schrodinger.trajectory.prody.mode module

This module defines classes for handling mode data.

class schrodinger.trajectory.prody.mode.VectorBase

Bases: object

A base class for Mode and Vector.

This base class defines some shared methods, such as scalar multiplication or addition of mode instances.

Defined operations are:

• Absolute value (abs(mode)) returns mode length

• Additive inverse (-mode)

• Mode addition (mode1 + mode2)

• Mode subtraction (mode1 - mode2)

• Scalar multiplication (x*mode or mode*x)

• Division by a scalar (mode/x)

• Dot product (mode1*mode2)

• Power (mode**x)

getArray()

Return a copy of array.

numAtoms()

Return number of atoms.

is3d()

Return True if vector is 3d.

getArrayNx3()

Return a copy of array with shape (N, 3).

numModes()

Return 1.

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.

__init__(model, index)

Initialize mode object as part of an NMA model.

Parameters

• model (NMA, GNM, or PCA) – a normal mode analysis instance

• index (int) – index of the mode

__len__()

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).

getTitle()

A descriptive title for the mode instance.

getIndex()

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

getModel()

Return the model that the mode instance belongs to.

getArray()

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

getEigvec()

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.

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.

getArrayNx3()

Return a copy of array with shape (N, 3).

numModes()

Return 1.

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.

__init__(array, title='Unknown', is3d=True)

Instantiate with a name, an array, and a 3d flag.

__len__()

is3d()

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

getTitle()

Get the descriptive title for the vector instance.

setTitle(title)

Set the descriptive title for the vector instance.

getArray()

Return a copy of array.

getNormed()

Return mode after normalizing it.

numDOF()

Return number of degrees of freedom.

numAtoms()

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

getArrayNx3()

Return a copy of array with shape (N, 3).

numModes()

Return 1.