schrodinger.trajectory.prody.nma module¶
This module defines a class handling normal mode analysis data.
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class
schrodinger.trajectory.prody.nma.
NMA
(title='Unknown')¶ Bases:
object
A class for handling Normal Mode Analysis (NMA) data.
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__init__
(title='Unknown')¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
()¶
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getModel
()¶ Return self.
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is3d
()¶ Return True if model is 3-dimensional.
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numAtoms
()¶ Return number of atoms.
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numModes
()¶ Return number of modes in the instance (not necessarily maximum number of possible modes).
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numDOF
()¶ Return number of degrees of freedom.
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getTitle
()¶ Return title of the model.
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setTitle
(title)¶ Set title of the model.
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getEigvals
()¶ Return eigenvalues. For
PCA
andEDA
models built using coordinate data in Å, unit of eigenvalues is |A2|. 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.
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getVariances
()¶ Return variances. For
PCA
andEDA
models built using coordinate data in Å, unit of variance is |A2|. ForANM
,GNM
, andRTB
, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.
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getArray
()¶ Return a copy of eigenvectors array.
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getEigvecs
()¶ Return a copy of eigenvectors array.
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getCovariance
()¶ Return covariance matrix. If covariance matrix is not set or yet calculated, it will be calculated using available modes.
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calcModes
()¶
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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.
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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.
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