schrodinger.trajectory.prody.modeset module¶
This module defines a pointer class for handling subsets of normal modes.
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class
schrodinger.trajectory.prody.modeset.
ModeSet
(model, indices)¶ Bases:
object
A class for providing access to subset of mode data. Instances are obtained by slicing an NMA model (
ANM
,GNM
, orPCA
). ModeSet’s contain a reference to the model and a list of mode indices. Methods common to NMA models are also defined for mode sets.-
__init__
(model, indices)¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
()¶
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is3d
()¶ Return True is 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 mode set.
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getModel
()¶ Return the model that the modes belongs to.
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getIndices
()¶ Return indices of modes in the mode set.
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getEigvals
()¶ Return eigenvalues. For
PCA
andEDA
models built using coordinate data in Å, unit of eigenvalues is |A2|. ForANM
andGNM
, 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
andGNM
, 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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