)
858 
859 
860  def __ge__(self, *args):
861  """
862  __ge__(Uncertainty self, Uncertainty o) -> bool
863  __ge__(Uncertainty self, Particle d) -> bool
864  """
865  return _IMP_pmi.Uncertainty___ge__(self, *args)
866 
867 
868  def __gt__(self, *args):
869  """
870  __gt__(Uncertainty self, Uncertainty o) -> bool
871  __gt__(Uncertainty self, Particle d) -> bool
872  """
873  return _IMP_pmi.Uncertainty___gt__(self, *args)
874 
875 
876  def __hash__(self):
877  """__hash__(Uncertainty self) -> std::size_t"""
878  return _IMP_pmi.Uncertainty___hash__(self)
879 
880 
881  def __str__(self):
882  """__str__(Uncertainty self) -> std::string"""
883  return _IMP_pmi.Uncertainty___str__(self)
884 
885 
886  def __repr__(self):
887  """__repr__(Uncertainty self) -> std::string"""
888  return _IMP_pmi.Uncertainty___repr__(self)
889 
890  __swig_destroy__ = _IMP_pmi.delete_Uncertainty
891  __del__ = lambda self: None
892 Uncertainty_swigregister = _IMP_pmi.Uncertainty_swigregister
893 Uncertainty_swigregister(Uncertainty)
894 
895 def Uncertainty_get_is_setup(*args):
896  """
897  get_is_setup(Model m, ParticleIndex pi) -> bool
898  Uncertainty_get_is_setup(_ParticleAdaptor p) -> bool
899  """
900  return _IMP_pmi.Uncertainty_get_is_setup(*args)
901 
902 def Uncertainty_setup_particle(*args):
903  """
904  setup_particle(Model m, ParticleIndex pi, IMP::Float uncertainty) -> Uncertainty
905  Uncertainty_setup_particle(_ParticleAdaptor decorator, IMP::Float uncertainty) -> Uncertainty
906  """
907  return _IMP_pmi.Uncertainty_setup_particle(*args)
908 
909 def Uncertainty_get_uncertainty_key():
910  """Uncertainty_get_uncertainty_key() -> FloatKey"""
911  return _IMP_pmi.Uncertainty_get_uncertainty_key()
912 
913 class Resolution(IMP.Decorator):
914  """Proxy of C++ IMP::pmi::Resolution class."""
915 
916  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
917 
918  def get_resolution(self):
919  """get_resolution(Resolution self) -> IMP::Float"""
920  return _IMP_pmi.Resolution_get_resolution(self)
921 
922 
923  def set_resolution(self, d):
924  """set_resolution(Resolution self, IMP::Float d)"""
925  return _IMP_pmi.Resolution_set_resolution(self, d)
926 
927 
928  def __init__(self, *args):
929  """
930  __init__(IMP::pmi::Resolution self) -> Resolution
931  __init__(IMP::pmi::Resolution self, Model m, ParticleIndex id) -> Resolution
932  __init__(IMP::pmi::Resolution self, _ParticleAdaptor d) -> Resolution
933  """
934  this = _IMP_pmi.new_Resolution(*args)
935  try:
936  self.this.append(this)
937  except __builtin__.Exception:
938  self.this = this
939 
940  def get_is_setup(*args):
941  """
942  get_is_setup(Model m, ParticleIndex pi) -> bool
943  get_is_setup(_ParticleAdaptor p) -> bool
944  """
945  return _IMP_pmi.Resolution_get_is_setup(*args)
946 
947  get_is_setup = staticmethod(get_is_setup)
948 
949  def show(self, *args):
950  """
951  show(Resolution self, _ostream out)
952  show(Resolution self)
953  """
954  return _IMP_pmi.Resolution_show(self, *args)
955 
956 
957  def setup_particle(*args):
958  """
959  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
960  setup_particle(_ParticleAdaptor decorator, IMP::Float resolution) -> Resolution
961  """
962  return _IMP_pmi.Resolution_setup_particle(*args)
963 
964  setup_particle = staticmethod(setup_particle)
965 
966  def get_resolution_key():
967  """get_resolution_key() -> FloatKey"""
968  return _IMP_pmi.Resolution_get_resolution_key()
969 
970  get_resolution_key = staticmethod(get_resolution_key)
971 
972  def add_attribute(self, *args):
973  """
974  add_attribute(Resolution self, FloatKey k, IMP::Float v, bool opt)
975  add_attribute(Resolution self, FloatKey a0, IMP::Float a1)
976  add_attribute(Resolution self, IntKey a0, IMP::Int a1)
977  add_attribute(Resolution self, StringKey a0, IMP::String a1)
978  add_attribute(Resolution self, ParticleIndexKey a0, Particle a1)
979  add_attribute(Resolution self, ObjectKey a0, Object a1)
980  """
981  return _IMP_pmi.Resolution_add_attribute(self, *args)
982 
983 
984  def get_value(self, *args):
985  """
986  get_value(Resolution self, FloatKey a0) -> IMP::Float
987  get_value(Resolution self, IntKey a0) -> IMP::Int
988  get_value(Resolution self, StringKey a0) -> IMP::String
989  get_value(Resolution self, ParticleIndexKey a0) -> Particle
990  get_value(Resolution self, ObjectKey a0) -> Object
991  """
992  return _IMP_pmi.Resolution_get_value(self, *args)
993 
994 
995  def set_value(self, *args):
996  """
997  set_value(Resolution self, FloatKey a0, IMP::Float a1)
998  set_value(Resolution self, IntKey a0, IMP::Int a1)
999  set_value(Resolution self, StringKey a0, IMP::String a1)
1000  set_value(Resolution self, ParticleIndexKey a0, Particle a1)
1001  set_value(Resolution self, ObjectKey a0, Object a1)
1002  """
1003  return _IMP_pmi.Resolution_set_value(self, *args)
1004 
1005 
1006  def remove_attribute(self, *args):
1007  """
1008  remove_attribute(Resolution self, FloatKey a0)
1009  remove_attribute(Resolution self, IntKey a0)
1010  remove_attribute(Resolution self, StringKey a0)
1011  remove_attribute(Resolution self, ParticleIndexKey a0)
1012  remove_attribute(Resolution self, ObjectKey a0)
1013  """
1014  return _IMP_pmi.Resolution_remove_attribute(self, *args)
1015 
1016 
1017  def has_attribute(self, *args):
1018  """
1019  has_attribute(Resolution self, FloatKey a0) -> bool
1020  has_attribute(Resolution self, IntKey a0) -> bool
1021  has_attribute(Resolution self, StringKey a0) -> bool
1022  has_attribute(Resolution self, ParticleIndexKey a0) -> bool
1023  has_attribute(Resolution self, ObjectKey a0) -> bool
1024  """
1025  return _IMP_pmi.Resolution_has_attribute(self, *args)
1026 
1027 
1028  def get_derivative(self, a0):
1029  """get_derivative(Resolution self, FloatKey a0) -> double"""
1030  return _IMP_pmi.Resolution_get_derivative(self, a0)
1031 
1032 
1033  def get_name(self):
1034  """get_name(Resolution self) -> std::string"""
1035  return _IMP_pmi.Resolution_get_name(self)
1036 
1037 
1038  def clear_caches(self):
1039  """clear_caches(Resolution self)"""
1040  return _IMP_pmi.Resolution_clear_caches(self)
1041 
1042 
1043  def set_name(self, a0):
1044  """set_name(Resolution self, std::string a0)"""
1045  return _IMP_pmi.Resolution_set_name(self, a0)
1046 
1047 
1048  def set_check_level(self, a0):
1049  """set_check_level(Resolution self, IMP::CheckLevel a0)"""
1050  return _IMP_pmi.Resolution_set_check_level(self, a0)
1051 
1052 
1053  def add_to_derivative(self, a0, a1, a2):
1054  """add_to_derivative(Resolution self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1055  return _IMP_pmi.Resolution_add_to_derivative(self, a0, a1, a2)
1056 
1057 
1058  def set_is_optimized(self, a0, a1):
1059  """set_is_optimized(Resolution self, FloatKey a0, bool a1)"""
1060  return _IMP_pmi.Resolution_set_is_optimized(self, a0, a1)
1061 
1062 
1063  def get_is_optimized(self, a0):
1064  """get_is_optimized(Resolution self, FloatKey a0) -> bool"""
1065  return _IMP_pmi.Resolution_get_is_optimized(self, a0)
1066 
1067 
1068  def get_check_level(self):
1069  """get_check_level(Resolution self) -> IMP::CheckLevel"""
1070  return _IMP_pmi.Resolution_get_check_level(self)
1071 
1072 
1073  def __eq__(self, *args):
1074  """
1075  __eq__(Resolution self, Resolution o) -> bool
1076  __eq__(Resolution self, Particle d) -> bool
1077  """
1078  return _IMP_pmi.Resolution___eq__(self, *args)
1079 
1080 
1081  def __ne__(self, *args):
1082  """
1083  __ne__(Resolution self, Resolution o) -> bool
1084  __ne__(Resolution self, Particle d) -> bool
1085  """
1086  return _IMP_pmi.Resolution___ne__(self, *args)
1087 
1088 
1089  def __le__(self, *args):
1090  """
1091  __le__(Resolution self, Resolution o) -> bool
1092  __le__(Resolution self, Particle d) -> bool
1093  """
1094  return _IMP_pmi.Resolution___le__(self, *args)
1095 
1096 
1097  def __lt__(self, *args):
1098  """
1099  __lt__(Resolution self, Resolution o) -> bool
1100  __lt__(Resolution self, Particle d) -> bool
1101  """
1102  return _IMP_pmi.Resolution___lt__(self, *args)
1103 
1104 
1105  def __ge__(self, *args):
1106  """
1107  __ge__(Resolution self, Resolution o) -> bool
1108  __ge__(Resolution self, Particle d) -> bool
1109  """
1110  return _IMP_pmi.Resolution___ge__(self, *args)
1111 
1112 
1113  def __gt__(self, *args):
1114  """
1115  __gt__(Resolution self, Resolution o) -> bool
1116  __gt__(Resolution self, Particle d) -> bool
1117  """
1118  return _IMP_pmi.Resolution___gt__(self, *args)
1119 
1120 
1121  def __hash__(self):
1122  """__hash__(Resolution self) -> std::size_t"""
1123  return _IMP_pmi.Resolution___hash__(self)
1124 
1125 
1126  def __str__(self):
1127  """__str__(Resolution self) -> std::string"""
1128  return _IMP_pmi.Resolution___str__(self)
1129 
1130 
1131  def __repr__(self):
1132  """__repr__(Resolution self) -> std::string"""
1133  return _IMP_pmi.Resolution___repr__(self)
1134 
1135  __swig_destroy__ = _IMP_pmi.delete_Resolution
1136  __del__ = lambda self: None
1137 Resolution_swigregister = _IMP_pmi.Resolution_swigregister
1138 Resolution_swigregister(Resolution)
1139 
1140 def Resolution_get_is_setup(*args):
1141  """
1142  get_is_setup(Model m, ParticleIndex pi) -> bool
1143  Resolution_get_is_setup(_ParticleAdaptor p) -> bool
1144  """
1145  return _IMP_pmi.Resolution_get_is_setup(*args)
1146 
1147 def Resolution_setup_particle(*args):
1148  """
1149  setup_particle(Model m, ParticleIndex pi, IMP::Float resolution) -> Resolution
1150  Resolution_setup_particle(_ParticleAdaptor decorator, IMP::Float resolution) -> Resolution
1151  """
1152  return _IMP_pmi.Resolution_setup_particle(*args)
1153 
1154 def Resolution_get_resolution_key():
1155  """Resolution_get_resolution_key() -> FloatKey"""
1156  return _IMP_pmi.Resolution_get_resolution_key()
1157 
1158 class Symmetric(IMP.Decorator):
1159  """Proxy of C++ IMP::pmi::Symmetric class."""
1160 
1161  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1162 
1163  def get_symmetric(self):
1164  """get_symmetric(Symmetric self) -> IMP::Float"""
1165  return _IMP_pmi.Symmetric_get_symmetric(self)
1166 
1167 
1168  def set_symmetric(self, d):
1169  """set_symmetric(Symmetric self, IMP::Float d)"""
1170  return _IMP_pmi.Symmetric_set_symmetric(self, d)
1171 
1172 
1173  def __init__(self, *args):
1174  """
1175  __init__(IMP::pmi::Symmetric self) -> Symmetric
1176  __init__(IMP::pmi::Symmetric self, Model m, ParticleIndex id) -> Symmetric
1177  __init__(IMP::pmi::Symmetric self, _ParticleAdaptor d) -> Symmetric
1178  """
1179  this = _IMP_pmi.new_Symmetric(*args)
1180  try:
1181  self.this.append(this)
1182  except __builtin__.Exception:
1183  self.this = this
1184 
1185  def get_is_setup(*args):
1186  """
1187  get_is_setup(Model m, ParticleIndex pi) -> bool
1188  get_is_setup(_ParticleAdaptor p) -> bool
1189  """
1190  return _IMP_pmi.Symmetric_get_is_setup(*args)
1191 
1192  get_is_setup = staticmethod(get_is_setup)
1193 
1194  def show(self, *args):
1195  """
1196  show(Symmetric self, _ostream out)
1197  show(Symmetric self)
1198  """
1199  return _IMP_pmi.Symmetric_show(self, *args)
1200 
1201 
1202  def setup_particle(*args):
1203  """
1204  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1205  setup_particle(_ParticleAdaptor decorator, IMP::Float symmetric) -> Symmetric
1206  """
1207  return _IMP_pmi.Symmetric_setup_particle(*args)
1208 
1209  setup_particle = staticmethod(setup_particle)
1210 
1211  def get_symmetric_key():
1212  """get_symmetric_key() -> FloatKey"""
1213  return _IMP_pmi.Symmetric_get_symmetric_key()
1214 
1215  get_symmetric_key = staticmethod(get_symmetric_key)
1216 
1217  def add_attribute(self, *args):
1218  """
1219  add_attribute(Symmetric self, FloatKey k, IMP::Float v, bool opt)
1220  add_attribute(Symmetric self, FloatKey a0, IMP::Float a1)
1221  add_attribute(Symmetric self, IntKey a0, IMP::Int a1)
1222  add_attribute(Symmetric self, StringKey a0, IMP::String a1)
1223  add_attribute(Symmetric self, ParticleIndexKey a0, Particle a1)
1224  add_attribute(Symmetric self, ObjectKey a0, Object a1)
1225  """
1226  return _IMP_pmi.Symmetric_add_attribute(self, *args)
1227 
1228 
1229  def get_value(self, *args):
1230  """
1231  get_value(Symmetric self, FloatKey a0) -> IMP::Float
1232  get_value(Symmetric self, IntKey a0) -> IMP::Int
1233  get_value(Symmetric self, StringKey a0) -> IMP::String
1234  get_value(Symmetric self, ParticleIndexKey a0) -> Particle
1235  get_value(Symmetric self, ObjectKey a0) -> Object
1236  """
1237  return _IMP_pmi.Symmetric_get_value(self, *args)
1238 
1239 
1240  def set_value(self, *args):
1241  """
1242  set_value(Symmetric self, FloatKey a0, IMP::Float a1)
1243  set_value(Symmetric self, IntKey a0, IMP::Int a1)
1244  set_value(Symmetric self, StringKey a0, IMP::String a1)
1245  set_value(Symmetric self, ParticleIndexKey a0, Particle a1)
1246  set_value(Symmetric self, ObjectKey a0, Object a1)
1247  """
1248  return _IMP_pmi.Symmetric_set_value(self, *args)
1249 
1250 
1251  def remove_attribute(self, *args):
1252  """
1253  remove_attribute(Symmetric self, FloatKey a0)
1254  remove_attribute(Symmetric self, IntKey a0)
1255  remove_attribute(Symmetric self, StringKey a0)
1256  remove_attribute(Symmetric self, ParticleIndexKey a0)
1257  remove_attribute(Symmetric self, ObjectKey a0)
1258  """
1259  return _IMP_pmi.Symmetric_remove_attribute(self, *args)
1260 
1261 
1262  def has_attribute(self, *args):
1263  """
1264  has_attribute(Symmetric self, FloatKey a0) -> bool
1265  has_attribute(Symmetric self, IntKey a0) -> bool
1266  has_attribute(Symmetric self, StringKey a0) -> bool
1267  has_attribute(Symmetric self, ParticleIndexKey a0) -> bool
1268  has_attribute(Symmetric self, ObjectKey a0) -> bool
1269  """
1270  return _IMP_pmi.Symmetric_has_attribute(self, *args)
1271 
1272 
1273  def get_derivative(self, a0):
1274  """get_derivative(Symmetric self, FloatKey a0) -> double"""
1275  return _IMP_pmi.Symmetric_get_derivative(self, a0)
1276 
1277 
1278  def get_name(self):
1279  """get_name(Symmetric self) -> std::string"""
1280  return _IMP_pmi.Symmetric_get_name(self)
1281 
1282 
1283  def clear_caches(self):
1284  """clear_caches(Symmetric self)"""
1285  return _IMP_pmi.Symmetric_clear_caches(self)
1286 
1287 
1288  def set_name(self, a0):
1289  """set_name(Symmetric self, std::string a0)"""
1290  return _IMP_pmi.Symmetric_set_name(self, a0)
1291 
1292 
1293  def set_check_level(self, a0):
1294  """set_check_level(Symmetric self, IMP::CheckLevel a0)"""
1295  return _IMP_pmi.Symmetric_set_check_level(self, a0)
1296 
1297 
1298  def add_to_derivative(self, a0, a1, a2):
1299  """add_to_derivative(Symmetric self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1300  return _IMP_pmi.Symmetric_add_to_derivative(self, a0, a1, a2)
1301 
1302 
1303  def set_is_optimized(self, a0, a1):
1304  """set_is_optimized(Symmetric self, FloatKey a0, bool a1)"""
1305  return _IMP_pmi.Symmetric_set_is_optimized(self, a0, a1)
1306 
1307 
1308  def get_is_optimized(self, a0):
1309  """get_is_optimized(Symmetric self, FloatKey a0) -> bool"""
1310  return _IMP_pmi.Symmetric_get_is_optimized(self, a0)
1311 
1312 
1313  def get_check_level(self):
1314  """get_check_level(Symmetric self) -> IMP::CheckLevel"""
1315  return _IMP_pmi.Symmetric_get_check_level(self)
1316 
1317 
1318  def __eq__(self, *args):
1319  """
1320  __eq__(Symmetric self, Symmetric o) -> bool
1321  __eq__(Symmetric self, Particle d) -> bool
1322  """
1323  return _IMP_pmi.Symmetric___eq__(self, *args)
1324 
1325 
1326  def __ne__(self, *args):
1327  """
1328  __ne__(Symmetric self, Symmetric o) -> bool
1329  __ne__(Symmetric self, Particle d) -> bool
1330  """
1331  return _IMP_pmi.Symmetric___ne__(self, *args)
1332 
1333 
1334  def __le__(self, *args):
1335  """
1336  __le__(Symmetric self, Symmetric o) -> bool
1337  __le__(Symmetric self, Particle d) -> bool
1338  """
1339  return _IMP_pmi.Symmetric___le__(self, *args)
1340 
1341 
1342  def __lt__(self, *args):
1343  """
1344  __lt__(Symmetric self, Symmetric o) -> bool
1345  __lt__(Symmetric self, Particle d) -> bool
1346  """
1347  return _IMP_pmi.Symmetric___lt__(self, *args)
1348 
1349 
1350  def __ge__(self, *args):
1351  """
1352  __ge__(Symmetric self, Symmetric o) -> bool
1353  __ge__(Symmetric self, Particle d) -> bool
1354  """
1355  return _IMP_pmi.Symmetric___ge__(self, *args)
1356 
1357 
1358  def __gt__(self, *args):
1359  """
1360  __gt__(Symmetric self, Symmetric o) -> bool
1361  __gt__(Symmetric self, Particle d) -> bool
1362  """
1363  return _IMP_pmi.Symmetric___gt__(self, *args)
1364 
1365 
1366  def __hash__(self):
1367  """__hash__(Symmetric self) -> std::size_t"""
1368  return _IMP_pmi.Symmetric___hash__(self)
1369 
1370 
1371  def __str__(self):
1372  """__str__(Symmetric self) -> std::string"""
1373  return _IMP_pmi.Symmetric___str__(self)
1374 
1375 
1376  def __repr__(self):
1377  """__repr__(Symmetric self) -> std::string"""
1378  return _IMP_pmi.Symmetric___repr__(self)
1379 
1380  __swig_destroy__ = _IMP_pmi.delete_Symmetric
1381  __del__ = lambda self: None
1382 Symmetric_swigregister = _IMP_pmi.Symmetric_swigregister
1383 Symmetric_swigregister(Symmetric)
1384 
1385 def Symmetric_get_is_setup(*args):
1386  """
1387  get_is_setup(Model m, ParticleIndex pi) -> bool
1388  Symmetric_get_is_setup(_ParticleAdaptor p) -> bool
1389  """
1390  return _IMP_pmi.Symmetric_get_is_setup(*args)
1391 
1392 def Symmetric_setup_particle(*args):
1393  """
1394  setup_particle(Model m, ParticleIndex pi, IMP::Float symmetric) -> Symmetric
1395  Symmetric_setup_particle(_ParticleAdaptor decorator, IMP::Float symmetric) -> Symmetric
1396  """
1397  return _IMP_pmi.Symmetric_setup_particle(*args)
1398 
1399 def Symmetric_get_symmetric_key():
1400  """Symmetric_get_symmetric_key() -> FloatKey"""
1401  return _IMP_pmi.Symmetric_get_symmetric_key()
1402 
1403 class SigmoidRestraintSphere(IMP.Restraint):
1404  """Proxy of C++ IMP::pmi::SigmoidRestraintSphere class."""
1405 
1406  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1407 
1408  def __init__(self, *args):
1409  """
1410  __init__(IMP::pmi::SigmoidRestraintSphere self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, double inflection, double slope, double amplitude, double line_slope_=0, std::string name) -> SigmoidRestraintSphere
1411  __init__(IMP::pmi::SigmoidRestraintSphere self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, double inflection, double slope, double amplitude, double line_slope_=0) -> SigmoidRestraintSphere
1412  __init__(IMP::pmi::SigmoidRestraintSphere self, Model m, _ParticleIndexAdaptor p1, _ParticleIndexAdaptor p2, double inflection, double slope, double amplitude) -> SigmoidRestraintSphere
1413  """
1414  this = _IMP_pmi.new_SigmoidRestraintSphere(*args)
1415  try:
1416  self.this.append(this)
1417  except __builtin__.Exception:
1418  self.this = this
1419 
1420  def set_amplitude(self, amplitude):
1421  """set_amplitude(SigmoidRestraintSphere self, double amplitude)"""
1422  return _IMP_pmi.SigmoidRestraintSphere_set_amplitude(self, amplitude)
1423 
1424 
1425  def increment_amplitude(self, amplitude):
1426  """increment_amplitude(SigmoidRestraintSphere self, double amplitude)"""
1427  return _IMP_pmi.SigmoidRestraintSphere_increment_amplitude(self, amplitude)
1428 
1429 
1430  def get_amplitude(self):
1431  """get_amplitude(SigmoidRestraintSphere self) -> double"""
1432  return _IMP_pmi.SigmoidRestraintSphere_get_amplitude(self)
1433 
1434 
1435  def do_get_inputs(self):
1436  """do_get_inputs(SigmoidRestraintSphere self) -> IMP::ModelObjectsTemp"""
1437  return _IMP_pmi.SigmoidRestraintSphere_do_get_inputs(self)
1438 
1439 
1440  def get_version_info(self):
1441  """get_version_info(SigmoidRestraintSphere self) -> VersionInfo"""
1442  return _IMP_pmi.SigmoidRestraintSphere_get_version_info(self)
1443 
1444 
1445  def __str__(self):
1446  """__str__(SigmoidRestraintSphere self) -> std::string"""
1447  return _IMP_pmi.SigmoidRestraintSphere___str__(self)
1448 
1449 
1450  def __repr__(self):
1451  """__repr__(SigmoidRestraintSphere self) -> std::string"""
1452  return _IMP_pmi.SigmoidRestraintSphere___repr__(self)
1453 
1454 
1455  @staticmethod
1456  def get_from(o):
1457  return _object_cast_to_SigmoidRestraintSphere(o)
1458 
1459 SigmoidRestraintSphere_swigregister = _IMP_pmi.SigmoidRestraintSphere_swigregister
1460 SigmoidRestraintSphere_swigregister(SigmoidRestraintSphere)
1461 
1462 class TransformMover(IMP.core.MonteCarloMover):
1463  """Proxy of C++ IMP::pmi::TransformMover class."""
1464 
1465  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1466 
1467  def __init__(self, *args):
1468  """
1469  __init__(IMP::pmi::TransformMover self, Model m, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1470  __init__(IMP::pmi::TransformMover self, Model m, Vector3D axis, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1471  __init__(IMP::pmi::TransformMover self, Model m, _ParticleIndexAdaptor p1i, _ParticleIndexAdaptor p2i, IMP::Float max_translation, IMP::Float max_rotation) -> TransformMover
1472  """
1473  this = _IMP_pmi.new_TransformMover(*args)
1474  try:
1475  self.this.append(this)
1476  except __builtin__.Exception:
1477  self.this = this
1478 
1479  def add_xyz_particle(self, pi):
1480  """add_xyz_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1481  return _IMP_pmi.TransformMover_add_xyz_particle(self, pi)
1482 
1483 
1484  def add_rigid_body_particle(self, pi):
1485  """add_rigid_body_particle(TransformMover self, _ParticleIndexAdaptor pi)"""
1486  return _IMP_pmi.TransformMover_add_rigid_body_particle(self, pi)
1487 
1488 
1489  def set_maximum_translation(self, mt):
1490  """set_maximum_translation(TransformMover self, IMP::Float mt)"""
1491  return _IMP_pmi.TransformMover_set_maximum_translation(self, mt)
1492 
1493 
1494  def set_maximum_rotation(self, mr):
1495  """set_maximum_rotation(TransformMover self, IMP::Float mr)"""
1496  return _IMP_pmi.TransformMover_set_maximum_rotation(self, mr)
1497 
1498 
1499  def get_maximum_translation(self):
1500  """get_maximum_translation(TransformMover self) -> IMP::Float"""
1501  return _IMP_pmi.TransformMover_get_maximum_translation(self)
1502 
1503 
1504  def get_maximum_rotation(self):
1505  """get_maximum_rotation(TransformMover self) -> IMP::Float"""
1506  return _IMP_pmi.TransformMover_get_maximum_rotation(self)
1507 
1508 
1509  def get_last_transformation(self):
1510  """get_last_transformation(TransformMover self) -> Transformation3D"""
1511  return _IMP_pmi.TransformMover_get_last_transformation(self)
1512 
1513 
1514  def get_version_info(self):
1515  """get_version_info(TransformMover self) -> VersionInfo"""
1516  return _IMP_pmi.TransformMover_get_version_info(self)
1517 
1518 
1519  def __str__(self):
1520  """__str__(TransformMover self) -> std::string"""
1521  return _IMP_pmi.TransformMover___str__(self)
1522 
1523 
1524  def __repr__(self):
1525  """__repr__(TransformMover self) -> std::string"""
1526  return _IMP_pmi.TransformMover___repr__(self)
1527 
1528 
1529  @staticmethod
1530  def get_from(o):
1531  return _object_cast_to_TransformMover(o)
1532 
1533 TransformMover_swigregister = _IMP_pmi.TransformMover_swigregister
1534 TransformMover_swigregister(TransformMover)
1535 
1536 
1537 def create_elastic_network(ps, dist_cutoff, strength):
1538  """create_elastic_network(IMP::Particles const & ps, IMP::Float dist_cutoff, IMP::Float strength) -> RestraintSet"""
1539  return _IMP_pmi.create_elastic_network(ps, dist_cutoff, strength)
1540 
1541 def get_dihedral_angle(p1, p2, p3, p4):
1542  """get_dihedral_angle(Atom p1, Atom p2, Atom p3, Atom p4) -> IMP::Float"""
1543  return _IMP_pmi.get_dihedral_angle(p1, p2, p3, p4)
1544 
1545 def get_bipartite_minimum_sphere_distance(m1, m2):
1546  """get_bipartite_minimum_sphere_distance(IMP::core::XYZRs const & m1, IMP::core::XYZRs const & m2) -> IMP::Float"""
1547  return _IMP_pmi.get_bipartite_minimum_sphere_distance(m1, m2)
1548 
1549 def get_list_of_bipartite_minimum_sphere_distance(pss):
1550  """get_list_of_bipartite_minimum_sphere_distance(IMP::ParticlesTemps const & pss) -> IMP::Floats"""
1551  return _IMP_pmi.get_list_of_bipartite_minimum_sphere_distance(pss)
1552 
1554  """get_molecule_name_and_copy(Hierarchy h) -> std::string"""
1555  return _IMP_pmi.get_molecule_name_and_copy(h)
1556 
1557 def get_is_canonical(h):
1558  """get_is_canonical(Hierarchy h) -> bool"""
1559  return _IMP_pmi.get_is_canonical(h)
1560 class InternalCoordinatesConstraint(IMP.SingletonModifier):
1561  """Proxy of C++ IMP::pmi::InternalCoordinatesConstraint class."""
1562 
1563  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1564 
1565  def __init__(self):
1566  """__init__(IMP::pmi::InternalCoordinatesConstraint self) -> InternalCoordinatesConstraint"""
1567  this = _IMP_pmi.new_InternalCoordinatesConstraint()
1568  try:
1569  self.this.append(this)
1570  except __builtin__.Exception:
1571  self.this = this
1572 
1573  def do_get_inputs(self, m, pis):
1574  """do_get_inputs(InternalCoordinatesConstraint self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1575  return _IMP_pmi.InternalCoordinatesConstraint_do_get_inputs(self, m, pis)
1576 
1577 
1578  def do_get_outputs(self, m, pis):
1579  """do_get_outputs(InternalCoordinatesConstraint self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1580  return _IMP_pmi.InternalCoordinatesConstraint_do_get_outputs(self, m, pis)
1581 
1582 
1583  def get_version_info(self):
1584  """get_version_info(InternalCoordinatesConstraint self) -> VersionInfo"""
1585  return _IMP_pmi.InternalCoordinatesConstraint_get_version_info(self)
1586 
1587 
1588  def __str__(self):
1589  """__str__(InternalCoordinatesConstraint self) -> std::string"""
1590  return _IMP_pmi.InternalCoordinatesConstraint___str__(self)
1591 
1592 
1593  def __repr__(self):
1594  """__repr__(InternalCoordinatesConstraint self) -> std::string"""
1595  return _IMP_pmi.InternalCoordinatesConstraint___repr__(self)
1596 
1597 
1598  @staticmethod
1599  def get_from(o):
1600  return _object_cast_to_InternalCoordinatesConstraint(o)
1601 
1602 InternalCoordinatesConstraint_swigregister = _IMP_pmi.InternalCoordinatesConstraint_swigregister
1603 InternalCoordinatesConstraint_swigregister(InternalCoordinatesConstraint)
1604 
1605 
1606 def get_module_version():
1607  """get_module_version() -> std::string const"""
1608  return _IMP_pmi.get_module_version()
1609 
1610 def get_example_path(fname):
1611  """get_example_path(std::string fname) -> std::string"""
1612  return _IMP_pmi.get_example_path(fname)
1613 
1614 def get_data_path(fname):
1615  """get_data_path(std::string fname) -> std::string"""
1616  return _IMP_pmi.get_data_path(fname)
1617 
1618 from . import _version_check
1619 _version_check.check_version(get_module_version())
1620 __version__ = get_module_version()
1621 
1622 
1623 
A base class for modifiers of ParticlesTemp.
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
A base class for ISD Restraints.
Various classes to hold sets of particles.
Support for output of models in mmCIF format.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
Warning related to handling of structures.
def deprecated_pmi1_object
Mark a PMI1 class as deprecated.
std::string get_molecule_name_and_copy(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and get the "molname.copynum".
Definition: utilities.h:85
RestraintSet * create_elastic_network(const Particles &ps, Float dist_cutoff, Float strength)
Create an elastic network restraint set.
Definition: utilities.h:26
A base class for classes which perturb particles.
Basic utilities for handling cryo-electron microscopy 3D density maps.
Warning for an expected, but missing, file.
bool get_is_canonical(atom::Hierarchy h)
Walk up a PMI2 hierarchy/representations and check if the root is named System.
Definition: utilities.h:91
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.
def deprecated_object
Python decorator to mark a class as deprecated.
Definition: __init__.py:9704
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...
double get_resolution(Model *m, ParticleIndex pi)
Estimate the resolution of the hierarchy as used by Representation.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
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
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54