Mode Set

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

class ModeSet(model, indices)[source]

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.

getArray()

Returns a copy of eigenvectors array.

getCovariance()

Returns covariance matrix. It will be calculated using available modes.

getEigvals()

Returns eigenvalues. For PCA and EDA models built using coordinate data in Å, unit of eigenvalues is Å2. 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.

getEigvecs()

Returns a copy of eigenvectors array.

getHinges()

Returns residue index of hinge sites.

getIndices()

Returns indices of modes in the mode set.

getModel()

Returns the model that the modes belongs to.

getTitle()

Returns title of the mode set.

getVariances()

Returns variances. For PCA and EDA models built using coordinate data in Å, unit of variance is Å2. For ANM and GNM, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

is3d()

Returns True is model is 3-dimensional.

numAtoms()

Returns number of atoms.

numDOF()

Returns number of degrees of freedom.

numModes()

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