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
()[source]
Returns a copy of eigenvectors array.

getCovariance
()[source]
Returns covariance matrix. It will be calculated using available modes.

getEigvals
()[source]
Returns eigenvalues. For PCA
and EDA
models
built using coordinate data in Å, unit of eigenvalues is Å^{2}. 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
()[source]
Returns residue index of hinge sites.

getIndices
()[source]
Returns indices of modes in the mode set.

getModel
()[source]
Returns the model that the modes belongs to.

getTitle
()[source]
Returns title of the mode set.

getVariances
()[source]
Returns variances. For PCA
and EDA
models
built using coordinate data in Å, unit of variance is Å^{2}. For
ANM
and GNM
, on the other hand, variance is the
inverse of the eigenvalue, so it has arbitrary or relative units.

is3d
()[source]
Returns True is model is 3dimensional.

numAtoms
()[source]
Returns number of atoms.

numDOF
()[source]
Returns number of degrees of freedom.

numModes
()[source]
Returns number of modes in the instance (not necessarily maximum
number of possible modes).