Explicit Membrane Gaussian Network Model

This module defines a class and a function for explicit membrane GNM calculations.

class prody.dynamics.exgnm.exGNM(name='Unknown')[source]

Class for explicit GNM (exGNM) method ([FT00]). Optional arguments build a membrane lattice permit analysis of membrane

effect on elastic network models in exGNM method described in [TL12].

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

__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.

buildKirchhoff(coords, cutoff=15.0, gamma=1.0, **kwargs)[source]

Build Kirchhoff matrix for given coordinate set. kwargs are passed to buildMembrane().

Parameters:

coords (numpy.ndarray) – a coordinate set or an object with getCoords method
cutoff (float) – cutoff distance (Å) for pairwise interactions, default is 15.0 Å
gamma (float) – spring constant, default is 1.0

buildMembrane(coords, **kwargs)[source]

Build Kirchhoff matrix for given coordinate set.

Parameters:

coords (numpy.ndarray) – a coordinate set or an object with getCoords method
membrane_high (float) – the maximum z coordinate of the membrane. Default is 13.0
membrane_low (float) – the minimum z coordinate of the membrane. Default is -13.0
R (float) – radius of all membrane in x-y direction. Default is 80
Ri (float) – inner radius of the membrane in x-y direction if it needs to be hollow. Default is 0, which is not hollow
r (float) – radius of each membrane node. Default is .1*
lat (str) – lattice type which could be FCC (face-centered-cubic, default), SC (simple cubic), SH (simple hexagonal)
exr (float) – exclusive radius of each protein node. Default is 5.0
hull (bool) – whether use convex hull to determine the protein’s interior. Turn it off if protein is multimer. Default is True
center (bool) – whether transform the structure to the origin (only x- and y-axis). Default is True

calcModes(n_modes=20, **kwargs)[source]

Calculate normal modes. This method uses scipy.linalg.eigh() function to diagonalize the Kirchhoff 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 True) – If True, modes with zero eigenvalues will be kept.
turbo (bool, default is True) – Use a memory intensive, but faster way to calculate modes.

getCombined()[source]: Returns a copy of the combined atoms or coordinates.

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.

getGamma(): Returns spring constant (or the gamma function or Gamma instance).

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.

numModes(): Returns 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.