Explicit Membrane Anisotropic Network Model¶
This module defines a class and a function for explicit membrane ANM calculations.

class
exANM
(name='Unknown')[source]¶ Class for explicit ANM (exANM) method ([FT00]). Optional arguments build a membrane lattice permit analysis of membrane
effect on elastic network models in exANM method described in [TL12].[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, cutoff=15.0, gamma=1.0, **kwargs)[source]¶ Build Hessian matrix for given coordinate set. kwargs are passed to :method:`.buildMembrane`.
Parameters:

buildMembrane
(coords, **kwargs)[source]¶ Build membrane lattice around coords.
Parameters:  coords (
numpy.ndarray
) – a coordinate set or an object withgetCoords
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 xy direction. Default is 80
 Ri (float) – inner radius of the membrane in xy direction if it needs to be hollow. Default is 0, which is not hollow
 r (float) – radius of each membrane node. Default is 3.1
 lat (str) – lattice type which could be FCC (facecenteredcubic, 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 yaxis). Default is True
 coords (

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 nonzero 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.

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.

getCutoff
()¶ Returns cutoff distance.

getEigvals
()¶ Returns eigenvalues. For
PCA
andEDA
models built using coordinate data in Å, unit of eigenvalues is Å^{2}. ForANM
,GNM
, andRTB
, 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.

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

getHessian
()¶ Returns a copy of the Hessian matrix.

getKirchhoff
()¶ Returns a copy of the Kirchhoff matrix.

getModel
()¶ Returns self.

getTitle
()¶ Returns title of the model.

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

is3d
()¶ Returns True if model is 3dimensional.

numAtoms
()¶ 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).

setHessian
(hessian)¶ Set Hessian matrix. A symmetric matrix is expected, i.e. not a lower or uppertriangular matrix.

setTitle
(title)¶ Set title of the model.
