10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_modeller')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_modeller')
25 _IMP_modeller = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_modeller', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_modeller', fp, pathname, description)
43 _IMP_modeller = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_MODELLER_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_MODELLER_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_modeller.delete_IMP_MODELLER_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
126 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_value(self)
131 incr(IMP_MODELLER_SwigPyIterator self, size_t n=1) -> IMP_MODELLER_SwigPyIterator
132 incr(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator
134 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_incr(self, n)
139 decr(IMP_MODELLER_SwigPyIterator self, size_t n=1) -> IMP_MODELLER_SwigPyIterator
140 decr(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator
142 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_distance(self, x)
151 """equal(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
152 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_equal(self, x)
156 """copy(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator"""
157 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_copy(self)
161 """next(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
162 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_next(self)
166 """__next__(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
167 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___next__(self)
171 """previous(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
172 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
177 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
182 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
187 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
192 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
197 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
202 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator
208 __sub__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___sub__(self, *args)
214 IMP_MODELLER_SwigPyIterator_swigregister = _IMP_modeller.IMP_MODELLER_SwigPyIterator_swigregister
215 IMP_MODELLER_SwigPyIterator_swigregister(IMP_MODELLER_SwigPyIterator)
223 IMP_DEBUG = _IMP_modeller.IMP_DEBUG
224 IMP_RELEASE = _IMP_modeller.IMP_RELEASE
225 IMP_SILENT = _IMP_modeller.IMP_SILENT
226 IMP_PROGRESS = _IMP_modeller.IMP_PROGRESS
227 IMP_TERSE = _IMP_modeller.IMP_TERSE
228 IMP_VERBOSE = _IMP_modeller.IMP_VERBOSE
229 IMP_MEMORY = _IMP_modeller.IMP_MEMORY
230 IMP_NONE = _IMP_modeller.IMP_NONE
231 IMP_USAGE = _IMP_modeller.IMP_USAGE
232 IMP_INTERNAL = _IMP_modeller.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_modeller.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_modeller.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_modeller.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_modeller.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_modeller.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_modeller.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_modeller.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_modeller.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_modeller.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_modeller._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_modeller._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_modeller.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_modeller.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_modeller.IMP_HAS_NOEXCEPT
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_modeller.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_modeller.IMPCGAL_SHOW_WARNINGS
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_modeller.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_modeller.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_modeller.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_modeller.IMPALGEBRA_SHOW_WARNINGS
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_modeller.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_modeller.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_modeller.IMPDISPLAY_SHOW_WARNINGS
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_modeller.IMPSCOREFUNCTOR_SHOW_WARNINGS
321 IMP_CORE_HAS_IMP_CGAL = _IMP_modeller.IMP_CORE_HAS_IMP_CGAL
322 IMP_CORE_HAS_IMP_KERNEL = _IMP_modeller.IMP_CORE_HAS_IMP_KERNEL
323 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_CORE_HAS_BOOST_FILESYSTEM
324 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
325 IMP_CORE_HAS_BOOST_RANDOM = _IMP_modeller.IMP_CORE_HAS_BOOST_RANDOM
326 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_CORE_HAS_BOOST_SYSTEM
327 IMP_CORE_HAS_CGAL = _IMP_modeller.IMP_CORE_HAS_CGAL
328 IMP_CORE_HAS_HDF5 = _IMP_modeller.IMP_CORE_HAS_HDF5
329 IMPCORE_SHOW_WARNINGS = _IMP_modeller.IMPCORE_SHOW_WARNINGS
331 IMP_MODELLER_HAS_IMP_ALGEBRA = _IMP_modeller.IMP_MODELLER_HAS_IMP_ALGEBRA
332 IMP_MODELLER_HAS_IMP_CGAL = _IMP_modeller.IMP_MODELLER_HAS_IMP_CGAL
333 IMP_MODELLER_HAS_IMP_DISPLAY = _IMP_modeller.IMP_MODELLER_HAS_IMP_DISPLAY
334 IMP_MODELLER_HAS_IMP_KERNEL = _IMP_modeller.IMP_MODELLER_HAS_IMP_KERNEL
335 IMP_MODELLER_HAS_IMP_SCORE_FUNCTOR = _IMP_modeller.IMP_MODELLER_HAS_IMP_SCORE_FUNCTOR
336 IMP_MODELLER_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_FILESYSTEM
337 IMP_MODELLER_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_MODELLER_HAS_BOOST_PROGRAMOPTIONS
338 IMP_MODELLER_HAS_BOOST_RANDOM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_RANDOM
339 IMP_MODELLER_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_SYSTEM
340 IMP_MODELLER_HAS_CGAL = _IMP_modeller.IMP_MODELLER_HAS_CGAL
341 IMP_MODELLER_HAS_HDF5 = _IMP_modeller.IMP_MODELLER_HAS_HDF5
342 IMPMODELLER_SHOW_WARNINGS = _IMP_modeller.IMPMODELLER_SHOW_WARNINGS
353 import modeller.scripts
354 import modeller.optimizers
356 class _TempDir(object):
357 """Make a temporary directory that is deleted when the object is."""
360 self.tmpdir = tempfile.mkdtemp()
363 shutil.rmtree(self.tmpdir, ignore_errors=
True)
367 """A Modeller restraint which evaluates an IMP scoring function.
368 This can be used to incorporate IMP Restraints into an existing
369 comparative modeling pipeline, or to use Modeller optimizers or
373 _physical_type = modeller.physical.absposition
375 def __init__(self, particles, scoring_function=None):
377 @param particles A list of the IMP atoms (as Particle objects),
378 same order as the Modeller atoms.
379 @param scoring_function An IMP::ScoringFunction object that will
380 be incorporated into the Modeller score (molpdf).
381 @note since Modeller, unlike IMP, is sensitive to the ordering
382 of atoms, it usually makes sense to create the model in
383 Modeller and then use ModelLoader to load it into IMP,
384 since that will preserve the Modeller atom ordering in IMP.
386 modeller.terms.energy_term.__init__(self)
387 self._particles = particles
389 self._sf = scoring_function
391 self._sf = particles[0].get_model()
393 def eval(self, mdl, deriv, indats):
394 atoms = self.indices_to_atoms(mdl, indats)
395 _copy_modeller_coords_to_imp(atoms, self._particles)
396 if len(self._particles) == 0:
399 score = self._sf.evaluate(deriv)
401 dvx = [0.] * len(indats)
402 dvy = [0.] * len(indats)
403 dvz = [0.] * len(indats)
404 _get_imp_derivs(self._particles, dvx, dvy, dvz)
405 return (score, dvx, dvy, dvz)
411 """An IMP restraint using all defined Modeller restraints.
412 This is useful if you want to use Modeller restraints with an IMP
413 optimizer, or in combination with IMP restraints.
415 @note Currently only the coordinates of the atoms are translated
416 between Modeller and IMP; thus, a Modeller restraint which
417 uses any other attribute (e.g. charge) will not react if
418 this attribute is changed by IMP.
421 def __init__(self, model, modeller_model, particles):
423 @param model The IMP Model object.
424 @param modeller_model The Modeller model object.
425 @param particles A list of the IMP atoms (as Particle objects),
426 in the same order as the Modeller atoms.
427 @note since Modeller, unlike IMP, is sensitive to the ordering
428 of atoms, it usually makes sense to create the model in
429 Modeller and then use ModelLoader to load it into IMP,
430 since that will preserve the Modeller atom ordering in IMP.
433 if hasattr(x,
'get_particle'):
434 return x.get_particle()
437 IMP.Restraint.__init__(self, model,
"ModellerRestraints %1%")
438 self._modeller_model = modeller_model
439 self._particles = [get_particle(x)
for x
in particles]
441 def unprotected_evaluate(self, accum):
442 atoms = self._modeller_model.atoms
443 sel = modeller.selection(self._modeller_model)
444 _copy_imp_coords_to_modeller(self._particles, atoms)
445 energies = sel.energy()
447 _add_modeller_derivs_to_imp(atoms, self._particles, accum)
453 def do_show(self, fh):
454 fh.write(
"ModellerRestraints")
456 return self._particles
459 def _copy_imp_coords_to_modeller(particles, atoms):
460 """Copy atom coordinates from IMP to Modeller"""
464 for (num, at)
in enumerate(atoms):
465 at.x = particles[num].get_value(xkey)
466 at.y = particles[num].get_value(ykey)
467 at.z = particles[num].get_value(zkey)
470 def _copy_modeller_coords_to_imp(atoms, particles):
471 """Copy atom coordinates from Modeller to IMP"""
475 for (num, at)
in enumerate(atoms):
476 particles[num].set_value(xkey, at.x)
477 particles[num].set_value(ykey, at.y)
478 particles[num].set_value(zkey, at.z)
481 def _add_modeller_derivs_to_imp(atoms, particles, accum):
482 """Add atom derivatives from Modeller to IMP"""
483 for (num, at)
in enumerate(atoms):
485 xyz.add_to_derivative(0, at.dvx, accum)
486 xyz.add_to_derivative(1, at.dvy, accum)
487 xyz.add_to_derivative(2, at.dvz, accum)
490 def _get_imp_derivs(particles, dvx, dvy, dvz):
491 """Move atom derivatives from IMP to Modeller"""
495 for idx
in range(0, len(dvx)):
496 dvx[idx] = particles[idx].get_derivative(xkey)
497 dvy[idx] = particles[idx].get_derivative(ykey)
498 dvz[idx] = particles[idx].get_derivative(zkey)
502 def _HarmonicLowerBoundGenerator(parameters, modalities):
503 (mean, stdev) = parameters
507 def _HarmonicUpperBoundGenerator(parameters, modalities):
508 (mean, stdev) = parameters
512 def _HarmonicGenerator(parameters, modalities):
513 (mean, stdev) = parameters
517 def _CosineGenerator(parameters, modalities):
518 (phase, force_constant) = parameters
519 (periodicity,) = modalities
522 def _LinearGenerator(parameters, modalities):
523 (scale,) = parameters
526 def _SplineGenerator(parameters, modalities):
527 (open, low, high, delta, lowderiv, highderiv) = parameters[:6]
529 for v
in parameters[6:]:
537 _unary_func_generators = {
538 1: _HarmonicLowerBoundGenerator,
539 2: _HarmonicUpperBoundGenerator,
540 3: _HarmonicGenerator,
543 10: _SplineGenerator,
547 def _DistanceRestraintGenerator(form, modalities, atoms, parameters):
548 unary_func_gen = _unary_func_generators[form]
550 unary_func_gen(parameters, modalities),
553 def _AngleRestraintGenerator(form, modalities, atoms, parameters):
554 unary_func_gen = _unary_func_generators[form]
556 unary_func_gen(parameters, modalities),
557 atoms[0], atoms[1], atoms[2])
559 def _MultiBinormalGenerator(form, modalities, atoms, parameters):
560 nterms = modalities[0]
561 if len(parameters) != nterms * 6:
562 raise ValueError(
"Incorrect number of parameters (%d) for multiple "
563 "binormal restraint - expecting %d (%d terms * 6)" \
564 % (len(parameters), nterms * 6, nterms))
566 atoms[:4], atoms[4:8])
567 for i
in range(nterms):
569 t.set_weight(parameters[i])
570 t.set_means((parameters[nterms + i * 2],
571 parameters[nterms + i * 2 + 1]))
572 t.set_standard_deviations((parameters[nterms * 3 + i * 2],
573 parameters[nterms * 3 + i * 2 + 1]))
574 t.set_correlation(parameters[nterms * 5 + i])
578 def _DihedralRestraintGenerator(form, modalities, atoms, parameters):
580 return _MultiBinormalGenerator(form, modalities, atoms, parameters)
581 unary_func_gen = _unary_func_generators[form]
583 unary_func_gen(parameters, modalities),
584 atoms[0], atoms[1], atoms[2], atoms[3])
586 def _get_protein_atom_particles(protein):
587 """Given a protein particle, get the flattened list of all child atoms"""
589 for ichain
in range(protein.get_number_of_children()):
590 chain = protein.get_child(ichain)
591 for ires
in range(chain.get_number_of_children()):
592 residue = chain.get_child(ires)
593 for iatom
in range(residue.get_number_of_children()):
594 atom = residue.get_child(iatom)
595 atom_particles.append(atom.get_particle())
596 return atom_particles
598 def _load_restraints_line(line, atom_particles):
599 """Parse a single Modeller restraints file line and return the
600 corresponding IMP restraint."""
603 if typ ==
'MODELLER5':
606 raise NotImplementedError(
"Only 'R' lines currently read from " + \
607 "Modeller restraints files")
608 form = int(spl.pop(0))
609 modalities = [int(spl.pop(0))]
610 features = [int(spl.pop(0))]
613 natoms = [int(spl.pop(0))]
614 nparam = int(spl.pop(0))
615 nfeat = int(spl.pop(0))
616 for i
in range(nfeat - 1):
617 modalities.append(int(spl.pop(0)))
618 features.append(int(spl.pop(0)))
619 natoms.append(int(spl.pop(0)))
620 atoms = [int(spl.pop(0))
for x
in range(natoms[0])]
621 for i
in range(len(atoms)):
622 atoms[i] = atom_particles[atoms[i] - 1]
623 parameters = [float(spl.pop(0))
for x
in range(nparam)]
624 restraint_generators = {
625 1 : _DistanceRestraintGenerator,
626 2 : _AngleRestraintGenerator,
627 3 : _DihedralRestraintGenerator,
629 restraint_gen = restraint_generators[features[0]]
630 return restraint_gen(form, modalities, atoms, parameters)
633 def _load_entire_restraints_file(filename, protein):
634 """Yield a set of IMP restraints from a Modeller restraints file."""
635 atoms = _get_protein_atom_particles(protein)
636 fh = open(filename,
'r')
639 rsr = _load_restraints_line(line, atoms)
642 except Exception
as err:
643 print(
"Cannot read restraints file line:\n" + line)
647 def _copy_residue(r, model):
648 """Copy residue information from modeller to imp"""
653 p.set_name(str(
"residue "+r.num));
657 def _copy_atom(a, model):
658 """Copy atom information from modeller"""
664 if hasattr(a,
'charge'):
666 if hasattr(a,
'type'):
668 ap.set_input_index(a.index)
671 def _copy_chain(c, model):
672 """Copy chain information from modeller"""
679 def _get_forcefield(submodel):
691 """Add radii to the hierarchy using the Modeller radius library, radii.lib.
692 Each radius is scaled by the given scale (Modeller usually scales radii
693 by a factor of 0.82). submodel specifies the topology submodel, which is
694 the column in radii.lib to use."""
698 for line
in open(filename):
699 if line.startswith(
'#'):
continue
702 radii[spl[0]] = float(spl[submodel])
703 atoms = IMP.atom.get_by_type(hierarchy, IMP.atom.ATOM_TYPE)
712 """Read a Modeller model into IMP. After creating this object, the atoms
713 in the Modeller model can be loaded into IMP using the load_atoms()
714 method, then optionally any Modeller static restraints can be read in
715 with load_static_restraints() or load_static_restraints_file().
717 This class can also be used to read Modeller alignment structures;
718 however, only load_atoms() will be useful in such a case (since
719 alignment structures don't have restraints or other information).
725 @param modeller_model The Modeller model or alignment structure
728 self._modeller_model = modeller_model
731 """Construct an IMP::atom::Hierarchy that contains the same atoms as
732 the Modeller model or alignment structure.
734 IMP atoms created from a Modeller model will be given charges and
735 CHARMM types, extracted from the model. Alignment structures don't
736 contain this information, so the IMP atoms won't either.
738 @param model The IMP::Model object in which the hierarchy will be
739 created. The highest level hierarchy node is a PROTEIN.
740 @return the newly-created root IMP::atom::Hierarchy.
745 for chain
in self._modeller_model.chains:
750 for residue
in chain.residues:
751 rp = _copy_residue(residue, model)
754 for atom
in residue.atoms:
755 ap = _copy_atom(atom, model)
758 self._atoms[atom.index] = ap
760 self._modeller_hierarchy = hpp
763 def _get_nonbonded_list(self, atoms, pair_filter, edat, distance):
768 if pair_filter
is None:
770 if edat.excl_local[0]:
771 pair_filter.set_bonds(list(self.
load_bonds()))
772 if edat.excl_local[1]:
774 if edat.excl_local[2]:
776 nbl.add_pair_filter(pair_filter)
780 """Load the Modeller bond topology into the IMP model. Each bond is
781 represented in IMP as an IMP::atom::Bond, with no defined length
782 or stiffness. These bonds are primarily useful as input to
783 IMP::atom::StereochemistryPairFilter, to exclude bond interactions
784 from the nonbonded list. Typically the contribution to the scoring
785 function from the bonds is included in the Modeller static restraints
786 (use load_static_restraints() or load_static_restraints_file() to
787 load these). If you want to regenerate the stereochemistry in IMP,
788 do not use these functions (as then stereochemistry scoring terms
789 and exclusions would be double-counted) and instead use the
790 IMP::atom::CHARMMTopology class.
792 You must call load_atoms() prior to using this function.
793 @see load_angles(), load_dihedrals(), load_impropers()
794 @return A generator listing all of the bonds.
796 if not hasattr(self,
'_modeller_hierarchy'):
797 raise ValueError(
"Call load_atoms() first.")
798 for (maa, mab)
in self._modeller_model.bonds:
799 pa = self._atoms[maa.index]
800 pb = self._atoms[mab.index]
810 IMP.atom.Bond.SINGLE).get_particle()
813 """Load the Modeller angle topology into the IMP model.
814 See load_bonds() for more details."""
815 return self._internal_load_angles(self._modeller_model.angles,
819 """Load the Modeller dihedral topology into the IMP model.
820 See load_bonds() for more details."""
821 return self._internal_load_angles(self._modeller_model.dihedrals,
825 """Load the Modeller improper topology into the IMP model.
826 See load_bonds() for more details."""
827 return self._internal_load_angles(self._modeller_model.impropers,
830 def _internal_load_angles(self, angles, angle_class):
831 if not hasattr(self,
'_modeller_hierarchy'):
832 raise ValueError(
"Call load_atoms() first.")
833 for modeller_atoms
in angles:
834 imp_particles = [self._atoms[x.index]
for x
in modeller_atoms]
836 a = angle_class.setup_particle(p,
838 yield a.get_particle()
841 """Convert a Modeller static restraints file into equivalent
842 IMP::Restraints. load_atoms() must have been called first to read
843 in the atoms that the restraints will act upon.
844 @param filename Name of the Modeller restraints file. The restraints
845 in this file are assumed to act upon the model read in by
846 load_atoms(); no checking is done to enforce this.
847 @return A Python generator of the newly-created IMP::Restraint
850 if not hasattr(self,
'_modeller_hierarchy'):
851 raise ValueError(
"Call load_atoms() first.")
852 return _load_entire_restraints_file(filename, self._modeller_hierarchy)
856 """Convert the current set of Modeller static restraints into equivalent
857 IMP::Restraints. load_atoms() must have been called first to read
858 in the atoms that the restraints will act upon.
859 @return A Python generator of the newly-created IMP::Restraint
862 class _RestraintGenerator(object):
863 """Simple generator wrapper"""
866 def __iter__(self, *args, **keys):
868 def close(self, *args, **keys):
869 return self._gen.close(*args, **keys)
871 return next(self._gen)
873 def send(self, *args, **keys):
874 return self._gen.send(*args, **keys)
875 def throw(self, *args, **keys):
876 return self._gen.throw(*args, **keys)
879 rsrfile = os.path.join(t.tmpdir,
'restraints.rsr')
880 self._modeller_model.restraints.write(file=rsrfile)
883 wrap = _RestraintGenerator(gen)
889 """Convert Modeller dynamic restraints into IMP::Restraint objects.
891 For each currently active Modeller dynamic restraint
892 (e.g. soft-sphere, electrostatics) an equivalent IMP::Restraint
894 load_atoms() must have been called first to read
895 in the atoms that the restraints will act upon.
897 If pair_filter is given, it is an IMP::PairFilter object to exclude
898 pairs from the nonbonded lists used by the dynamic restraints.
899 Otherwise, an IMP::atom::StereochemistryPairFilter object is created
900 to exclude Modeller bonds, angles and dihedrals, as specified by
901 edat.excl_local. (Note that this calls load_bonds(), load_angles()
902 and load_dihedrals(), so will create duplicate lists of bonds if
903 those methods are called manually as well.)
905 @note Currently only soft-sphere, electrostatic and Lennard-Jones
906 restraints are loaded.
907 @return A Python generator of the newly-created IMP::Restraint
910 if not hasattr(self,
'_modeller_hierarchy'):
911 raise ValueError(
"Call load_atoms() first.")
912 edat = self._modeller_model.env.edat
913 libs = self._modeller_model.env.libs
915 m = atoms[0].get_model()
918 if edat.dynamic_sphere:
921 nbl = self._get_nonbonded_list(atoms, pair_filter, edat, 0.)
924 libs.topology.submodel, edat.radii_factor)
931 if edat.dynamic_lennard
or edat.dynamic_coulomb:
933 d = max(edat.contact_shell - 3.0, 0.0)
934 nbl = self._get_nonbonded_list(atoms, pair_filter, edat, d)
935 ff = _get_forcefield(libs.topology.submodel)
936 ff.add_radii(self._modeller_hierarchy)
938 if edat.dynamic_lennard:
939 ff.add_well_depths(self._modeller_hierarchy)
941 edat.lennard_jones_switch[1])
945 if edat.dynamic_coulomb:
947 edat.coulomb_switch[1])
949 ps.set_relative_dielectric(edat.relative_dielectric)
954 def get_module_version():
955 """get_module_version() -> std::string const"""
956 return _IMP_modeller.get_module_version()
959 """get_example_path(std::string fname) -> std::string"""
960 return _IMP_modeller.get_example_path(fname)
963 """get_data_path(std::string fname) -> std::string"""
964 return _IMP_modeller.get_data_path(fname)
966 from .
import _version_check
967 _version_check.check_version(get_module_version())
968 __version__ = get_module_version()
static CHARMMAtom setup_particle(Model *m, ParticleIndex pi, String charmm_type)
static Charged setup_particle(Model *m, ParticleIndex pi, Float charge)
Lower bound harmonic function (non-zero when feature < mean)
def load_static_restraints
Convert the current set of Modeller static restraints into equivalent IMP::Restraints.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
def load_bonds
Load the Modeller bond topology into the IMP model.
A Modeller restraint which evaluates an IMP scoring function.
Coulomb (electrostatic) score between a pair of particles.
static Atom setup_particle(Model *m, ParticleIndex pi, Atom other)
Various classes to hold sets of particles.
Upper bound harmonic function (non-zero when feature > mean)
static XYZR setup_particle(Model *m, ParticleIndex pi)
A decorator for a particle which has bonds.
def load_impropers
Load the Modeller improper topology into the IMP model.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Dihedral restraint between four particles.
def load_static_restraints_file
Convert a Modeller static restraints file into equivalent IMP::Restraints.
A score on the distance between the surfaces of two spheres.
Return all close unordered pairs of particles taken from the SingletonContainer.
static Residue setup_particle(Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
A single binormal term in a MultipleBinormalRestraint.
def load_dynamic_restraints
Convert Modeller dynamic restraints into IMP::Restraint objects.
Distance restraint between two particles.
static XYZ setup_particle(Model *m, ParticleIndex pi)
Composable functors to implement scores via compile-time composition.
An IMP restraint using all defined Modeller restraints.
CHARMM force field parameters.
Bond create_bond(Bonded a, Bonded b, Bond o)
Connect the two wrapped particles by a custom bond.
def load_dihedrals
Load the Modeller dihedral topology into the IMP model.
static Float get_k_from_standard_deviation(Float sd, Float t=297.15)
Return the k to use for a given Gaussian standard deviation.
Angle restraint between three particles.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
ParticleIndexPairs get_indexes(const ParticlePairsTemp &ps)
Lennard-Jones score between a pair of particles.
A particle that describes an angle between three particles.
The standard decorator for manipulating molecular structures.
Store a list of ParticleIndexes.
static Bonded setup_particle(Model *m, ParticleIndex pi)
def load_atoms
Construct an IMP::atom::Hierarchy that contains the same atoms as the Modeller model or alignment str...
Version and module information for Objects.
A decorator for a particle with x,y,z coordinates.
Modeller-style multiple binormal (phi/psi) restraint.
def add_soft_sphere_radii
Add radii to the hierarchy using the Modeller radius library, radii.lib.
A particle that describes a dihedral angle between four particles.
def load_angles
Load the Modeller angle topology into the IMP model.
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...
static bool get_is_setup(const IMP::ParticleAdaptor &p)
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
A filter that excludes bonds, angles and dihedrals.
Read a Modeller model into IMP.
Class to handle individual particles of a Model object.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Smooth interaction scores by switching the derivatives (force switch).
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
Hierarchies get_leaves(const Selection &h)
Applies a PairScore to each Pair in a list.
virtual ModelObjectsTemp do_get_inputs() const =0
Closed cubic spline function.
A decorator for an atom that has a defined CHARMM type.
A restraint is a term in an IMP ScoringFunction.
Harmonic function (symmetric about the mean)