Normal Mode Analysis

This module defines a class handling normal mode analysis data.

class prody.dynamics.nma.MaskedNMA(name='Unknown', mask=False, masked=True)[source]

__getitem__(index): A list or tuple of integers can be used for indexing.

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.

getArray(): Returns a copy of eigenvectors array.

getCovariance(): Returns covariance matrix. If covariance matrix is not set or yet calculated, it will be calculated using available modes.

getEigvals(): Returns 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.

getEigvecs(): Returns a copy of eigenvectors array.

getModel(): Returns self.

getTitle(): Returns title of the model.

getVariances(): Returns 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.

is3d(): Returns True if model is 3-dimensional.

numAtoms()[source]: Returns number of atoms.

numDOF(): Returns number of degrees of freedom.

numEntries(): Returns number of entries in one eigenvector.

numModes(): Returns number of modes in the instance (not necessarily maximum number of possible modes).

setEigens(vectors, values=None)[source]: Set eigen vectors and eigen values. If eigen values are omitted, they will be set to 1. Inverse eigenvalues are set as variances.

setNumAtoms(n_atoms)[source]

Fixes the tail of the model. If n_atoms is greater than the original size (number of nodes), then extra hidden nodes will be added to the model, and if not, the model will be trimmed so that the total number of nodes, including the hidden ones, will be equal to the n_atoms. Note that if masked is True, the n_atoms should be the number of visible nodes.

Parameters:: n_atoms (int) – number of atoms of the model

setTitle(title): Set title of the model.

class prody.dynamics.nma.NMA(title='Unknown')[source]

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

__getitem__(index)[source]: A list or tuple of integers can be used for indexing.

addEigenpair(vector, value=None)[source]: 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.

getArray()[source]: Returns a copy of eigenvectors array.

getCovariance()[source]: Returns covariance matrix. If covariance matrix is not set or yet calculated, it will be calculated using available modes.

getEigvals()[source]: Returns 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.

getEigvecs(): Returns a copy of eigenvectors array.

getModel()[source]: Returns self.

getTitle()[source]: Returns title of the model.

getVariances()[source]: Returns 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.

is3d()[source]: Returns True if model is 3-dimensional.

numAtoms()[source]: Returns number of atoms.

numDOF()[source]: Returns number of degrees of freedom.

numEntries()[source]: Returns number of entries in one eigenvector.

numModes()[source]: Returns number of modes in the instance (not necessarily maximum number of possible modes).

setEigens(vectors, values=None)[source]: Set eigen vectors and eigen values. If eigen values are omitted, they will be set to 1. Inverse eigenvalues are set as variances.

setTitle(title)[source]: Set title of the model.