schrodinger.trajectory.prody.mode module

This module defines classes for handling mode data.

class schrodinger.trajectory.prody.mode.Mode(model, index)

Bases: schrodinger.trajectory.prody.mode.VectorBase

A class to provide access to and operations on mode data.

getArray()

Return a copy of the normal mode array (eigenvector).

getEigval()

Return normal mode eigenvalue. 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.

getEigvec()

Return a copy of the normal mode array (eigenvector).

getIndex()

Return the index of the mode. Note that mode indices are zero-based.

getModel()

Return the model that the mode instance belongs to.

getTitle()

A descriptive title for the mode instance.

getVariance()

Return variance along the mode. 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()

Return True if mode instance is from a 3-dimensional model.

numAtoms()

Return number of atoms.

numDOF()

Return number of degrees of freedom (three times the number of atoms).

class schrodinger.trajectory.prody.mode.Vector(array, title='Unknown', is3d=True)

Bases: schrodinger.trajectory.prody.mode.VectorBase

A class to provide operations on a modified mode array. This class holds only mode array (i.e. eigenvector) data, and has no associations with an NMA instance. Scalar multiplication of Mode instance or addition of two Mode instances results in a Vector instance.

getArray()

Return a copy of array.

getNormed()

Return mode after normalizing it.

getTitle()

Get the descriptive title for the vector instance.

is3d()

Return True if vector instance describes a 3-dimensional property, such as a deformation for a set of atoms.

numAtoms()

Return number of atoms. For a 3-dimensional vector, returns length of the vector divided by 3.

numDOF()

Return number of degrees of freedom.

setTitle(title)

Set the descriptive title for the vector instance.