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.

__init__(model, indices)

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

__len__()

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.