schrodinger.trajectory.prody.modeset module

This module defines a pointer class for handling subsets of normal modes.

class schrodinger.trajectory.prody.modeset.ModeSet(model, indices)

Bases: object

A class for providing access to subset of mode data. Instances are obtained by slicing an NMA model (ANM, GNM, or PCA). ModeSet’s contain a reference to the model and a list of mode indices. Methods common to NMA models are also defined for mode sets.

__slots__ = ['_model', '_indices']

__init__(model, indices)

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

__len__()

__iter__()

__repr__()

Return repr(self).

__str__()

Return str(self).

is3d()

Return True is model is 3-dimensional.

numAtoms()

Return number of atoms.

numModes()

Return number of modes in the instance (not necessarily maximum number of possible modes).

numDOF()

Return number of degrees of freedom.

getTitle()

Return title of the mode set.

getModel()

Return the model that the modes belongs to.

getIndices()

Return indices of modes in the mode set.

getEigvals()

Return eigenvalues. For PCA and EDA models built using coordinate data in Å, unit of eigenvalues is |A2|. For ANM and GNM, on the other hand, eigenvalues are in arbitrary or relative units but they correlate with stiffness of the motion along associated eigenvector.

getVariances()

Return variances. For PCA and EDA models built using coordinate data in Å, unit of variance is |A2|. For ANM and GNM, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

getArray()

Return a copy of eigenvectors array.

getEigvecs()

Return a copy of eigenvectors array.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__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.modeset'

__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

__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).