IMP logo
IMP Reference Guide  2.18.0
The Integrative Modeling Platform
kmeans/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.7
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 2007-2022 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 
16 
17 from sys import version_info
18 if version_info >= (2, 6, 0):
19  def swig_import_helper():
20  from os.path import dirname
21  import imp
22  fp = None
23  try:
24  fp, pathname, description = imp.find_module('_IMP_kmeans', [dirname(__file__)])
25  except ImportError:
26  import _IMP_kmeans
27  return _IMP_kmeans
28  if fp is not None:
29  try:
30  _mod = imp.load_module('_IMP_kmeans', fp, pathname, description)
31  finally:
32  fp.close()
33  return _mod
34  _IMP_kmeans = swig_import_helper()
35  del swig_import_helper
36 else:
37  import _IMP_kmeans
38 del version_info
39 try:
40  _swig_property = property
41 except NameError:
42  pass # Python < 2.2 doesn't have 'property'.
43 
44 
45 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
46  if (name == "thisown"):
47  return self.this.own(value)
48  if (name == "this"):
49  if type(value).__name__ == 'SwigPyObject':
50  self.__dict__[name] = value
51  return
52  method = class_type.__swig_setmethods__.get(name, None)
53  if method:
54  return method(self, value)
55  if (not static):
56  object.__setattr__(self, name, value)
57  else:
58  raise AttributeError("You cannot add attributes to %s" % self)
59 
60 
61 def _swig_setattr(self, class_type, name, value):
62  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
63 
64 
65 def _swig_getattr_nondynamic(self, class_type, name, static=1):
66  if (name == "thisown"):
67  return self.this.own()
68  method = class_type.__swig_getmethods__.get(name, None)
69  if method:
70  return method(self)
71  if (not static):
72  return object.__getattr__(self, name)
73  else:
74  raise AttributeError(name)
75 
76 def _swig_getattr(self, class_type, name):
77  return _swig_getattr_nondynamic(self, class_type, name, 0)
78 
79 
80 def _swig_repr(self):
81  try:
82  strthis = "proxy of " + self.this.__repr__()
83  except:
84  strthis = ""
85  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
86 
87 try:
88  _object = object
89  _newclass = 1
90 except AttributeError:
91  class _object:
92  pass
93  _newclass = 0
94 
95 
96 
97 def _swig_setattr_nondynamic_method(set):
98  def set_attr(self, name, value):
99  if (name == "thisown"):
100  return self.this.own(value)
101  if hasattr(self, name) or (name == "this"):
102  set(self, name, value)
103  else:
104  raise AttributeError("You cannot add attributes to %s" % self)
105  return set_attr
106 
107 
108 try:
109  import weakref
110  weakref_proxy = weakref.proxy
111 except:
112  weakref_proxy = lambda x: x
113 
114 
115 class IMP_KMEANS_SwigPyIterator(object):
116  """Proxy of C++ swig::IMP_KMEANS_SwigPyIterator class"""
117  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
118 
119  def __init__(self, *args, **kwargs):
120  raise AttributeError("No constructor defined - class is abstract")
121  __repr__ = _swig_repr
122  __swig_destroy__ = _IMP_kmeans.delete_IMP_KMEANS_SwigPyIterator
123  __del__ = lambda self: None
124 
125  def value(self):
126  """value(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
127  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_value(self)
128 
129 
130  def incr(self, n=1):
131  """
132  incr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
133  incr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
134  """
135  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_incr(self, n)
136 
137 
138  def decr(self, n=1):
139  """
140  decr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
141  decr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
142  """
143  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_decr(self, n)
144 
145 
146  def distance(self, x):
147  """distance(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t"""
148  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_distance(self, x)
149 
150 
151  def equal(self, x):
152  """equal(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
153  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_equal(self, x)
154 
155 
156  def copy(self):
157  """copy(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator"""
158  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_copy(self)
159 
160 
161  def next(self):
162  """next(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
163  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_next(self)
164 
165 
166  def __next__(self):
167  """__next__(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
168  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___next__(self)
169 
170 
171  def previous(self):
172  """previous(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
173  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_previous(self)
174 
175 
176  def advance(self, n):
177  """advance(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
178  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_advance(self, n)
179 
180 
181  def __eq__(self, x):
182  """__eq__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
183  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___eq__(self, x)
184 
185 
186  def __ne__(self, x):
187  """__ne__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
188  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___ne__(self, x)
189 
190 
191  def __iadd__(self, n):
192  """__iadd__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
193  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___iadd__(self, n)
194 
195 
196  def __isub__(self, n):
197  """__isub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
198  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___isub__(self, n)
199 
200 
201  def __add__(self, n):
202  """__add__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
203  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___add__(self, n)
204 
205 
206  def __sub__(self, *args):
207  """
208  __sub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator
209  __sub__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t
210  """
211  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___sub__(self, *args)
212 
213  def __iter__(self):
214  return self
215 IMP_KMEANS_SwigPyIterator_swigregister = _IMP_kmeans.IMP_KMEANS_SwigPyIterator_swigregister
216 IMP_KMEANS_SwigPyIterator_swigregister(IMP_KMEANS_SwigPyIterator)
217 
218 
219 _value_types=[]
220 _object_types=[]
221 _raii_types=[]
222 _plural_types=[]
223 
224 
225 _IMP_kmeans.IMP_DEBUG_swigconstant(_IMP_kmeans)
226 IMP_DEBUG = _IMP_kmeans.IMP_DEBUG
227 
228 _IMP_kmeans.IMP_RELEASE_swigconstant(_IMP_kmeans)
229 IMP_RELEASE = _IMP_kmeans.IMP_RELEASE
230 
231 _IMP_kmeans.IMP_SILENT_swigconstant(_IMP_kmeans)
232 IMP_SILENT = _IMP_kmeans.IMP_SILENT
233 
234 _IMP_kmeans.IMP_PROGRESS_swigconstant(_IMP_kmeans)
235 IMP_PROGRESS = _IMP_kmeans.IMP_PROGRESS
236 
237 _IMP_kmeans.IMP_TERSE_swigconstant(_IMP_kmeans)
238 IMP_TERSE = _IMP_kmeans.IMP_TERSE
239 
240 _IMP_kmeans.IMP_VERBOSE_swigconstant(_IMP_kmeans)
241 IMP_VERBOSE = _IMP_kmeans.IMP_VERBOSE
242 
243 _IMP_kmeans.IMP_MEMORY_swigconstant(_IMP_kmeans)
244 IMP_MEMORY = _IMP_kmeans.IMP_MEMORY
245 
246 _IMP_kmeans.IMP_NONE_swigconstant(_IMP_kmeans)
247 IMP_NONE = _IMP_kmeans.IMP_NONE
248 
249 _IMP_kmeans.IMP_USAGE_swigconstant(_IMP_kmeans)
250 IMP_USAGE = _IMP_kmeans.IMP_USAGE
251 
252 _IMP_kmeans.IMP_INTERNAL_swigconstant(_IMP_kmeans)
253 IMP_INTERNAL = _IMP_kmeans.IMP_INTERNAL
254 
255 _IMP_kmeans.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_kmeans)
256 IMP_KERNEL_HAS_LOG4CXX = _IMP_kmeans.IMP_KERNEL_HAS_LOG4CXX
257 
258 _IMP_kmeans.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_kmeans)
259 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kmeans.IMP_COMPILER_HAS_DEBUG_VECTOR
260 
261 _IMP_kmeans.IMP_COMPILER_HAS_RANDOM_SHUFFLE_swigconstant(_IMP_kmeans)
262 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_kmeans.IMP_COMPILER_HAS_RANDOM_SHUFFLE
263 
264 _IMP_kmeans.IMP_COMPILER_HAS_THREE_WAY_swigconstant(_IMP_kmeans)
265 IMP_COMPILER_HAS_THREE_WAY = _IMP_kmeans.IMP_COMPILER_HAS_THREE_WAY
266 
267 _IMP_kmeans.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_kmeans)
268 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KERNEL_HAS_BOOST_RANDOM
269 
270 _IMP_kmeans.IMP_KERNEL_HAS_NUMPY_swigconstant(_IMP_kmeans)
271 IMP_KERNEL_HAS_NUMPY = _IMP_kmeans.IMP_KERNEL_HAS_NUMPY
272 
273 _IMP_kmeans.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_kmeans)
274 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kmeans.IMP_KERNEL_HAS_GPERFTOOLS
275 
276 _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_kmeans)
277 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
278 
279 _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_kmeans)
280 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
281 
282 _IMP_kmeans.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_kmeans)
283 IMPKERNEL_SHOW_WARNINGS = _IMP_kmeans.IMPKERNEL_SHOW_WARNINGS
284 
285 import sys
286 class _DirectorObjects(object):
287  """@internal Simple class to keep references to director objects
288  to prevent premature deletion."""
289  def __init__(self):
290  self._objects = []
291  def register(self, obj):
292  """Take a reference to a director object; will only work for
293  refcounted C++ classes"""
294  if hasattr(obj, 'get_ref_count'):
295  self._objects.append(obj)
296  def cleanup(self):
297  """Only drop our reference and allow cleanup by Python if no other
298  Python references exist (we hold 3 references: one in self._objects,
299  one in x, and one in the argument list for getrefcount) *and* no
300  other C++ references exist (the Python object always holds one)"""
301  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
302  or x.get_ref_count() > 1]
303 # Do in two steps so the references are kept until the end of the
304 # function (deleting references may trigger a fresh call to this method)
305  self._objects = objs
306  def get_object_count(self):
307  """Get number of director objects (useful for testing only)"""
308  return len(self._objects)
309 _director_objects = _DirectorObjects()
310 
311 class _ostream(object):
312  """Proxy of C++ std::ostream class"""
313  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
314 
315  def __init__(self, *args, **kwargs):
316  raise AttributeError("No constructor defined")
317  __repr__ = _swig_repr
318 
319  def write(self, osa_buf):
320  """write(_ostream self, char const * osa_buf)"""
321  return _IMP_kmeans._ostream_write(self, osa_buf)
322 
323 _ostream_swigregister = _IMP_kmeans._ostream_swigregister
324 _ostream_swigregister(_ostream)
325 
326 
327 _IMP_kmeans.IMP_HAS_NOEXCEPT_swigconstant(_IMP_kmeans)
328 IMP_HAS_NOEXCEPT = _IMP_kmeans.IMP_HAS_NOEXCEPT
329 
330 _IMP_kmeans.IMP_C_OPEN_BINARY_swigconstant(_IMP_kmeans)
331 IMP_C_OPEN_BINARY = _IMP_kmeans.IMP_C_OPEN_BINARY
332 import IMP
333 
334 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_kmeans)
335 IMP_KMEANS_HAS_BOOST_FILESYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_FILESYSTEM
336 
337 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_kmeans)
338 IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS
339 
340 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_RANDOM_swigconstant(_IMP_kmeans)
341 IMP_KMEANS_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_RANDOM
342 
343 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SERIALIZATION_swigconstant(_IMP_kmeans)
344 IMP_KMEANS_HAS_BOOST_SERIALIZATION = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SERIALIZATION
345 
346 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SYSTEM_swigconstant(_IMP_kmeans)
347 IMP_KMEANS_HAS_BOOST_SYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SYSTEM
348 
349 _IMP_kmeans.IMP_KMEANS_HAS_NUMPY_swigconstant(_IMP_kmeans)
350 IMP_KMEANS_HAS_NUMPY = _IMP_kmeans.IMP_KMEANS_HAS_NUMPY
351 
352 _IMP_kmeans.IMPKMEANS_SHOW_WARNINGS_swigconstant(_IMP_kmeans)
353 IMPKMEANS_SHOW_WARNINGS = _IMP_kmeans.IMPKMEANS_SHOW_WARNINGS
354 
355 _object_types.append("KMeans")
356 
357 
358 def _object_cast_to_KMeans(o):
359  """_object_cast_to_KMeans(Object o) -> KMeans"""
360  return _IMP_kmeans._object_cast_to_KMeans(o)
361 
362 _IMP_kmeans.KM_LLOYDS_swigconstant(_IMP_kmeans)
363 KM_LLOYDS = _IMP_kmeans.KM_LLOYDS
364 
365 _IMP_kmeans.KM_LOCAL_SWAP_swigconstant(_IMP_kmeans)
366 KM_LOCAL_SWAP = _IMP_kmeans.KM_LOCAL_SWAP
367 
368 _IMP_kmeans.KM_LOCAL_EZ_HYBRID_swigconstant(_IMP_kmeans)
369 KM_LOCAL_EZ_HYBRID = _IMP_kmeans.KM_LOCAL_EZ_HYBRID
370 
371 _IMP_kmeans.KM_HYBRID_swigconstant(_IMP_kmeans)
372 KM_HYBRID = _IMP_kmeans.KM_HYBRID
373 class KMeans(IMP.Object):
374  """Proxy of C++ IMP::kmeans::KMeans class"""
375  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
376 
377  def __init__(self, *args):
378  """
379  __init__(IMP::kmeans::KMeans self, std::string const & fname_data, int dim, unsigned int max_nPts) -> KMeans
380  __init__(IMP::kmeans::KMeans self) -> KMeans
381  """
382  this = _IMP_kmeans.new_KMeans(*args)
383  try:
384  self.this.append(this)
385  except:
386  self.this = this
387 
388  def get_version_info(self):
389  """get_version_info(KMeans self) -> VersionInfo"""
390  return _IMP_kmeans.KMeans_get_version_info(self)
391 
392 
393  def execute(self, *args):
394  """
395  execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type, int stages=100)
396  execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type)
397  execute(KMeans self, unsigned int k)
398  """
399  return _IMP_kmeans.KMeans_execute(self, *args)
400 
401 
402  def add_data_pt(self, p):
403  """add_data_pt(KMeans self, IMP::Floats const & p)"""
404  return _IMP_kmeans.KMeans_add_data_pt(self, p)
405 
406 
407  def clear_data(self):
408  """clear_data(KMeans self)"""
409  return _IMP_kmeans.KMeans_clear_data(self)
410 
411 
412  def get_data_point(self, i):
413  """get_data_point(KMeans self, unsigned int i) -> IMP::Floats const &"""
414  return _IMP_kmeans.KMeans_get_data_point(self, i)
415 
416 
417  def get_number_of_data_points(self):
418  """get_number_of_data_points(KMeans self) -> unsigned int"""
419  return _IMP_kmeans.KMeans_get_number_of_data_points(self)
420 
421 
422  def print_centers(self, *args):
423  """
424  print_centers(KMeans self, IMP::LogLevel ll)
425  print_centers(KMeans self)
426  """
427  return _IMP_kmeans.KMeans_print_centers(self, *args)
428 
429 
430  def get_center(self, i):
431  """get_center(KMeans self, unsigned int i) -> IMP::Floats"""
432  return _IMP_kmeans.KMeans_get_center(self, i)
433 
434 
435  def get_assignments(self):
436  """get_assignments(KMeans self) -> IMP::Ints"""
437  return _IMP_kmeans.KMeans_get_assignments(self)
438 
439 
440  def get_squared_distance_to_centers(self):
441  """get_squared_distance_to_centers(KMeans self) -> IMP::Floats"""
442  return _IMP_kmeans.KMeans_get_squared_distance_to_centers(self)
443 
444 
445  def get_number_of_centers(self):
446  """get_number_of_centers(KMeans self) -> unsigned int"""
447  return _IMP_kmeans.KMeans_get_number_of_centers(self)
448 
449 
450  def __str__(self):
451  """__str__(KMeans self) -> std::string"""
452  return _IMP_kmeans.KMeans___str__(self)
453 
454 
455  def __repr__(self):
456  """__repr__(KMeans self) -> std::string"""
457  return _IMP_kmeans.KMeans___repr__(self)
458 
459 
460  @staticmethod
461  def get_from(o):
462  return _object_cast_to_KMeans(o)
463 
464 KMeans_swigregister = _IMP_kmeans.KMeans_swigregister
465 KMeans_swigregister(KMeans)
466 
467 
468 def get_module_version():
469  """get_module_version() -> std::string const"""
470  return _IMP_kmeans.get_module_version()
471 
472 def get_example_path(fname):
473  """get_example_path(std::string fname) -> std::string"""
474  return _IMP_kmeans.get_example_path(fname)
475 
476 def get_data_path(fname):
477  """get_data_path(std::string fname) -> std::string"""
478  return _IMP_kmeans.get_data_path(fname)
479 
480 from . import _version_check
481 _version_check.check_version(get_module_version())
482 __version__ = get_module_version()
483 
484 
485 
Common base class for heavy weight IMP objects.
Definition: Object.h:106
std::string get_module_version()
Return the version of this module, as a string.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.