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 :class: Mode and :class: 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 – 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 :class: PCA and :class: EDA models built using coordinate data in Å, unit of eigenvalues is |A2|. For :class: ANM and :class: 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 :class: PCA and :class: EDA models built using coordinate data in Å, unit of variance is |A2|. For :class: ANM and :class: GNM, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

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 :class: Mode instance or addition of two :class: Mode instances results in a :class: 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.