Normal Mode¶
This module defines classes for handling mode data.

class
Mode
(model, index)[source]¶ A class to provide access to and operations on mode data.
Initialize mode object as part of an NMA model.
Parameters: 
getArrayNx3
()¶ Returns a copy of array with shape (N, 3).

getEigval
()[source]¶ Returns normal mode eigenvalue. For
PCA
andEDA
models built using coordinate data in Å, unit of eigenvalues is Å^{2}. ForANM
andGNM
, on the other hand, eigenvalues are in arbitrary or relative units but they correlate with stiffness of the motion along associated eigenvector.

getEigvals
()¶ Returns normal mode eigenvalue. For
PCA
andEDA
models built using coordinate data in Å, unit of eigenvalues is Å^{2}. ForANM
andGNM
, on the other hand, eigenvalues are in arbitrary or relative units but they correlate with stiffness of the motion along associated eigenvector.

getEigvec
()¶ Returns a copy of the normal mode array (eigenvector).

getEigvecs
()¶ Returns a copy of the normal mode array (eigenvector).

getVariance
()[source]¶ Returns variance along the mode. For
PCA
andEDA
models built using coordinate data in Å, unit of variance is Å^{2}. ForANM
andGNM
, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

getVariances
()¶ Returns variance along the mode. For
PCA
andEDA
models built using coordinate data in Å, unit of variance is Å^{2}. ForANM
andGNM
, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

numModes
()¶ Returns 1.


class
Vector
(array, title='Unknown', is3d=True)[source]¶ 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 twoMode
instances results in aVector
instance.Instantiate with a name, an array, and a 3d flag.

getArrayNx3
()¶ Returns a copy of array with shape (N, 3).

is3d
()[source]¶ Returns True if vector instance describes a 3dimensional property, such as a deformation for a set of atoms.

numAtoms
()[source]¶ Returns number of atoms. For a 3dimensional vector, returns length of the vector divided by 3.

numModes
()¶ Returns 1.
