IMP logo
IMP Reference Guide  2.6.0
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 # This wrapper is part of IMP,
8 # Copyright 2007-2016 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_kmeans', [dirname(__file__)])
23  except ImportError:
24  import _IMP_kmeans
25  return _IMP_kmeans
26  if fp is not None:
27  try:
28  _mod = imp.load_module('_IMP_kmeans', fp, pathname, description)
29  finally:
30  fp.close()
31  return _mod
32  _IMP_kmeans = swig_import_helper()
33  del swig_import_helper
34 else:
35  import _IMP_kmeans
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_KMEANS_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_KMEANS_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_kmeans.delete_IMP_KMEANS_SwigPyIterator
121  __del__ = lambda self: None
122 
123  def value(self):
124  """value(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
125  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_value(self)
126 
127 
128  def incr(self, n=1):
129  """
130  incr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
131  incr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
132  """
133  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_incr(self, n)
134 
135 
136  def decr(self, n=1):
137  """
138  decr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
139  decr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
140  """
141  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_decr(self, n)
142 
143 
144  def distance(self, x):
145  """distance(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t"""
146  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_distance(self, x)
147 
148 
149  def equal(self, x):
150  """equal(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
151  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_equal(self, x)
152 
153 
154  def copy(self):
155  """copy(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator"""
156  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_copy(self)
157 
158 
159  def next(self):
160  """next(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
161  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_next(self)
162 
163 
164  def __next__(self):
165  """__next__(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
166  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___next__(self)
167 
168 
169  def previous(self):
170  """previous(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
171  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_previous(self)
172 
173 
174  def advance(self, n):
175  """advance(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
176  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_advance(self, n)
177 
178 
179  def __eq__(self, x):
180  """__eq__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
181  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___eq__(self, x)
182 
183 
184  def __ne__(self, x):
185  """__ne__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
186  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___ne__(self, x)
187 
188 
189  def __iadd__(self, n):
190  """__iadd__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
191  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___iadd__(self, n)
192 
193 
194  def __isub__(self, n):
195  """__isub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
196  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___isub__(self, n)
197 
198 
199  def __add__(self, n):
200  """__add__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
201  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___add__(self, n)
202 
203 
204  def __sub__(self, *args):
205  """
206  __sub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator
207  __sub__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t
208  """
209  return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___sub__(self, *args)
210 
211  def __iter__(self):
212  return self
213 IMP_KMEANS_SwigPyIterator_swigregister = _IMP_kmeans.IMP_KMEANS_SwigPyIterator_swigregister
214 IMP_KMEANS_SwigPyIterator_swigregister(IMP_KMEANS_SwigPyIterator)
215 
216 
217 _value_types=[]
218 _object_types=[]
219 _raii_types=[]
220 _plural_types=[]
221 
222 
223 _IMP_kmeans.IMP_DEBUG_swigconstant(_IMP_kmeans)
224 IMP_DEBUG = _IMP_kmeans.IMP_DEBUG
225 
226 _IMP_kmeans.IMP_RELEASE_swigconstant(_IMP_kmeans)
227 IMP_RELEASE = _IMP_kmeans.IMP_RELEASE
228 
229 _IMP_kmeans.IMP_SILENT_swigconstant(_IMP_kmeans)
230 IMP_SILENT = _IMP_kmeans.IMP_SILENT
231 
232 _IMP_kmeans.IMP_PROGRESS_swigconstant(_IMP_kmeans)
233 IMP_PROGRESS = _IMP_kmeans.IMP_PROGRESS
234 
235 _IMP_kmeans.IMP_TERSE_swigconstant(_IMP_kmeans)
236 IMP_TERSE = _IMP_kmeans.IMP_TERSE
237 
238 _IMP_kmeans.IMP_VERBOSE_swigconstant(_IMP_kmeans)
239 IMP_VERBOSE = _IMP_kmeans.IMP_VERBOSE
240 
241 _IMP_kmeans.IMP_MEMORY_swigconstant(_IMP_kmeans)
242 IMP_MEMORY = _IMP_kmeans.IMP_MEMORY
243 
244 _IMP_kmeans.IMP_NONE_swigconstant(_IMP_kmeans)
245 IMP_NONE = _IMP_kmeans.IMP_NONE
246 
247 _IMP_kmeans.IMP_USAGE_swigconstant(_IMP_kmeans)
248 IMP_USAGE = _IMP_kmeans.IMP_USAGE
249 
250 _IMP_kmeans.IMP_INTERNAL_swigconstant(_IMP_kmeans)
251 IMP_INTERNAL = _IMP_kmeans.IMP_INTERNAL
252 
253 _IMP_kmeans.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_kmeans)
254 IMP_KERNEL_HAS_LOG4CXX = _IMP_kmeans.IMP_KERNEL_HAS_LOG4CXX
255 
256 _IMP_kmeans.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_kmeans)
257 IMP_COMPILER_HAS_AUTO = _IMP_kmeans.IMP_COMPILER_HAS_AUTO
258 
259 _IMP_kmeans.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_kmeans)
260 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kmeans.IMP_COMPILER_HAS_DEBUG_VECTOR
261 
262 _IMP_kmeans.IMP_COMPILER_HAS_UNIQUE_PTR_swigconstant(_IMP_kmeans)
263 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_kmeans.IMP_COMPILER_HAS_UNIQUE_PTR
264 
265 _IMP_kmeans.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_kmeans)
266 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KERNEL_HAS_BOOST_RANDOM
267 
268 _IMP_kmeans.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_kmeans)
269 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kmeans.IMP_KERNEL_HAS_GPERFTOOLS
270 
271 _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_kmeans)
272 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
273 
274 _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_kmeans)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
276 
277 _IMP_kmeans.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_kmeans)
278 IMPKERNEL_SHOW_WARNINGS = _IMP_kmeans.IMPKERNEL_SHOW_WARNINGS
279 
280 import sys
281 class _DirectorObjects(object):
282  """@internal Simple class to keep references to director objects
283  to prevent premature deletion."""
284  def __init__(self):
285  self._objects = []
286  def register(self, obj):
287  """Take a reference to a director object; will only work for
288  refcounted C++ classes"""
289  if hasattr(obj, 'get_ref_count'):
290  self._objects.append(obj)
291  def cleanup(self):
292  """Only drop our reference and allow cleanup by Python if no other
293  Python references exist (we hold 3 references: one in self._objects,
294  one in x, and one in the argument list for getrefcount) *and* no
295  other C++ references exist (the Python object always holds one)"""
296  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
297  or x.get_ref_count() > 1]
298 # Do in two steps so the references are kept until the end of the
299 # function (deleting references may trigger a fresh call to this method)
300  self._objects = objs
301  def get_object_count(self):
302  """Get number of director objects (useful for testing only)"""
303  return len(self._objects)
304 _director_objects = _DirectorObjects()
305 
306 class _ostream(object):
307  """Proxy of C++ std::ostream class"""
308  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
309 
310  def __init__(self, *args, **kwargs):
311  raise AttributeError("No constructor defined")
312  __repr__ = _swig_repr
313 
314  def write(self, osa_buf):
315  """write(_ostream self, char const * osa_buf)"""
316  return _IMP_kmeans._ostream_write(self, osa_buf)
317 
318 _ostream_swigregister = _IMP_kmeans._ostream_swigregister
319 _ostream_swigregister(_ostream)
320 
321 
322 _IMP_kmeans.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_kmeans)
323 IMP_COMPILER_HAS_OVERRIDE = _IMP_kmeans.IMP_COMPILER_HAS_OVERRIDE
324 
325 _IMP_kmeans.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_kmeans)
326 IMP_COMPILER_HAS_FINAL = _IMP_kmeans.IMP_COMPILER_HAS_FINAL
327 
328 _IMP_kmeans.IMP_HAS_NOEXCEPT_swigconstant(_IMP_kmeans)
329 IMP_HAS_NOEXCEPT = _IMP_kmeans.IMP_HAS_NOEXCEPT
330 import IMP
331 
332 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_kmeans)
333 IMP_KMEANS_HAS_BOOST_FILESYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_FILESYSTEM
334 
335 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_kmeans)
336 IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS
337 
338 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_RANDOM_swigconstant(_IMP_kmeans)
339 IMP_KMEANS_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_RANDOM
340 
341 _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SYSTEM_swigconstant(_IMP_kmeans)
342 IMP_KMEANS_HAS_BOOST_SYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SYSTEM
343 
344 _IMP_kmeans.IMPKMEANS_SHOW_WARNINGS_swigconstant(_IMP_kmeans)
345 IMPKMEANS_SHOW_WARNINGS = _IMP_kmeans.IMPKMEANS_SHOW_WARNINGS
346 
347 _object_types.append("KMeans")
348 
349 
350 def _object_cast_to_KMeans(o):
351  """_object_cast_to_KMeans(Object o) -> KMeans"""
352  return _IMP_kmeans._object_cast_to_KMeans(o)
353 
354 _IMP_kmeans.KM_LLOYDS_swigconstant(_IMP_kmeans)
355 KM_LLOYDS = _IMP_kmeans.KM_LLOYDS
356 
357 _IMP_kmeans.KM_LOCAL_SWAP_swigconstant(_IMP_kmeans)
358 KM_LOCAL_SWAP = _IMP_kmeans.KM_LOCAL_SWAP
359 
360 _IMP_kmeans.KM_LOCAL_EZ_HYBRID_swigconstant(_IMP_kmeans)
361 KM_LOCAL_EZ_HYBRID = _IMP_kmeans.KM_LOCAL_EZ_HYBRID
362 
363 _IMP_kmeans.KM_HYBRID_swigconstant(_IMP_kmeans)
364 KM_HYBRID = _IMP_kmeans.KM_HYBRID
365 class KMeans(IMP.Object):
366  """Proxy of C++ IMP::kmeans::KMeans class"""
367  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
368 
369  def __init__(self, *args):
370  """
371  __init__(IMP::kmeans::KMeans self, std::string const & fname_data, int dim, unsigned int max_nPts) -> KMeans
372  __init__(IMP::kmeans::KMeans self) -> KMeans
373  """
374  this = _IMP_kmeans.new_KMeans(*args)
375  try:
376  self.this.append(this)
377  except:
378  self.this = this
379 
380  def get_version_info(self):
381  """get_version_info(KMeans self) -> VersionInfo"""
382  return _IMP_kmeans.KMeans_get_version_info(self)
383 
384 
385  def execute(self, *args):
386  """
387  execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type, int stages=100)
388  execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type)
389  execute(KMeans self, unsigned int k)
390  """
391  return _IMP_kmeans.KMeans_execute(self, *args)
392 
393 
394  def add_data_pt(self, p):
395  """add_data_pt(KMeans self, IMP::Floats const & p)"""
396  return _IMP_kmeans.KMeans_add_data_pt(self, p)
397 
398 
399  def clear_data(self):
400  """clear_data(KMeans self)"""
401  return _IMP_kmeans.KMeans_clear_data(self)
402 
403 
404  def get_data_point(self, i):
405  """get_data_point(KMeans self, unsigned int i) -> IMP::Floats const &"""
406  return _IMP_kmeans.KMeans_get_data_point(self, i)
407 
408 
409  def get_number_of_data_points(self):
410  """get_number_of_data_points(KMeans self) -> unsigned int"""
411  return _IMP_kmeans.KMeans_get_number_of_data_points(self)
412 
413 
414  def print_centers(self, *args):
415  """
416  print_centers(KMeans self, IMP::LogLevel ll)
417  print_centers(KMeans self)
418  """
419  return _IMP_kmeans.KMeans_print_centers(self, *args)
420 
421 
422  def get_center(self, i):
423  """get_center(KMeans self, unsigned int i) -> IMP::Floats"""
424  return _IMP_kmeans.KMeans_get_center(self, i)
425 
426 
427  def get_assignments(self):
428  """get_assignments(KMeans self) -> IMP::Ints"""
429  return _IMP_kmeans.KMeans_get_assignments(self)
430 
431 
432  def get_squared_distance_to_centers(self):
433  """get_squared_distance_to_centers(KMeans self) -> IMP::Floats"""
434  return _IMP_kmeans.KMeans_get_squared_distance_to_centers(self)
435 
436 
437  def get_number_of_centers(self):
438  """get_number_of_centers(KMeans self) -> unsigned int"""
439  return _IMP_kmeans.KMeans_get_number_of_centers(self)
440 
441 
442  def __str__(self):
443  """__str__(KMeans self) -> std::string"""
444  return _IMP_kmeans.KMeans___str__(self)
445 
446 
447  def __repr__(self):
448  """__repr__(KMeans self) -> std::string"""
449  return _IMP_kmeans.KMeans___repr__(self)
450 
451 
452  @staticmethod
453  def get_from(o):
454  return _object_cast_to_KMeans(o)
455 
456 KMeans_swigregister = _IMP_kmeans.KMeans_swigregister
457 KMeans_swigregister(KMeans)
458 
459 
460 def get_module_version():
461  """get_module_version() -> std::string const"""
462  return _IMP_kmeans.get_module_version()
463 
464 def get_example_path(fname):
465  """get_example_path(std::string fname) -> std::string"""
466  return _IMP_kmeans.get_example_path(fname)
467 
468 def get_data_path(fname):
469  """get_data_path(std::string fname) -> std::string"""
470  return _IMP_kmeans.get_data_path(fname)
471 
472 from . import _version_check
473 _version_check.check_version(get_module_version())
474 __version__ = get_module_version()
475 
476 
477 
Common base class for heavy weight IMP objects.
Definition: Object.h:106
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.