Mode Set

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

class prody.dynamics.modeset.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.

__getitem__(index)[source]: A list or tuple of integers can be used for indexing.

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 |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.

getEigvecs(): Returns a copy of eigenvectors array.

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 |A2|. 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 3-dimensional.

numAtoms()[source]: Returns number of atoms.

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

numEntries()[source]: Returns number of entries in one eigenvector.

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