Mode Set
This module defines a pointer class for handling subsets of normal modes.
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class ModeSet(model, indices)[source]
A class for providing access to subset of mode data. Instances
are obtained by slicing an NMA model (ANM, GNM, or
PCA). 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.
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getArray()[source]
Return a copy of eigenvectors array.
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getEigvals()[source]
Return eigenvalues. For PCA and EDA models
built using coordinate data in Å, unit of eigenvalues is Å2. For
ANM and GNM, 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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getEigvecs()
Return a copy of eigenvectors array.
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getIndices()[source]
Return indices of modes in the mode set.
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getModel()[source]
Return the model that the modes belongs to.
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getTitle()[source]
Return title of the mode set.
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getVariances()[source]
Return variances. For PCA and EDA models
built using coordinate data in Å, unit of variance is Å2. For
ANM and GNM, on the other hand, variance is the
inverse of the eigenvalue, so it has arbitrary or relative units.
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is3d()[source]
Return True is model is 3-dimensional.
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numAtoms()[source]
Return number of atoms.
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numDOF()[source]
Return number of degrees of freedom.
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numModes()[source]
Return number of modes in the instance (not necessarily maximum
number of possible modes).