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IMP Reference Guide  develop.63b38c487d,2024/12/22
The Integrative Modeling Platform
scratch/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.3.0
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2024 IMP Inventors. All rights reserved.
10 
11 
12 
13 
14 from sys import version_info as _swig_python_version_info
15 import _IMP_scratch
16 
17 try:
18  import builtins as __builtin__
19 except ImportError:
20  import __builtin__
21 
22 def _swig_repr(self):
23  try:
24  strthis = "proxy of " + self.this.__repr__()
25  except __builtin__.Exception:
26  strthis = ""
27  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
28 
29 
30 def _swig_setattr_nondynamic_instance_variable(set):
31  def set_instance_attr(self, name, value):
32  if name == "this":
33  set(self, name, value)
34  elif name == "thisown":
35  self.this.own(value)
36  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
37  set(self, name, value)
38  else:
39  raise AttributeError("You cannot add instance attributes to %s" % self)
40  return set_instance_attr
41 
42 
43 def _swig_setattr_nondynamic_class_variable(set):
44  def set_class_attr(cls, name, value):
45  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
46  set(cls, name, value)
47  else:
48  raise AttributeError("You cannot add class attributes to %s" % cls)
49  return set_class_attr
50 
51 
52 def _swig_add_metaclass(metaclass):
53  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
54  def wrapper(cls):
55  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
56  return wrapper
57 
58 
59 class _SwigNonDynamicMeta(type):
60  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
62 
63 
64 import weakref
65 
66 class IMP_SCRATCH_SwigPyIterator(object):
67  r"""Proxy of C++ swig::IMP_SCRATCH_SwigPyIterator class."""
68 
69  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
70 
71  def __init__(self, *args, **kwargs):
72  raise AttributeError("No constructor defined - class is abstract")
73  __repr__ = _swig_repr
74  __swig_destroy__ = _IMP_scratch.delete_IMP_SCRATCH_SwigPyIterator
75 
76  def value(self):
77  r"""value(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
78  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_value(self)
79 
80  def incr(self, n=1):
81  r"""incr(IMP_SCRATCH_SwigPyIterator self, size_t n=1) -> IMP_SCRATCH_SwigPyIterator"""
82  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_incr(self, n)
83 
84  def decr(self, n=1):
85  r"""decr(IMP_SCRATCH_SwigPyIterator self, size_t n=1) -> IMP_SCRATCH_SwigPyIterator"""
86  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_decr(self, n)
87 
88  def distance(self, x):
89  r"""distance(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> ptrdiff_t"""
90  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_distance(self, x)
91 
92  def equal(self, x):
93  r"""equal(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
94  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_equal(self, x)
95 
96  def copy(self):
97  r"""copy(IMP_SCRATCH_SwigPyIterator self) -> IMP_SCRATCH_SwigPyIterator"""
98  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_copy(self)
99 
100  def next(self):
101  r"""next(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
102  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_next(self)
103 
104  def __next__(self):
105  r"""__next__(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
106  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___next__(self)
107 
108  def previous(self):
109  r"""previous(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
110  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_previous(self)
111 
112  def advance(self, n):
113  r"""advance(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
114  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_advance(self, n)
115 
116  def __eq__(self, x):
117  r"""__eq__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
118  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___eq__(self, x)
119 
120  def __ne__(self, x):
121  r"""__ne__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
122  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___ne__(self, x)
123 
124  def __iadd__(self, n):
125  r"""__iadd__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
126  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___iadd__(self, n)
127 
128  def __isub__(self, n):
129  r"""__isub__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
130  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___isub__(self, n)
131 
132  def __add__(self, n):
133  r"""__add__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
134  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___add__(self, n)
135 
136  def __sub__(self, *args):
137  r"""
138  __sub__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator
139  __sub__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> ptrdiff_t
140  """
141  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___sub__(self, *args)
142  def __iter__(self):
143  return self
144 
145 # Register IMP_SCRATCH_SwigPyIterator in _IMP_scratch:
146 _IMP_scratch.IMP_SCRATCH_SwigPyIterator_swigregister(IMP_SCRATCH_SwigPyIterator)
147 
148 _value_types=[]
149 _object_types=[]
150 _raii_types=[]
151 _plural_types=[]
152 
153 IMP_DEBUG = _IMP_scratch.IMP_DEBUG
154 
155 IMP_RELEASE = _IMP_scratch.IMP_RELEASE
156 
157 IMP_SILENT = _IMP_scratch.IMP_SILENT
158 
159 IMP_PROGRESS = _IMP_scratch.IMP_PROGRESS
160 
161 IMP_TERSE = _IMP_scratch.IMP_TERSE
162 
163 IMP_VERBOSE = _IMP_scratch.IMP_VERBOSE
164 
165 IMP_MEMORY = _IMP_scratch.IMP_MEMORY
166 
167 IMP_NONE = _IMP_scratch.IMP_NONE
168 
169 IMP_USAGE = _IMP_scratch.IMP_USAGE
170 
171 IMP_INTERNAL = _IMP_scratch.IMP_INTERNAL
172 
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_scratch.IMP_KERNEL_HAS_LOG4CXX
174 
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_scratch.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
176 
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_scratch.IMP_COMPILER_HAS_DEBUG_VECTOR
178 
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_scratch.IMP_COMPILER_HAS_RANDOM_SHUFFLE
180 
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_scratch.IMP_COMPILER_HAS_THREE_WAY
182 
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_scratch.IMP_KERNEL_HAS_BOOST_RANDOM
184 
185 IMP_KERNEL_HAS_NUMPY = _IMP_scratch.IMP_KERNEL_HAS_NUMPY
186 
187 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_scratch.IMP_KERNEL_HAS_GPERFTOOLS
188 
189 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_scratch.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
190 
191 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_scratch.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
192 
193 IMPKERNEL_SHOW_WARNINGS = _IMP_scratch.IMPKERNEL_SHOW_WARNINGS
194 
195 
196 import sys
197 class _DirectorObjects:
198  """@internal Simple class to keep references to director objects
199  to prevent premature deletion."""
200  def __init__(self):
201  self._objects = []
202  def register(self, obj):
203  """Take a reference to a director object; will only work for
204  refcounted C++ classes"""
205  if hasattr(obj, 'get_ref_count'):
206  self._objects.append(obj)
207  def cleanup(self):
208  """Only drop our reference and allow cleanup by Python if no other
209  Python references exist (we hold 3 references: one in self._objects,
210  one in x, and one in the argument list for getrefcount) *and* no
211  other C++ references exist (the Python object always holds one)"""
212  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
213  or x.get_ref_count() > 1]
214 # Do in two steps so the references are kept until the end of the
215 # function (deleting references may trigger a fresh call to this method)
216  self._objects = objs
217  def get_object_count(self):
218  """Get number of director objects (useful for testing only)"""
219  return len(self._objects)
220 _director_objects = _DirectorObjects()
221 
222 class _ostream(object):
223  r"""Proxy of C++ std::ostream class."""
224 
225  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
226 
227  def __init__(self, *args, **kwargs):
228  raise AttributeError("No constructor defined")
229  __repr__ = _swig_repr
230 
231  def write(self, osa_buf):
232  r"""write(_ostream self, char const * osa_buf)"""
233  return _IMP_scratch._ostream_write(self, osa_buf)
234 
235 # Register _ostream in _IMP_scratch:
236 _IMP_scratch._ostream_swigregister(_ostream)
237 IMP_C_OPEN_BINARY = _IMP_scratch.IMP_C_OPEN_BINARY
238 
239 import IMP
240 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CGAL_HAS_BOOST_FILESYSTEM
241 
242 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
243 
244 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CGAL_HAS_BOOST_RANDOM
245 
246 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CGAL_HAS_BOOST_SYSTEM
247 
248 IMP_CGAL_HAS_NUMPY = _IMP_scratch.IMP_CGAL_HAS_NUMPY
249 
250 IMPCGAL_SHOW_WARNINGS = _IMP_scratch.IMPCGAL_SHOW_WARNINGS
251 
252 import IMP.cgal
253 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_scratch.IMP_ALGEBRA_HAS_IMP_CGAL
254 
255 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
256 
257 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
258 
259 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_RANDOM
260 
261 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_SYSTEM
262 
263 IMP_ALGEBRA_HAS_CGAL = _IMP_scratch.IMP_ALGEBRA_HAS_CGAL
264 
265 IMP_ALGEBRA_HAS_NUMPY = _IMP_scratch.IMP_ALGEBRA_HAS_NUMPY
266 
267 IMP_ALGEBRA_HAS_ANN = _IMP_scratch.IMP_ALGEBRA_HAS_ANN
268 
269 IMPALGEBRA_SHOW_WARNINGS = _IMP_scratch.IMPALGEBRA_SHOW_WARNINGS
270 
271 import IMP.algebra
272 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_scratch.IMP_DISPLAY_HAS_IMP_CGAL
273 
274 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
275 
276 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
277 
278 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_RANDOM
279 
280 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_SYSTEM
281 
282 IMP_DISPLAY_HAS_CGAL = _IMP_scratch.IMP_DISPLAY_HAS_CGAL
283 
284 IMP_DISPLAY_HAS_NUMPY = _IMP_scratch.IMP_DISPLAY_HAS_NUMPY
285 
286 IMPDISPLAY_SHOW_WARNINGS = _IMP_scratch.IMPDISPLAY_SHOW_WARNINGS
287 
288 import IMP.display
289 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
290 
291 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
292 
293 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
294 
295 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
296 
297 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
298 
299 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_CGAL
300 
301 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_HDF5
302 
303 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_NUMPY
304 
305 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_scratch.IMPSCOREFUNCTOR_SHOW_WARNINGS
306 
307 import IMP.score_functor
308 IMP_CORE_HAS_IMP_CGAL = _IMP_scratch.IMP_CORE_HAS_IMP_CGAL
309 
310 IMP_CORE_HAS_IMP_KERNEL = _IMP_scratch.IMP_CORE_HAS_IMP_KERNEL
311 
312 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CORE_HAS_BOOST_FILESYSTEM
313 
314 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
315 
316 IMP_CORE_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CORE_HAS_BOOST_RANDOM
317 
318 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CORE_HAS_BOOST_SYSTEM
319 
320 IMP_CORE_HAS_CGAL = _IMP_scratch.IMP_CORE_HAS_CGAL
321 
322 IMP_CORE_HAS_HDF5 = _IMP_scratch.IMP_CORE_HAS_HDF5
323 
324 IMP_CORE_HAS_NUMPY = _IMP_scratch.IMP_CORE_HAS_NUMPY
325 
326 IMPCORE_SHOW_WARNINGS = _IMP_scratch.IMPCORE_SHOW_WARNINGS
327 
328 import IMP.core
329 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_scratch.IMP_CONTAINER_HAS_IMP_ALGEBRA
330 
331 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_scratch.IMP_CONTAINER_HAS_IMP_CGAL
332 
333 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_scratch.IMP_CONTAINER_HAS_IMP_DISPLAY
334 
335 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_scratch.IMP_CONTAINER_HAS_IMP_KERNEL
336 
337 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_scratch.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
338 
339 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
340 
341 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
342 
343 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_RANDOM
344 
345 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_SYSTEM
346 
347 IMP_CONTAINER_HAS_CGAL = _IMP_scratch.IMP_CONTAINER_HAS_CGAL
348 
349 IMP_CONTAINER_HAS_HDF5 = _IMP_scratch.IMP_CONTAINER_HAS_HDF5
350 
351 IMP_CONTAINER_HAS_NUMPY = _IMP_scratch.IMP_CONTAINER_HAS_NUMPY
352 
353 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_scratch.IMP_CONTAINER_HAS_PYTHON_IHM
354 
355 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_scratch.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
356 
357 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_scratch.IMP_CONTAINER_HAS_ROBIN_MAP
358 
359 IMPCONTAINER_SHOW_WARNINGS = _IMP_scratch.IMPCONTAINER_SHOW_WARNINGS
360 
361 import IMP.container
362 IMP_SCRATCH_HAS_IMP_ALGEBRA = _IMP_scratch.IMP_SCRATCH_HAS_IMP_ALGEBRA
363 
364 IMP_SCRATCH_HAS_IMP_CGAL = _IMP_scratch.IMP_SCRATCH_HAS_IMP_CGAL
365 
366 IMP_SCRATCH_HAS_IMP_DISPLAY = _IMP_scratch.IMP_SCRATCH_HAS_IMP_DISPLAY
367 
368 IMP_SCRATCH_HAS_IMP_KERNEL = _IMP_scratch.IMP_SCRATCH_HAS_IMP_KERNEL
369 
370 IMP_SCRATCH_HAS_IMP_SCORE_FUNCTOR = _IMP_scratch.IMP_SCRATCH_HAS_IMP_SCORE_FUNCTOR
371 
372 IMP_SCRATCH_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_FILESYSTEM
373 
374 IMP_SCRATCH_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_PROGRAMOPTIONS
375 
376 IMP_SCRATCH_HAS_BOOST_RANDOM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_RANDOM
377 
378 IMP_SCRATCH_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_SYSTEM
379 
380 IMP_SCRATCH_HAS_CGAL = _IMP_scratch.IMP_SCRATCH_HAS_CGAL
381 
382 IMP_SCRATCH_HAS_HDF5 = _IMP_scratch.IMP_SCRATCH_HAS_HDF5
383 
384 IMP_SCRATCH_HAS_NUMPY = _IMP_scratch.IMP_SCRATCH_HAS_NUMPY
385 
386 IMP_SCRATCH_HAS_PYTHON_IHM = _IMP_scratch.IMP_SCRATCH_HAS_PYTHON_IHM
387 
388 IMPSCRATCH_SHOW_WARNINGS = _IMP_scratch.IMPSCRATCH_SHOW_WARNINGS
389 
390 
391 def get_module_version():
392  r"""get_module_version() -> std::string const"""
393  return _IMP_scratch.get_module_version()
394 
395 def get_example_path(fname):
396  r"""get_example_path(std::string fname) -> std::string"""
397  return _IMP_scratch.get_example_path(fname)
398 
399 def get_data_path(fname):
400  r"""get_data_path(std::string fname) -> std::string"""
401  return _IMP_scratch.get_data_path(fname)
402 
403 from . import _version_check
404 _version_check.check_version(get_module_version())
405 __version__ = get_module_version()
406 
407 
def get_data_path
Return the full path to one of this module's data files.
def get_module_version
Return the version of this module, as a string.
def get_example_path
Return the full path to one of this module's example files.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
Composable functors to implement scores via compile-time composition.
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...
Output IMP model data in various file formats.