schrodinger.trajectory.prody.ensemble module

schrodinger.trajectory.prody.ensemble.importLA()

Return one of scipy.linalg or numpy.linalg.

schrodinger.trajectory.prody.ensemble.checkWeights(weights, natoms, ncsets=None, dtype=<class 'float'>)

Return weights if it has correct shape ([ncsets, ]natoms, 1). after its shape and data type is corrected. otherwise raise an exception. All items of weights must be greater than zero.

schrodinger.trajectory.prody.ensemble.getRMSD(ref, tar, weights=None)

class schrodinger.trajectory.prody.ensemble.Ensemble(cms_model, tr, asl_sel='(protein and atom.ptype " CA ")')

Bases: object

A class for analysis of arbitrary conformational ensembles. Adopted from ProDy project (prody.csb.pitt.edu)

solute_asl = 'not ((water) or (ions) or (membrane))'

__init__(cms_model, tr, asl_sel='(protein and atom.ptype " CA ")')

Initialize self. See help(type(self)) for accurate signature.

__len__()

__str__()

Return str(self).

set_solute_structure()

Sets structure of the solute molecule (sans water, ions, membrane)

setSoluteCoords()

Coordinate of the solute

setCoords()

Coodinates is a reference structure

getCoords()

Return a copy of reference coordinates for selected atoms.

setWeight(weights)

Set atomic weights.

getWeights()

Return a copy of weights of selected atoms.

setConfs()

superpose()

Superpose the ensemble onto the reference coordinates.

iterpose(rmsd=1e-05)

Iteratively superpose the ensemble until convergence.

1. Conformations are aligned with the reference coordinates
2. mean coordiantes are calculated
3. mean coordiantes are used as reference coordinates
4. repeat until mean coordinates do not change

At the end of the procedure, the reference coordinates set will be averate of conformations in the ensemble.

getDeviations()

Return deviations from reference coordinates for selected atoms. Conformations can be aligned using one of superpose() or iterpose() methods prior to calculating deviations.

write_reference_structure(name='ref.mae')

Writes maestro structure

get_solute_st()

return maestro structure of solute atoms.

get_selected_st()

return maestro structure of selected atoms.

numAtoms()

Return number of atoms.

numConfs()

Return number of frames.

numSelected()

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.trajectory.prody.ensemble', '__doc__': '\n A class for analysis of arbitrary conformational ensembles.\n Adopted from ProDy project (prody.csb.pitt.edu)\n ', 'solute_asl': 'not ((water) or (ions) or (membrane))', '__init__': <function Ensemble.__init__>, '__len__': <function Ensemble.__len__>, '__str__': <function Ensemble.__str__>, 'set_solute_structure': <function Ensemble.set_solute_structure>, '_indices': <property object>, 'setSoluteCoords': <function Ensemble.setSoluteCoords>, 'setCoords': <function Ensemble.setCoords>, 'getCoords': <function Ensemble.getCoords>, 'setWeight': <function Ensemble.setWeight>, 'getWeights': <function Ensemble.getWeights>, 'setConfs': <function Ensemble.setConfs>, '_getCoordsets': <function Ensemble._getCoordsets>, 'superpose': <function Ensemble.superpose>, '_superpose': <function Ensemble._superpose>, 'iterpose': <function Ensemble.iterpose>, 'getDeviations': <function Ensemble.getDeviations>, 'write_reference_structure': <function Ensemble.write_reference_structure>, 'get_solute_st': <function Ensemble.get_solute_st>, 'get_selected_st': <function Ensemble.get_selected_st>, 'numAtoms': <function Ensemble.numAtoms>, 'numConfs': <function Ensemble.numConfs>, 'numSelected': <function Ensemble.numSelected>, '__dict__': <attribute '__dict__' of 'Ensemble' objects>, '__weakref__': <attribute '__weakref__' of 'Ensemble' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.trajectory.prody.ensemble'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)