Rotation Translation Blocks¶

This module defines a class and a function for rotating translating blocks (RTB) calculations.

class RTB(name='Unknown')[source]¶

Class for Rotations and Translations of Blocks (RTB) method ([FT00]). Optional arguments permit imposing constrains along Z-direction as in imANM method described in [TL12].

[FT00]

Tama F, Gadea FJ, Marques O, Sanejouand YH. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000 41:1-7.

[TL12]

Lezon TR, Bahar I, Constraints Imposed by the Membrane Selectively Guide the Alternating Access Dynamics of the Glutamate Transporter GltPh

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.

buildHessian(coords, blocks, cutoff=15.0, gamma=1.0, **kwargs)[source]¶

Build Hessian matrix for given coordinate set.

Parameters:	coords (numpy.ndarray) – a coordinate set or an object with getCoords method blocks (list, numpy.ndarray) – a list or array of block identifiers cutoff (float) – cutoff distance (Å) for pairwise interactions, default is 15.0 Å gamma (float) – spring constant, default is 1.0 scale (float) – scaling factor for force constant along Z-direction, default is 1.0

calcModes(n_modes=20, zeros=False, turbo=True)[source]¶

Calculate normal modes. This method uses scipy.linalg.eigh() function to diagonalize the Hessian matrix. When Scipy is not found, numpy.linalg.eigh() is used.

Parameters:	n_modes (int or None, default is 20) – number of non-zero eigenvalues/vectors to calculate. If None is given, all modes will be calculated. zeros (bool, default is False) – If True, modes with zero eigenvalues will be kept. turbo (bool, default is True) – Use a memory intensive, but faster way to calculate modes.

getArray()¶

Return a copy of eigenvectors array.

getCovariance()¶

Return covariance matrix. If covariance matrix is not set or yet calculated, it will be calculated using available modes.

getEigvals()¶

Return eigenvalues. For PCA and EDA models built using coordinate data in Å, unit of eigenvalues is Ų. 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()¶

Return a copy of eigenvectors array.

getHessian()¶

Return a copy of the Hessian matrix.

getModel()¶

Return self.

getProjection()[source]¶

Return a copy of the projection matrix.

getTitle()¶

Return title of the model.

getVariances()¶

Return variances. For PCA and EDA models built using coordinate data in Å, unit of variance is Ų. For ANM, GNM, and RTB, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

is3d()¶

Return True if model is 3-dimensional.

numAtoms()¶

Return number of atoms.

numDOF()¶

Return number of degrees of freedom.

numModes()¶

Return number of modes in the instance (not necessarily maximum number of possible modes).

setEigens(vectors, values=None)¶

Set eigen vectors and eigen values. If eigen values are omitted, they will be set to 1. Inverse eigenvalues are set as variances.

setHessian(hessian)¶

Set Hessian matrix. A symmetric matrix is expected, i.e. not a lower- or upper-triangular matrix.

setTitle(title)¶

Set title of the model.