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IMP Reference Guide  2.5.0
The Integrative Modeling Platform
misc/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.5
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 2007-2015 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
16 if version_info >= (2, 6, 0):
17  def swig_import_helper():
18  from os.path import dirname
19  import imp
20  fp = None
21  try:
22  fp, pathname, description = imp.find_module('_IMP_misc', [dirname(__file__)])
23  except ImportError:
24  import _IMP_misc
25  return _IMP_misc
26  if fp is not None:
27  try:
28  _mod = imp.load_module('_IMP_misc', fp, pathname, description)
29  finally:
30  fp.close()
31  return _mod
32  _IMP_misc = swig_import_helper()
33  del swig_import_helper
34 else:
35  import _IMP_misc
36 del version_info
37 try:
38  _swig_property = property
39 except NameError:
40  pass # Python < 2.2 doesn't have 'property'.
41 
42 
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44  if (name == "thisown"):
45  return self.this.own(value)
46  if (name == "this"):
47  if type(value).__name__ == 'SwigPyObject':
48  self.__dict__[name] = value
49  return
50  method = class_type.__swig_setmethods__.get(name, None)
51  if method:
52  return method(self, value)
53  if (not static):
54  object.__setattr__(self, name, value)
55  else:
56  raise AttributeError("You cannot add attributes to %s" % self)
57 
58 
59 def _swig_setattr(self, class_type, name, value):
60  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
61 
62 
63 def _swig_getattr_nondynamic(self, class_type, name, static=1):
64  if (name == "thisown"):
65  return self.this.own()
66  method = class_type.__swig_getmethods__.get(name, None)
67  if method:
68  return method(self)
69  if (not static):
70  return object.__getattr__(self, name)
71  else:
72  raise AttributeError(name)
73 
74 def _swig_getattr(self, class_type, name):
75  return _swig_getattr_nondynamic(self, class_type, name, 0)
76 
77 
78 def _swig_repr(self):
79  try:
80  strthis = "proxy of " + self.this.__repr__()
81  except:
82  strthis = ""
83  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
84 
85 try:
86  _object = object
87  _newclass = 1
88 except AttributeError:
89  class _object:
90  pass
91  _newclass = 0
92 
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:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_MISC_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_MISC_SwigPyIterator class"""
115  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
116 
117  def __init__(self, *args, **kwargs):
118  raise AttributeError("No constructor defined - class is abstract")
119  __repr__ = _swig_repr
120  __swig_destroy__ = _IMP_misc.delete_IMP_MISC_SwigPyIterator
121  __del__ = lambda self: None
122 
123  def value(self):
124  """value(IMP_MISC_SwigPyIterator self) -> PyObject *"""
125  return _IMP_misc.IMP_MISC_SwigPyIterator_value(self)
126 
127 
128  def incr(self, n=1):
129  """
130  incr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator
131  incr(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator
132  """
133  return _IMP_misc.IMP_MISC_SwigPyIterator_incr(self, n)
134 
135 
136  def decr(self, n=1):
137  """
138  decr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator
139  decr(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator
140  """
141  return _IMP_misc.IMP_MISC_SwigPyIterator_decr(self, n)
142 
143 
144  def distance(self, x):
145  """distance(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t"""
146  return _IMP_misc.IMP_MISC_SwigPyIterator_distance(self, x)
147 
148 
149  def equal(self, x):
150  """equal(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
151  return _IMP_misc.IMP_MISC_SwigPyIterator_equal(self, x)
152 
153 
154  def copy(self):
155  """copy(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator"""
156  return _IMP_misc.IMP_MISC_SwigPyIterator_copy(self)
157 
158 
159  def next(self):
160  """next(IMP_MISC_SwigPyIterator self) -> PyObject *"""
161  return _IMP_misc.IMP_MISC_SwigPyIterator_next(self)
162 
163 
164  def __next__(self):
165  """__next__(IMP_MISC_SwigPyIterator self) -> PyObject *"""
166  return _IMP_misc.IMP_MISC_SwigPyIterator___next__(self)
167 
168 
169  def previous(self):
170  """previous(IMP_MISC_SwigPyIterator self) -> PyObject *"""
171  return _IMP_misc.IMP_MISC_SwigPyIterator_previous(self)
172 
173 
174  def advance(self, n):
175  """advance(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
176  return _IMP_misc.IMP_MISC_SwigPyIterator_advance(self, n)
177 
178 
179  def __eq__(self, x):
180  """__eq__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
181  return _IMP_misc.IMP_MISC_SwigPyIterator___eq__(self, x)
182 
183 
184  def __ne__(self, x):
185  """__ne__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
186  return _IMP_misc.IMP_MISC_SwigPyIterator___ne__(self, x)
187 
188 
189  def __iadd__(self, n):
190  """__iadd__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
191  return _IMP_misc.IMP_MISC_SwigPyIterator___iadd__(self, n)
192 
193 
194  def __isub__(self, n):
195  """__isub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
196  return _IMP_misc.IMP_MISC_SwigPyIterator___isub__(self, n)
197 
198 
199  def __add__(self, n):
200  """__add__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
201  return _IMP_misc.IMP_MISC_SwigPyIterator___add__(self, n)
202 
203 
204  def __sub__(self, *args):
205  """
206  __sub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator
207  __sub__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t
208  """
209  return _IMP_misc.IMP_MISC_SwigPyIterator___sub__(self, *args)
210 
211  def __iter__(self):
212  return self
213 IMP_MISC_SwigPyIterator_swigregister = _IMP_misc.IMP_MISC_SwigPyIterator_swigregister
214 IMP_MISC_SwigPyIterator_swigregister(IMP_MISC_SwigPyIterator)
215 
216 _value_types=[]
217 _object_types=[]
218 _raii_types=[]
219 _plural_types=[]
220 
221 
222 _IMP_misc.IMP_DEBUG_swigconstant(_IMP_misc)
223 IMP_DEBUG = _IMP_misc.IMP_DEBUG
224 
225 _IMP_misc.IMP_RELEASE_swigconstant(_IMP_misc)
226 IMP_RELEASE = _IMP_misc.IMP_RELEASE
227 
228 _IMP_misc.IMP_SILENT_swigconstant(_IMP_misc)
229 IMP_SILENT = _IMP_misc.IMP_SILENT
230 
231 _IMP_misc.IMP_PROGRESS_swigconstant(_IMP_misc)
232 IMP_PROGRESS = _IMP_misc.IMP_PROGRESS
233 
234 _IMP_misc.IMP_TERSE_swigconstant(_IMP_misc)
235 IMP_TERSE = _IMP_misc.IMP_TERSE
236 
237 _IMP_misc.IMP_VERBOSE_swigconstant(_IMP_misc)
238 IMP_VERBOSE = _IMP_misc.IMP_VERBOSE
239 
240 _IMP_misc.IMP_MEMORY_swigconstant(_IMP_misc)
241 IMP_MEMORY = _IMP_misc.IMP_MEMORY
242 
243 _IMP_misc.IMP_NONE_swigconstant(_IMP_misc)
244 IMP_NONE = _IMP_misc.IMP_NONE
245 
246 _IMP_misc.IMP_USAGE_swigconstant(_IMP_misc)
247 IMP_USAGE = _IMP_misc.IMP_USAGE
248 
249 _IMP_misc.IMP_INTERNAL_swigconstant(_IMP_misc)
250 IMP_INTERNAL = _IMP_misc.IMP_INTERNAL
251 
252 _IMP_misc.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_misc)
253 IMP_KERNEL_HAS_LOG4CXX = _IMP_misc.IMP_KERNEL_HAS_LOG4CXX
254 
255 _IMP_misc.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_misc)
256 IMP_COMPILER_HAS_AUTO = _IMP_misc.IMP_COMPILER_HAS_AUTO
257 
258 _IMP_misc.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_misc)
259 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_misc.IMP_COMPILER_HAS_DEBUG_VECTOR
260 
261 _IMP_misc.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
262 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_misc.IMP_KERNEL_HAS_BOOST_RANDOM
263 
264 _IMP_misc.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_misc)
265 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_misc.IMP_KERNEL_HAS_GPERFTOOLS
266 
267 _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_misc)
268 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
269 
270 _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_misc)
271 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
272 
273 _IMP_misc.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_misc)
274 IMPKERNEL_SHOW_WARNINGS = _IMP_misc.IMPKERNEL_SHOW_WARNINGS
275 import sys
276 class _DirectorObjects(object):
277  """@internal Simple class to keep references to director objects
278  to prevent premature deletion."""
279  def __init__(self):
280  self._objects = []
281  def register(self, obj):
282  """Take a reference to a director object; will only work for
283  refcounted C++ classes"""
284  if hasattr(obj, 'get_ref_count'):
285  self._objects.append(obj)
286  def cleanup(self):
287  """Only drop our reference and allow cleanup by Python if no other
288  Python references exist (we hold 3 references: one in self._objects,
289  one in x, and one in the argument list for getrefcount) *and* no
290  other C++ references exist (the Python object always holds one)"""
291  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
292  or x.get_ref_count() > 1]
293  # Do in two steps so the references are kept until the end of the
294  # function (deleting references may trigger a fresh call to this method)
295  self._objects = objs
296  def get_object_count(self):
297  """Get number of director objects (useful for testing only)"""
298  return len(self._objects)
299 _director_objects = _DirectorObjects()
300 
301 class _ostream(object):
302  """Proxy of C++ std::ostream class"""
303  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
304 
305  def __init__(self, *args, **kwargs):
306  raise AttributeError("No constructor defined")
307  __repr__ = _swig_repr
308 
309  def write(self, osa_buf):
310  """write(_ostream self, char const * osa_buf)"""
311  return _IMP_misc._ostream_write(self, osa_buf)
312 
313 _ostream_swigregister = _IMP_misc._ostream_swigregister
314 _ostream_swigregister(_ostream)
315 
316 
317 _IMP_misc.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_misc)
318 IMP_COMPILER_HAS_OVERRIDE = _IMP_misc.IMP_COMPILER_HAS_OVERRIDE
319 
320 _IMP_misc.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_misc)
321 IMP_COMPILER_HAS_FINAL = _IMP_misc.IMP_COMPILER_HAS_FINAL
322 
323 _IMP_misc.IMP_HAS_NOEXCEPT_swigconstant(_IMP_misc)
324 IMP_HAS_NOEXCEPT = _IMP_misc.IMP_HAS_NOEXCEPT
325 import IMP
326 
327 _IMP_misc.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
328 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_FILESYSTEM
329 
330 _IMP_misc.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
331 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
332 
333 _IMP_misc.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
334 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_misc.IMP_CGAL_HAS_BOOST_RANDOM
335 
336 _IMP_misc.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
337 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_SYSTEM
338 
339 _IMP_misc.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_misc)
340 IMPCGAL_SHOW_WARNINGS = _IMP_misc.IMPCGAL_SHOW_WARNINGS
341 import IMP.cgal
342 
343 _IMP_misc.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_misc)
344 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_IMP_CGAL
345 
346 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
347 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
348 
349 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
350 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
351 
352 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
353 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_RANDOM
354 
355 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
356 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_SYSTEM
357 
358 _IMP_misc.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_misc)
359 IMP_ALGEBRA_HAS_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_CGAL
360 
361 _IMP_misc.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_misc)
362 IMP_ALGEBRA_HAS_ANN = _IMP_misc.IMP_ALGEBRA_HAS_ANN
363 
364 _IMP_misc.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_misc)
365 IMPALGEBRA_SHOW_WARNINGS = _IMP_misc.IMPALGEBRA_SHOW_WARNINGS
366 import IMP.algebra
367 
368 _IMP_misc.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_misc)
369 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_misc.IMP_DISPLAY_HAS_IMP_CGAL
370 
371 _IMP_misc.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
372 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
373 
374 _IMP_misc.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
375 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
376 
377 _IMP_misc.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
378 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_RANDOM
379 
380 _IMP_misc.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
381 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_SYSTEM
382 
383 _IMP_misc.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_misc)
384 IMP_DISPLAY_HAS_CGAL = _IMP_misc.IMP_DISPLAY_HAS_CGAL
385 
386 _IMP_misc.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_misc)
387 IMPDISPLAY_SHOW_WARNINGS = _IMP_misc.IMPDISPLAY_SHOW_WARNINGS
388 import IMP.display
389 
390 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_misc)
391 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
392 
393 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
394 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
395 
396 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
397 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
398 
399 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
400 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
401 
402 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
403 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
404 
405 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_misc)
406 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_CGAL
407 
408 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_misc)
409 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_HDF5
410 
411 _IMP_misc.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_misc)
412 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_misc.IMPSCOREFUNCTOR_SHOW_WARNINGS
413 import IMP.score_functor
414 
415 _IMP_misc.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_misc)
416 IMP_CORE_HAS_IMP_CGAL = _IMP_misc.IMP_CORE_HAS_IMP_CGAL
417 
418 _IMP_misc.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
419 IMP_CORE_HAS_IMP_KERNEL = _IMP_misc.IMP_CORE_HAS_IMP_KERNEL
420 
421 _IMP_misc.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
422 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_FILESYSTEM
423 
424 _IMP_misc.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
425 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
426 
427 _IMP_misc.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
428 IMP_CORE_HAS_BOOST_RANDOM = _IMP_misc.IMP_CORE_HAS_BOOST_RANDOM
429 
430 _IMP_misc.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
431 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_SYSTEM
432 
433 _IMP_misc.IMP_CORE_HAS_CGAL_swigconstant(_IMP_misc)
434 IMP_CORE_HAS_CGAL = _IMP_misc.IMP_CORE_HAS_CGAL
435 
436 _IMP_misc.IMP_CORE_HAS_HDF5_swigconstant(_IMP_misc)
437 IMP_CORE_HAS_HDF5 = _IMP_misc.IMP_CORE_HAS_HDF5
438 
439 _IMP_misc.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_misc)
440 IMPCORE_SHOW_WARNINGS = _IMP_misc.IMPCORE_SHOW_WARNINGS
441 import IMP.core
442 
443 _IMP_misc.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_misc)
444 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_misc.IMP_CONTAINER_HAS_IMP_ALGEBRA
445 
446 _IMP_misc.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_misc)
447 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_misc.IMP_CONTAINER_HAS_IMP_CGAL
448 
449 _IMP_misc.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_misc)
450 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_misc.IMP_CONTAINER_HAS_IMP_DISPLAY
451 
452 _IMP_misc.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
453 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_misc.IMP_CONTAINER_HAS_IMP_KERNEL
454 
455 _IMP_misc.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_misc)
456 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
457 
458 _IMP_misc.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
459 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
460 
461 _IMP_misc.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
462 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
463 
464 _IMP_misc.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
465 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_RANDOM
466 
467 _IMP_misc.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
468 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_SYSTEM
469 
470 _IMP_misc.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_misc)
471 IMP_CONTAINER_HAS_CGAL = _IMP_misc.IMP_CONTAINER_HAS_CGAL
472 
473 _IMP_misc.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_misc)
474 IMP_CONTAINER_HAS_HDF5 = _IMP_misc.IMP_CONTAINER_HAS_HDF5
475 
476 _IMP_misc.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_misc)
477 IMPCONTAINER_SHOW_WARNINGS = _IMP_misc.IMPCONTAINER_SHOW_WARNINGS
478 import IMP.container
479 
480 _IMP_misc.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_misc)
481 IMP_ATOM_HAS_IMP_CGAL = _IMP_misc.IMP_ATOM_HAS_IMP_CGAL
482 
483 _IMP_misc.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
484 IMP_ATOM_HAS_IMP_KERNEL = _IMP_misc.IMP_ATOM_HAS_IMP_KERNEL
485 
486 _IMP_misc.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_misc)
487 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
488 
489 _IMP_misc.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
490 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
491 
492 _IMP_misc.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
493 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_misc.IMP_ATOM_HAS_BOOST_RANDOM
494 
495 _IMP_misc.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_misc)
496 IMP_ATOM_HAS_BOOST_REGEX = _IMP_misc.IMP_ATOM_HAS_BOOST_REGEX
497 
498 _IMP_misc.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
499 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ATOM_HAS_BOOST_SYSTEM
500 
501 _IMP_misc.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_misc)
502 IMP_ATOM_HAS_CGAL = _IMP_misc.IMP_ATOM_HAS_CGAL
503 
504 _IMP_misc.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_misc)
505 IMP_ATOM_HAS_HDF5 = _IMP_misc.IMP_ATOM_HAS_HDF5
506 
507 _IMP_misc.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_misc)
508 IMPATOM_SHOW_WARNINGS = _IMP_misc.IMPATOM_SHOW_WARNINGS
509 
510 _IMP_misc.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_misc)
511 IMP_ATOM_TYPE_INDEX = _IMP_misc.IMP_ATOM_TYPE_INDEX
512 
513 _IMP_misc.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_misc)
514 IMP_RESIDUE_TYPE_INDEX = _IMP_misc.IMP_RESIDUE_TYPE_INDEX
515 
516 _IMP_misc.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_misc)
517 IMP_HIERARCHY_TYPE_INDEX = _IMP_misc.IMP_HIERARCHY_TYPE_INDEX
518 import IMP.atom
519 
520 _IMP_misc.IMP_MISC_HAS_IMP_ALGEBRA_swigconstant(_IMP_misc)
521 IMP_MISC_HAS_IMP_ALGEBRA = _IMP_misc.IMP_MISC_HAS_IMP_ALGEBRA
522 
523 _IMP_misc.IMP_MISC_HAS_IMP_CGAL_swigconstant(_IMP_misc)
524 IMP_MISC_HAS_IMP_CGAL = _IMP_misc.IMP_MISC_HAS_IMP_CGAL
525 
526 _IMP_misc.IMP_MISC_HAS_IMP_CONTAINER_swigconstant(_IMP_misc)
527 IMP_MISC_HAS_IMP_CONTAINER = _IMP_misc.IMP_MISC_HAS_IMP_CONTAINER
528 
529 _IMP_misc.IMP_MISC_HAS_IMP_DISPLAY_swigconstant(_IMP_misc)
530 IMP_MISC_HAS_IMP_DISPLAY = _IMP_misc.IMP_MISC_HAS_IMP_DISPLAY
531 
532 _IMP_misc.IMP_MISC_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
533 IMP_MISC_HAS_IMP_KERNEL = _IMP_misc.IMP_MISC_HAS_IMP_KERNEL
534 
535 _IMP_misc.IMP_MISC_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_misc)
536 IMP_MISC_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_MISC_HAS_IMP_SCORE_FUNCTOR
537 
538 _IMP_misc.IMP_MISC_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
539 IMP_MISC_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_FILESYSTEM
540 
541 _IMP_misc.IMP_MISC_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
542 IMP_MISC_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_MISC_HAS_BOOST_PROGRAMOPTIONS
543 
544 _IMP_misc.IMP_MISC_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
545 IMP_MISC_HAS_BOOST_RANDOM = _IMP_misc.IMP_MISC_HAS_BOOST_RANDOM
546 
547 _IMP_misc.IMP_MISC_HAS_BOOST_REGEX_swigconstant(_IMP_misc)
548 IMP_MISC_HAS_BOOST_REGEX = _IMP_misc.IMP_MISC_HAS_BOOST_REGEX
549 
550 _IMP_misc.IMP_MISC_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
551 IMP_MISC_HAS_BOOST_SYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_SYSTEM
552 
553 _IMP_misc.IMP_MISC_HAS_CGAL_swigconstant(_IMP_misc)
554 IMP_MISC_HAS_CGAL = _IMP_misc.IMP_MISC_HAS_CGAL
555 
556 _IMP_misc.IMP_MISC_HAS_HDF5_swigconstant(_IMP_misc)
557 IMP_MISC_HAS_HDF5 = _IMP_misc.IMP_MISC_HAS_HDF5
558 
559 _IMP_misc.IMPMISC_SHOW_WARNINGS_swigconstant(_IMP_misc)
560 IMPMISC_SHOW_WARNINGS = _IMP_misc.IMPMISC_SHOW_WARNINGS
561 _object_types.append("WormLikeChain")
562 
563 
564 def _object_cast_to_WormLikeChain(o):
565  """_object_cast_to_WormLikeChain(Object o) -> WormLikeChain"""
566  return _IMP_misc._object_cast_to_WormLikeChain(o)
567 _object_types.append("StateAdaptor")
568 
569 
570 def _object_cast_to_StateAdaptor(o):
571  """_object_cast_to_StateAdaptor(Object o) -> StateAdaptor"""
572  return _IMP_misc._object_cast_to_StateAdaptor(o)
573 _object_types.append("CommonEndpointPairFilter")
574 
575 
576 def _object_cast_to_CommonEndpointPairFilter(o):
577  """_object_cast_to_CommonEndpointPairFilter(Object o) -> CommonEndpointPairFilter"""
578  return _IMP_misc._object_cast_to_CommonEndpointPairFilter(o)
579 _object_types.append("LogPairScore")
580 
581 
582 def _object_cast_to_LogPairScore(o):
583  """_object_cast_to_LogPairScore(Object o) -> LogPairScore"""
584  return _IMP_misc._object_cast_to_LogPairScore(o)
585 _object_types.append("LowestRefinedPairScore")
586 
587 
588 def _object_cast_to_LowestRefinedPairScore(o):
589  """_object_cast_to_LowestRefinedPairScore(Object o) -> LowestRefinedPairScore"""
590  return _IMP_misc._object_cast_to_LowestRefinedPairScore(o)
591 _object_types.append("SoftCylinderPairScore")
592 
593 
594 def _object_cast_to_SoftCylinderPairScore(o):
595  """_object_cast_to_SoftCylinderPairScore(Object o) -> SoftCylinderPairScore"""
596  return _IMP_misc._object_cast_to_SoftCylinderPairScore(o)
597 _object_types.append("DecayPairContainerOptimizerState")
598 
599 
600 def _object_cast_to_DecayPairContainerOptimizerState(o):
601  """_object_cast_to_DecayPairContainerOptimizerState(Object o) -> DecayPairContainerOptimizerState"""
602  return _IMP_misc._object_cast_to_DecayPairContainerOptimizerState(o)
603 def CustomXYZRs(l=[]):
604  return [CustomXYZR(x) for x in l]
605 _plural_types.append("CustomXYZRs")
606 
607 _value_types.append("CustomXYZR")
608 
609 class WormLikeChain(IMP.UnaryFunction):
610  """Proxy of C++ IMP::misc::WormLikeChain class"""
611  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
612 
613  def __init__(self, l_max, lp):
614  """__init__(IMP::misc::WormLikeChain self, IMP::Float l_max, IMP::Float lp) -> WormLikeChain"""
615  this = _IMP_misc.new_WormLikeChain(l_max, lp)
616  try:
617  self.this.append(this)
618  except:
619  self.this = this
620 
621  def get_version_info(self):
622  """get_version_info(WormLikeChain self) -> VersionInfo"""
623  return _IMP_misc.WormLikeChain_get_version_info(self)
624 
625 
626  def do_show(self, out):
627  """do_show(WormLikeChain self, _ostream out)"""
628  return _IMP_misc.WormLikeChain_do_show(self, out)
629 
630 
631  def __str__(self):
632  """__str__(WormLikeChain self) -> std::string"""
633  return _IMP_misc.WormLikeChain___str__(self)
634 
635 
636  def __repr__(self):
637  """__repr__(WormLikeChain self) -> std::string"""
638  return _IMP_misc.WormLikeChain___repr__(self)
639 
640  def get_from(o):
641  return _object_cast_to_WormLikeChain(o)
642  get_from = staticmethod(get_from)
643 
644 WormLikeChain_swigregister = _IMP_misc.WormLikeChain_swigregister
645 WormLikeChain_swigregister(WormLikeChain)
646 
647 class LowestRefinedPairScore(IMP.PairScore):
648  """Proxy of C++ IMP::misc::LowestRefinedPairScore class"""
649  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
650 
651  def __init__(self, r, f):
652  """__init__(IMP::misc::LowestRefinedPairScore self, Refiner r, PairScore f) -> LowestRefinedPairScore"""
653  this = _IMP_misc.new_LowestRefinedPairScore(r, f)
654  try:
655  self.this.append(this)
656  except:
657  self.this = this
658 
659  def do_get_inputs(self, m, pis):
660  """do_get_inputs(LowestRefinedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
661  return _IMP_misc.LowestRefinedPairScore_do_get_inputs(self, m, pis)
662 
663 
664  def get_version_info(self):
665  """get_version_info(LowestRefinedPairScore self) -> VersionInfo"""
666  return _IMP_misc.LowestRefinedPairScore_get_version_info(self)
667 
668 
669  def __str__(self):
670  """__str__(LowestRefinedPairScore self) -> std::string"""
671  return _IMP_misc.LowestRefinedPairScore___str__(self)
672 
673 
674  def __repr__(self):
675  """__repr__(LowestRefinedPairScore self) -> std::string"""
676  return _IMP_misc.LowestRefinedPairScore___repr__(self)
677 
678  def get_from(o):
679  return _object_cast_to_LowestRefinedPairScore(o)
680  get_from = staticmethod(get_from)
681 
682 LowestRefinedPairScore_swigregister = _IMP_misc.LowestRefinedPairScore_swigregister
683 LowestRefinedPairScore_swigregister(LowestRefinedPairScore)
684 
685 class LogPairScore(IMP.PairScore):
686  """Proxy of C++ IMP::misc::LogPairScore class"""
687  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
688 
689  def __init__(self):
690  """__init__(IMP::misc::LogPairScore self) -> LogPairScore"""
691  this = _IMP_misc.new_LogPairScore()
692  try:
693  self.this.append(this)
694  except:
695  self.this = this
696 
697  def do_get_inputs(self, arg2, arg3):
698  """do_get_inputs(LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
699  return _IMP_misc.LogPairScore_do_get_inputs(self, arg2, arg3)
700 
701 
702  def get_version_info(self):
703  """get_version_info(LogPairScore self) -> VersionInfo"""
704  return _IMP_misc.LogPairScore_get_version_info(self)
705 
706 
707  def get_particle_pairs(self):
708  """get_particle_pairs(LogPairScore self) -> IMP::ParticlePairsTemp"""
709  return _IMP_misc.LogPairScore_get_particle_pairs(self)
710 
711 
712  def clear(self):
713  """clear(LogPairScore self)"""
714  return _IMP_misc.LogPairScore_clear(self)
715 
716 
717  def get_contains(self, pp):
718  """get_contains(LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
719  return _IMP_misc.LogPairScore_get_contains(self, pp)
720 
721 
722  def __str__(self):
723  """__str__(LogPairScore self) -> std::string"""
724  return _IMP_misc.LogPairScore___str__(self)
725 
726 
727  def __repr__(self):
728  """__repr__(LogPairScore self) -> std::string"""
729  return _IMP_misc.LogPairScore___repr__(self)
730 
731  def get_from(o):
732  return _object_cast_to_LogPairScore(o)
733  get_from = staticmethod(get_from)
734 
735 LogPairScore_swigregister = _IMP_misc.LogPairScore_swigregister
736 LogPairScore_swigregister(LogPairScore)
737 
738 class StateAdaptor(IMP.ScoreState):
739  """Proxy of C++ IMP::misc::StateAdaptor class"""
740  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
741 
742  def __init__(self, m, before, after):
743  """__init__(IMP::misc::StateAdaptor self, Model m, OptimizerState before, OptimizerState after) -> StateAdaptor"""
744  this = _IMP_misc.new_StateAdaptor(m, before, after)
745  try:
746  self.this.append(this)
747  except:
748  self.this = this
749 
750  def do_before_evaluate(self):
751  """do_before_evaluate(StateAdaptor self)"""
752  return _IMP_misc.StateAdaptor_do_before_evaluate(self)
753 
754 
755  def do_after_evaluate(self, da):
756  """do_after_evaluate(StateAdaptor self, DerivativeAccumulator da)"""
757  return _IMP_misc.StateAdaptor_do_after_evaluate(self, da)
758 
759 
760  def do_get_inputs(self):
761  """do_get_inputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
762  return _IMP_misc.StateAdaptor_do_get_inputs(self)
763 
764 
765  def do_get_outputs(self):
766  """do_get_outputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
767  return _IMP_misc.StateAdaptor_do_get_outputs(self)
768 
769 
770  def get_version_info(self):
771  """get_version_info(StateAdaptor self) -> VersionInfo"""
772  return _IMP_misc.StateAdaptor_get_version_info(self)
773 
774 
775  def __str__(self):
776  """__str__(StateAdaptor self) -> std::string"""
777  return _IMP_misc.StateAdaptor___str__(self)
778 
779 
780  def __repr__(self):
781  """__repr__(StateAdaptor self) -> std::string"""
782  return _IMP_misc.StateAdaptor___repr__(self)
783 
784  def get_from(o):
785  return _object_cast_to_StateAdaptor(o)
786  get_from = staticmethod(get_from)
787 
788 StateAdaptor_swigregister = _IMP_misc.StateAdaptor_swigregister
789 StateAdaptor_swigregister(StateAdaptor)
790 
791 class CommonEndpointPairFilter(IMP.PairPredicate):
792  """Proxy of C++ IMP::misc::CommonEndpointPairFilter class"""
793  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
794 
795  def __init__(self):
796  """__init__(IMP::misc::CommonEndpointPairFilter self) -> CommonEndpointPairFilter"""
797  this = _IMP_misc.new_CommonEndpointPairFilter()
798  try:
799  self.this.append(this)
800  except:
801  self.this = this
802 
803  def do_get_inputs(self, m, pis):
804  """do_get_inputs(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
805  return _IMP_misc.CommonEndpointPairFilter_do_get_inputs(self, m, pis)
806 
807 
808  def get_value(self, *args):
809  """
810  get_value(CommonEndpointPairFilter self, IMP::ParticlePair const & a) -> int
811  get_value(CommonEndpointPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
812  """
813  return _IMP_misc.CommonEndpointPairFilter_get_value(self, *args)
814 
815 
816  def get_value_index(self, *args):
817  """
818  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
819  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
820  """
821  return _IMP_misc.CommonEndpointPairFilter_get_value_index(self, *args)
822 
823 
824  def get_version_info(self):
825  """get_version_info(CommonEndpointPairFilter self) -> VersionInfo"""
826  return _IMP_misc.CommonEndpointPairFilter_get_version_info(self)
827 
828 
829  def __str__(self):
830  """__str__(CommonEndpointPairFilter self) -> std::string"""
831  return _IMP_misc.CommonEndpointPairFilter___str__(self)
832 
833 
834  def __repr__(self):
835  """__repr__(CommonEndpointPairFilter self) -> std::string"""
836  return _IMP_misc.CommonEndpointPairFilter___repr__(self)
837 
838  def get_from(o):
839  return _object_cast_to_CommonEndpointPairFilter(o)
840  get_from = staticmethod(get_from)
841 
842 CommonEndpointPairFilter_swigregister = _IMP_misc.CommonEndpointPairFilter_swigregister
843 CommonEndpointPairFilter_swigregister(CommonEndpointPairFilter)
844 
845 class CustomXYZR(IMP.core.XYZ):
846  """Proxy of C++ IMP::misc::CustomXYZR class"""
847  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
848 
849  def get_decorator_traits(self):
850  """get_decorator_traits(CustomXYZR self) -> FloatKey"""
851  return _IMP_misc.CustomXYZR_get_decorator_traits(self)
852 
853 
854  def get_default_decorator_traits():
855  """get_default_decorator_traits() -> FloatKey"""
856  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
857 
858  get_default_decorator_traits = staticmethod(get_default_decorator_traits)
859 
860  def __init__(self, *args):
861  """
862  __init__(IMP::misc::CustomXYZR self) -> CustomXYZR
863  __init__(IMP::misc::CustomXYZR self, Model m, ParticleIndex id, FloatKey tr) -> CustomXYZR
864  __init__(IMP::misc::CustomXYZR self, Model m, ParticleIndex id) -> CustomXYZR
865  __init__(IMP::misc::CustomXYZR self, _ParticleAdaptor d, FloatKey tr) -> CustomXYZR
866  __init__(IMP::misc::CustomXYZR self, _ParticleAdaptor d) -> CustomXYZR
867  """
868  this = _IMP_misc.new_CustomXYZR(*args)
869  try:
870  self.this.append(this)
871  except:
872  self.this = this
873 
874  def show(self, *args):
875  """
876  show(CustomXYZR self, _ostream out)
877  show(CustomXYZR self)
878  """
879  return _IMP_misc.CustomXYZR_show(self, *args)
880 
881 
882  def setup_particle(*args):
883  """
884  setup_particle(Model m, ParticleIndex pi, FloatKey tr) -> CustomXYZR
885  setup_particle(Model m, ParticleIndex pi) -> CustomXYZR
886  setup_particle(_ParticleAdaptor d, FloatKey tr) -> CustomXYZR
887  setup_particle(_ParticleAdaptor d) -> CustomXYZR
888  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr) -> CustomXYZR
889  setup_particle(Model m, ParticleIndex pi, double radius) -> CustomXYZR
890  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr) -> CustomXYZR
891  setup_particle(_ParticleAdaptor d, double radius) -> CustomXYZR
892  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr) -> CustomXYZR
893  setup_particle(Model m, ParticleIndex pi, Sphere3D ball) -> CustomXYZR
894  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr) -> CustomXYZR
895  setup_particle(_ParticleAdaptor d, Sphere3D ball) -> CustomXYZR
896  """
897  return _IMP_misc.CustomXYZR_setup_particle(*args)
898 
899  setup_particle = staticmethod(setup_particle)
900 
901  def get_is_setup(*args):
902  """
903  get_is_setup(_ParticleAdaptor p, FloatKey tr) -> bool
904  get_is_setup(_ParticleAdaptor p) -> bool
905  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key) -> bool
906  get_is_setup(Model m, ParticleIndex pi) -> bool
907  """
908  return _IMP_misc.CustomXYZR_get_is_setup(*args)
909 
910  get_is_setup = staticmethod(get_is_setup)
911 
912  def get_radius(self):
913  """get_radius(CustomXYZR self) -> IMP::Float"""
914  return _IMP_misc.CustomXYZR_get_radius(self)
915 
916 
917  def set_radius(self, t):
918  """set_radius(CustomXYZR self, IMP::Float t)"""
919  return _IMP_misc.CustomXYZR_set_radius(self, t)
920 
921 
922  def get_sphere(self):
923  """get_sphere(CustomXYZR self) -> Sphere3D"""
924  return _IMP_misc.CustomXYZR_get_sphere(self)
925 
926 
927  def set_sphere(self, s):
928  """set_sphere(CustomXYZR self, Sphere3D s)"""
929  return _IMP_misc.CustomXYZR_set_sphere(self, s)
930 
931 
932  def get_default_radius_key():
933  """get_default_radius_key() -> FloatKey"""
934  return _IMP_misc.CustomXYZR_get_default_radius_key()
935 
936  get_default_radius_key = staticmethod(get_default_radius_key)
937 
938  def add_to_radius_derivative(self, v, d):
939  """add_to_radius_derivative(CustomXYZR self, double v, DerivativeAccumulator d)"""
940  return _IMP_misc.CustomXYZR_add_to_radius_derivative(self, v, d)
941 
942 
943  def get_traits(self):
944  """get_traits(CustomXYZR self) -> FloatKey"""
945  return _IMP_misc.CustomXYZR_get_traits(self)
946 
947 
948  def add_attribute(self, *args):
949  """
950  add_attribute(CustomXYZR self, FloatKey k, IMP::Float v, bool opt)
951  add_attribute(CustomXYZR self, FloatKey a0, IMP::Float a1)
952  add_attribute(CustomXYZR self, IntKey a0, IMP::Int a1)
953  add_attribute(CustomXYZR self, StringKey a0, IMP::String a1)
954  add_attribute(CustomXYZR self, ParticleIndexKey a0, Particle a1)
955  add_attribute(CustomXYZR self, ObjectKey a0, Object a1)
956  """
957  return _IMP_misc.CustomXYZR_add_attribute(self, *args)
958 
959 
960  def get_value(self, *args):
961  """
962  get_value(CustomXYZR self, FloatKey a0) -> IMP::Float
963  get_value(CustomXYZR self, IntKey a0) -> IMP::Int
964  get_value(CustomXYZR self, StringKey a0) -> IMP::String
965  get_value(CustomXYZR self, ParticleIndexKey a0) -> Particle
966  get_value(CustomXYZR self, ObjectKey a0) -> Object
967  """
968  return _IMP_misc.CustomXYZR_get_value(self, *args)
969 
970 
971  def set_value(self, *args):
972  """
973  set_value(CustomXYZR self, FloatKey a0, IMP::Float a1)
974  set_value(CustomXYZR self, IntKey a0, IMP::Int a1)
975  set_value(CustomXYZR self, StringKey a0, IMP::String a1)
976  set_value(CustomXYZR self, ParticleIndexKey a0, Particle a1)
977  set_value(CustomXYZR self, ObjectKey a0, Object a1)
978  """
979  return _IMP_misc.CustomXYZR_set_value(self, *args)
980 
981 
982  def remove_attribute(self, *args):
983  """
984  remove_attribute(CustomXYZR self, FloatKey a0)
985  remove_attribute(CustomXYZR self, IntKey a0)
986  remove_attribute(CustomXYZR self, StringKey a0)
987  remove_attribute(CustomXYZR self, ParticleIndexKey a0)
988  remove_attribute(CustomXYZR self, ObjectKey a0)
989  """
990  return _IMP_misc.CustomXYZR_remove_attribute(self, *args)
991 
992 
993  def has_attribute(self, *args):
994  """
995  has_attribute(CustomXYZR self, FloatKey a0) -> bool
996  has_attribute(CustomXYZR self, IntKey a0) -> bool
997  has_attribute(CustomXYZR self, StringKey a0) -> bool
998  has_attribute(CustomXYZR self, ParticleIndexKey a0) -> bool
999  has_attribute(CustomXYZR self, ObjectKey a0) -> bool
1000  """
1001  return _IMP_misc.CustomXYZR_has_attribute(self, *args)
1002 
1003 
1004  def get_derivative(self, a0):
1005  """get_derivative(CustomXYZR self, FloatKey a0) -> double"""
1006  return _IMP_misc.CustomXYZR_get_derivative(self, a0)
1007 
1008 
1009  def get_name(self):
1010  """get_name(CustomXYZR self) -> std::string"""
1011  return _IMP_misc.CustomXYZR_get_name(self)
1012 
1013 
1014  def clear_caches(self):
1015  """clear_caches(CustomXYZR self)"""
1016  return _IMP_misc.CustomXYZR_clear_caches(self)
1017 
1018 
1019  def set_name(self, a0):
1020  """set_name(CustomXYZR self, std::string a0)"""
1021  return _IMP_misc.CustomXYZR_set_name(self, a0)
1022 
1023 
1024  def set_check_level(self, a0):
1025  """set_check_level(CustomXYZR self, IMP::CheckLevel a0)"""
1026  return _IMP_misc.CustomXYZR_set_check_level(self, a0)
1027 
1028 
1029  def add_to_derivative(self, a0, a1, a2):
1030  """add_to_derivative(CustomXYZR self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1031  return _IMP_misc.CustomXYZR_add_to_derivative(self, a0, a1, a2)
1032 
1033 
1034  def set_is_optimized(self, a0, a1):
1035  """set_is_optimized(CustomXYZR self, FloatKey a0, bool a1)"""
1036  return _IMP_misc.CustomXYZR_set_is_optimized(self, a0, a1)
1037 
1038 
1039  def get_is_optimized(self, a0):
1040  """get_is_optimized(CustomXYZR self, FloatKey a0) -> bool"""
1041  return _IMP_misc.CustomXYZR_get_is_optimized(self, a0)
1042 
1043 
1044  def get_check_level(self):
1045  """get_check_level(CustomXYZR self) -> IMP::CheckLevel"""
1046  return _IMP_misc.CustomXYZR_get_check_level(self)
1047 
1048 
1049  def __eq__(self, *args):
1050  """
1051  __eq__(CustomXYZR self, CustomXYZR o) -> bool
1052  __eq__(CustomXYZR self, Particle d) -> bool
1053  """
1054  return _IMP_misc.CustomXYZR___eq__(self, *args)
1055 
1056 
1057  def __ne__(self, *args):
1058  """
1059  __ne__(CustomXYZR self, CustomXYZR o) -> bool
1060  __ne__(CustomXYZR self, Particle d) -> bool
1061  """
1062  return _IMP_misc.CustomXYZR___ne__(self, *args)
1063 
1064 
1065  def __le__(self, *args):
1066  """
1067  __le__(CustomXYZR self, CustomXYZR o) -> bool
1068  __le__(CustomXYZR self, Particle d) -> bool
1069  """
1070  return _IMP_misc.CustomXYZR___le__(self, *args)
1071 
1072 
1073  def __lt__(self, *args):
1074  """
1075  __lt__(CustomXYZR self, CustomXYZR o) -> bool
1076  __lt__(CustomXYZR self, Particle d) -> bool
1077  """
1078  return _IMP_misc.CustomXYZR___lt__(self, *args)
1079 
1080 
1081  def __ge__(self, *args):
1082  """
1083  __ge__(CustomXYZR self, CustomXYZR o) -> bool
1084  __ge__(CustomXYZR self, Particle d) -> bool
1085  """
1086  return _IMP_misc.CustomXYZR___ge__(self, *args)
1087 
1088 
1089  def __gt__(self, *args):
1090  """
1091  __gt__(CustomXYZR self, CustomXYZR o) -> bool
1092  __gt__(CustomXYZR self, Particle d) -> bool
1093  """
1094  return _IMP_misc.CustomXYZR___gt__(self, *args)
1095 
1096 
1097  def __hash__(self):
1098  """__hash__(CustomXYZR self) -> std::size_t"""
1099  return _IMP_misc.CustomXYZR___hash__(self)
1100 
1101 
1102  def __str__(self):
1103  """__str__(CustomXYZR self) -> std::string"""
1104  return _IMP_misc.CustomXYZR___str__(self)
1105 
1106 
1107  def __repr__(self):
1108  """__repr__(CustomXYZR self) -> std::string"""
1109  return _IMP_misc.CustomXYZR___repr__(self)
1110 
1111  __swig_destroy__ = _IMP_misc.delete_CustomXYZR
1112  __del__ = lambda self: None
1113 CustomXYZR_swigregister = _IMP_misc.CustomXYZR_swigregister
1114 CustomXYZR_swigregister(CustomXYZR)
1115 
1116 def CustomXYZR_get_default_decorator_traits():
1117  """CustomXYZR_get_default_decorator_traits() -> FloatKey"""
1118  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
1119 
1120 def CustomXYZR_setup_particle(*args):
1121  """
1122  setup_particle(Model m, ParticleIndex pi, FloatKey tr) -> CustomXYZR
1123  setup_particle(Model m, ParticleIndex pi) -> CustomXYZR
1124  setup_particle(_ParticleAdaptor d, FloatKey tr) -> CustomXYZR
1125  setup_particle(_ParticleAdaptor d) -> CustomXYZR
1126  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr) -> CustomXYZR
1127  setup_particle(Model m, ParticleIndex pi, double radius) -> CustomXYZR
1128  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr) -> CustomXYZR
1129  setup_particle(_ParticleAdaptor d, double radius) -> CustomXYZR
1130  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr) -> CustomXYZR
1131  setup_particle(Model m, ParticleIndex pi, Sphere3D ball) -> CustomXYZR
1132  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr) -> CustomXYZR
1133  CustomXYZR_setup_particle(_ParticleAdaptor d, Sphere3D ball) -> CustomXYZR
1134  """
1135  return _IMP_misc.CustomXYZR_setup_particle(*args)
1136 
1137 def CustomXYZR_get_is_setup(*args):
1138  """
1139  get_is_setup(_ParticleAdaptor p, FloatKey tr) -> bool
1140  get_is_setup(_ParticleAdaptor p) -> bool
1141  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key) -> bool
1142  CustomXYZR_get_is_setup(Model m, ParticleIndex pi) -> bool
1143  """
1144  return _IMP_misc.CustomXYZR_get_is_setup(*args)
1145 
1146 def CustomXYZR_get_default_radius_key():
1147  """CustomXYZR_get_default_radius_key() -> FloatKey"""
1148  return _IMP_misc.CustomXYZR_get_default_radius_key()
1149 
1150 
1151 def __lshift__(out, n):
1152  """__lshift__(_ostream out, CustomXYZR n) -> _ostream"""
1153  return _IMP_misc.__lshift__(out, n)
1154 
1155 def get_distance(a, b):
1156  """get_distance(CustomXYZR a, CustomXYZR b) -> double"""
1157  return _IMP_misc.get_distance(a, b)
1158 
1159 def get_sphere_d_geometry(d):
1160  """get_sphere_d_geometry(CustomXYZR d) -> Sphere3D"""
1161  return _IMP_misc.get_sphere_d_geometry(d)
1162 
1163 def set_sphere_d_geometry(d, v):
1164  """set_sphere_d_geometry(CustomXYZR d, Sphere3D v)"""
1165  return _IMP_misc.set_sphere_d_geometry(d, v)
1166 class SoftCylinderPairScore(IMP.PairScore):
1167  """Proxy of C++ IMP::misc::SoftCylinderPairScore class"""
1168  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1169 
1170  def __init__(self, k):
1171  """__init__(IMP::misc::SoftCylinderPairScore self, double k) -> SoftCylinderPairScore"""
1172  this = _IMP_misc.new_SoftCylinderPairScore(k)
1173  try:
1174  self.this.append(this)
1175  except:
1176  self.this = this
1177 
1178  def do_get_inputs(self, m, pis):
1179  """do_get_inputs(SoftCylinderPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1180  return _IMP_misc.SoftCylinderPairScore_do_get_inputs(self, m, pis)
1181 
1182 
1183  def get_version_info(self):
1184  """get_version_info(SoftCylinderPairScore self) -> VersionInfo"""
1185  return _IMP_misc.SoftCylinderPairScore_get_version_info(self)
1186 
1187 
1188  def __str__(self):
1189  """__str__(SoftCylinderPairScore self) -> std::string"""
1190  return _IMP_misc.SoftCylinderPairScore___str__(self)
1191 
1192 
1193  def __repr__(self):
1194  """__repr__(SoftCylinderPairScore self) -> std::string"""
1195  return _IMP_misc.SoftCylinderPairScore___repr__(self)
1196 
1197  def get_from(o):
1198  return _object_cast_to_SoftCylinderPairScore(o)
1199  get_from = staticmethod(get_from)
1200 
1201 SoftCylinderPairScore_swigregister = _IMP_misc.SoftCylinderPairScore_swigregister
1202 SoftCylinderPairScore_swigregister(SoftCylinderPairScore)
1203 
1204 class DecayPairContainerOptimizerState(IMP.OptimizerState):
1205  """Proxy of C++ IMP::misc::DecayPairContainerOptimizerState class"""
1206  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1207 
1208  def __init__(self, *args):
1209  """
1210  __init__(IMP::misc::DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list, std::string name) -> DecayPairContainerOptimizerState
1211  __init__(IMP::misc::DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list) -> DecayPairContainerOptimizerState
1212  __init__(IMP::misc::DecayPairContainerOptimizerState self, PairPredicate pred, IMP::ParticlePairsTemp const & initial_list, std::string name) -> DecayPairContainerOptimizerState
1213  __init__(IMP::misc::DecayPairContainerOptimizerState self, PairPredicate pred, IMP::ParticlePairsTemp const & initial_list) -> DecayPairContainerOptimizerState
1214  """
1215  this = _IMP_misc.new_DecayPairContainerOptimizerState(*args)
1216  try:
1217  self.this.append(this)
1218  except:
1219  self.this = this
1220 
1221  def get_output_container(self):
1222  """get_output_container(DecayPairContainerOptimizerState self) -> PairContainer"""
1223  return _IMP_misc.DecayPairContainerOptimizerState_get_output_container(self)
1224 
1225 
1226  def do_update(self, call_num):
1227  """do_update(DecayPairContainerOptimizerState self, unsigned int call_num)"""
1228  return _IMP_misc.DecayPairContainerOptimizerState_do_update(self, call_num)
1229 
1230 
1231  def get_version_info(self):
1232  """get_version_info(DecayPairContainerOptimizerState self) -> VersionInfo"""
1233  return _IMP_misc.DecayPairContainerOptimizerState_get_version_info(self)
1234 
1235 
1236  def __str__(self):
1237  """__str__(DecayPairContainerOptimizerState self) -> std::string"""
1238  return _IMP_misc.DecayPairContainerOptimizerState___str__(self)
1239 
1240 
1241  def __repr__(self):
1242  """__repr__(DecayPairContainerOptimizerState self) -> std::string"""
1243  return _IMP_misc.DecayPairContainerOptimizerState___repr__(self)
1244 
1245  def get_from(o):
1246  return _object_cast_to_DecayPairContainerOptimizerState(o)
1247  get_from = staticmethod(get_from)
1248 
1249 DecayPairContainerOptimizerState_swigregister = _IMP_misc.DecayPairContainerOptimizerState_swigregister
1250 DecayPairContainerOptimizerState_swigregister(DecayPairContainerOptimizerState)
1251 
1252 
1253 def get_module_version():
1254  """get_module_version() -> std::string const"""
1255  return _IMP_misc.get_module_version()
1256 
1257 def get_example_path(fname):
1258  """get_example_path(std::string fname) -> std::string"""
1259  return _IMP_misc.get_example_path(fname)
1260 
1261 def get_data_path(fname):
1262  """get_data_path(std::string fname) -> std::string"""
1263  return _IMP_misc.get_data_path(fname)
1264 from . import _version_check
1265 _version_check.check_version(get_module_version())
1266 __version__ = get_module_version()
1267 
1268 
1269 
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:38
Various classes to hold sets of particles.
const algebra::Sphere3D get_sphere_d_geometry(CustomXYZR d)
Definition: CustomXYZR.h:90
Make CGAL functionality available to IMP.
virtual void clear_caches()
Definition: Object.h:227
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Composable functors to implement scores via compile-time composition.
double get_distance(const Plane3D &pln, const Vector3D &p)
Return the distance between a plane and a point in 3D.
Definition: Plane3D.h:63
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:53
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
void set_sphere_d_geometry(CustomXYZR d, const algebra::Sphere3D &v)
Definition: CustomXYZR.h:95
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
Definition: PairPredicate.h:32
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
Shared optimizer state that is invoked upon commitment of new coordinates.
void set_check_level(CheckLevel l)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:25