schrodinger.trajectory.prody.nma module

This module defines a class handling normal mode analysis data.

class schrodinger.trajectory.prody.nma.NMA(title='Unknown')

Bases: object

A class for handling Normal Mode Analysis (NMA) data.

__init__(title='Unknown')

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

__len__()

getTrace()

Return trace, and emit a warning message if trace is calculated using eigenvalues of a subset of variances (eigenvalues or inverse eigenvalues).

getModel()

Return self.

is3d()

Return True if 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 model.

setTitle(title)

Set title of the model.

getEigvals()

Return eigenvalues. For PCA and EDA models built using coordinate data in Å, unit of eigenvalues is |A2|. For ANM, GNM, and RTB, 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, GNM, and RTB, 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.

getCovariance()

Return covariance matrix. If covariance matrix is not set or yet calculated, it will be calculated using available modes.

calcModes()

addEigenpair(vector, value=None)

Add eigen vector and eigen value pair(s) to the instance. If eigen value is omitted, it will be set to 1. Inverse eigenvalues are set as variances.

setEigens(vectors, values=None)

Set eigen vectors and eigen values. If eigen values are omitted, they will be set to 1. Inverse eigenvalues are set as variances.