Source code for prody.dynamics.modeset
# -*- coding: utf-8 -*-
"""This module defines a pointer class for handling subsets of normal modes."""
from numpy import array
__all__ = ['ModeSet']
[docs]class ModeSet(object):
"""A class for providing access to subset of mode data. Instances
are obtained by slicing an NMA model (:class:`.ANM`, :class:`.GNM`, or
:class:`.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."""
__slots__ = ['_model', '_indices']
def __init__(self, model, indices):
self._model = model
self._indices = array(indices, int)
def __len__(self):
return len(self._indices)
def __iter__(self):
for i in self._indices:
yield self._model[i]
def __repr__(self):
return '<ModeSet: {0} modes from {1}>'.format(len(self),
str(self._model))
def __str__(self):
return '{0} modes from {1}'.format(len(self._indices),
str(self._model))
[docs] def is3d(self):
"""Return **True** is model is 3-dimensional."""
return self._model._is3d
[docs] def numAtoms(self):
"""Return number of atoms."""
return self._model._n_atoms
[docs] def numModes(self):
"""Return number of modes in the instance (not necessarily maximum
number of possible modes)."""
return len(self._indices)
[docs] def numDOF(self):
"""Return number of degrees of freedom."""
return self._model._dof
[docs] def getTitle(self):
"""Return title of the mode set."""
return str(self)
[docs] def getModel(self):
"""Return the model that the modes belongs to."""
return self._model
[docs] def getIndices(self):
"""Return indices of modes in the mode set."""
return self._indices
[docs] def getEigvals(self):
"""Return eigenvalues. For :class:`.PCA` and :class:`.EDA` models
built using coordinate data in Å, unit of eigenvalues is |A2|. For
:class:`.ANM` and :class:`.GNM`, on the other hand, eigenvalues are
in arbitrary or relative units but they correlate with stiffness of
the motion along associated eigenvector."""
return self._model._eigvals[self._indices]
[docs] def getVariances(self):
"""Return variances. For :class:`.PCA` and :class:`.EDA` models
built using coordinate data in Å, unit of variance is |A2|. For
:class:`.ANM` and :class:`.GNM`, on the other hand, variance is the
inverse of the eigenvalue, so it has arbitrary or relative units."""
return self._model._vars[self._indices]
[docs] def getArray(self):
"""Return a copy of eigenvectors array."""
return self._model._array[:, self._indices]
getEigvecs = getArray
def _getArray(self):
"""Return eigenvectors array."""
return self._model._array[:, self._indices]