Analysis Functions¶
This module defines functions for calculating physical properties from normal modes.

calcCollectivity
(mode, masses=None, is3d=None)[source]¶ Returns collectivity of the mode. This function implements collectivity as defined in equation 5 of [BR95]. If masses are provided, they will be incorporated in the calculation. Otherwise, atoms are assumed to have uniform masses.
[BR95] Bruschweiler R. Collective protein dynamics and nuclear spin relaxation. J Chem Phys 1995 102:33963403. Parameters:

calcCrossCorr
(modes, n_cpu=1, norm=True)[source]¶ Returns crosscorrelations matrix. For a 3d model, crosscorrelations matrix is an NxN matrix, where N is the number of atoms. Each element of this matrix is the trace of the submatrix corresponding to a pair of atoms. Covariance matrix may be calculated using all modes or a subset of modes of an NMA instance. For large systems, calculation of crosscorrelations matrix may be time consuming. Optionally, multiple processors may be employed to perform calculations by passing
n_cpu=2
or more.

calcFractVariance
(mode)[source]¶ Returns fraction of variance explained by the mode. Fraction of variance is the ratio of the variance along a mode to the trace of the covariance matrix of the model.

calcSqFlucts
(modes)[source]¶ Returns sum of squarefluctuations for given set of normal modes. Square fluctuations for a single mode is obtained by multiplying the square of the mode array with the variance (
Mode.getVariance()
) along the mode. ForPCA
andEDA
models built using coordinate data in Å, unit of squarefluctuations is Å^{2}, forANM
andGNM
, on the other hand, it is arbitrary or relative units.

calcTempFactors
(modes, atoms)[source]¶ Returns temperature (β) factors calculated using modes from a
ANM
orGNM
instance scaled according to the experimental Bfactors from atoms.

calcProjection
(ensemble, modes, rmsd=True, norm=False)[source]¶ Returns projection of conformational deviations onto given modes. ensemble coordinates are used to calculate the deviations that are projected onto modes. For K conformations and M modes, a (K,M) matrix is returned.
Parameters:  ensemble (
Ensemble
,Conformation
,Vector
,Trajectory
) – an ensemble, trajectory or a conformation for which deviation(s) will be projected, or a deformation vector  modes (
Mode
,ModeSet
,NMA
) – up to three normal modes
By default, rootmeansquare deviation (RMSD) along the normal mode is calculated. To calculate the raw projection pass
rmsd=False
.By default, the projection is not normalized. If you would like it to be, pass
norm=True
.Vector
instances are accepted as ensemble argument to allow for projecting a deformation vector onto normal modes. ensemble (

calcCrossProjection
(ensemble, mode1, mode2, scale=None, **kwargs)[source]¶ Returns projection of conformational deviations onto modes from different models.
Parameters:  ensemble (
Ensemble
) – ensemble for which deviations will be projected  mode1 (
Mode
,Vector
) – normal mode to project conformations onto  mode2 (
Mode
,Vector
) – normal mode to project conformations onto  scale – scale width of the projection onto mode1 (
x
) or mode2(y
), an optimized scaling factor (scalar) will be calculated by default or a value of scalar can be passed.
This function uses calcProjection and its arguments can be passed to it as keyword arguments. By default, this function applies RMSD scaling and normalisation. These can be turned off with
rmsd=False
andnorm=False
. ensemble (

calcPairDeformationDist
(model, coords, ind1, ind2, kbt=1.0)[source]¶ Returns distribution of the deformations in the distance contributed by each mode for selected pair of residues ind1 ind2 using model from a
ANM
. Method described in [EB08] equation (10) and figure (2).[EB08] Eyal E., Bahar I. Toward a Molecular Understanding of the Anisotropic Response of Proteins to External Forces: Insights from Elastic Network Models. Biophys J 2008 94:342434355. Parameters:

calcDistFlucts
(modes, n_cpu=1, norm=True)[source]¶ Returns the matrix of distance fluctuations (i.e. an NxN matrix where N is the number of residues, of MSFs in the interresidue distances) computed from the crosscorrelation matrix (see Eq. 12.E.1 in [IB18]). The arguments are the same as in
calcCrossCorr()
.[IB18] Dill K, Jernigan RL, Bahar I. Protein Actions: Principles and Modeling. Garland Science 2017.

calcHinges
(modes, atoms=None, flag=False)[source]¶ Returns the hinge sites identified using normal modes.
Parameters:

calcHitTime
(model, method='standard')[source]¶ Returns the hit and commute times between pairs of nodes calculated based on a
NMA
object.[CB95] Chennubhotla C., Bahar I. Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput Biol 2007 3(9).
Parameters: Returns: (
ndarray
,ndarray
)

calcHitTime
(model, method='standard')[source] Returns the hit and commute times between pairs of nodes calculated based on a
NMA
object.[CB95] Chennubhotla C., Bahar I. Signal Propagation in Proteins and Relation to Equilibrium Fluctuations. PLoS Comput Biol 2007 3(9).
Parameters: Returns: (
ndarray
,ndarray
)

calcAnisousFromModel
(model)[source]¶ Returns a 3Nx6 matrix containing anisotropic B factors (ANISOU lines) from a covariance matrix calculated from model.
Parameters: model ( ANM
,PCA
) – 3D model from which to calculate covariance matrixIn [1]: from prody import * In [2]: protein = parsePDB('1ejg') In [3]: anm, calphas = calcANM(protein) In [4]: adp_matrix = calcAnisousFromModel(anm)