Perturbation Response Scanning¶
This module defines functions for performing perturbation response scanning from PCA and normal modes.

calcPerturbResponse
(model, **kwargs)[source]¶ This function implements the perturbation response scanning (PRS) method described in [CA09] and [IG14]. It returns a PRS matrix, and effectiveness and sensitivity profiles.
Rows of the matrix are the average magnitude of the responses obtained by perturbing the atom/node position at that row index, i.e.
prs_matrix[i,j]
will give the response of residue/node j to perturbations in residue/node i.PRS is performed using the covariance matrix from a model, e.g. a
ANM
instance. To use an external matrix, please provide it to aPCA
instance using thePCA.setCovariance()
.When an atoms instance is given, the PRS matrix will be added as data, which can be retrieved with
atoms.getData('prs_matrix')
.model and atoms must have the same number of atoms. atoms must be an
AtomGroup
instance.[CA09] Atilgan C, Atilgan AR, PerturbationResponse Scanning Reveals Ligand EntryExit Mechanisms of Ferric Binding Protein. PLoS Comput Biol 2009 5(10):e1000544. [IG14] General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. PLoS Comput. Biol. 2014 10:e1003624.

calcDynamicFlexibilityIndex
(model, atoms, select, **kwargs)[source]¶ Calculate the dynamic flexibility index for the selected residue(s). This function implements the dynamic flexibility index (Dfi) method described in [ZNG13].
Parameters: [ZNG13] Gerek ZN, Kumar S, Ozkan SB, Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl. 2013 6(3):42333.

calcDynamicCouplingIndex
(model, atoms, select, func_sel, **kwargs)[source]¶ Calculate the dynamic coupling index for the selected residue(s). This function implements the dynamic coupling index (DCI) or functional DFI method described in [AK15].
Parameters:  model (
ANM
,PCA
) – 3D model from which to calculate covariance matrix  atoms (
Atomic
) – an Atomic object from which residues are selected  select (str,
Selection
) – a selection string or selection for residues of interest  func_sel (str,
Selection
) – a selection string or selection for functional residues  norm (bool) – whether to normalise the covariance, default False
[AK15]  Kumar A, Glembo TJ, Ozkan SB. The Role of Conformational Dynamics and Allostery
 in the Disease Development of Human Ferritin.
Biophys J. 2015 109(6):127381.
 model (