Package schrodinger :: Package trajectory :: Package prody :: Module modeset :: Class ModeSet

Class ModeSet

object --+
         |
        ModeSet

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.

Instance Methods

[hide private]

__init__(self, model, indices)
x.__init__(...) initializes x; see help(type(x)) for signature

__len__(self)

__iter__(self)

__repr__(self)
repr(x)

__str__(self)
str(x)

is3d(self)
Return **True** is model is 3-dimensional.

numAtoms(self)
Return number of atoms.

numModes(self)
Return number of modes in the instance (not necessarily maximum number of possible modes).

numDOF(self)
Return number of degrees of freedom.

getTitle(self)
Return title of the mode set.

getModel(self)
Return the model that the modes belongs to.

getIndices(self)
Return indices of modes in the mode set.

getEigvals(self)
Return eigenvalues.

getVariances(self)
Return variances.

getArray(self)
Return a copy of eigenvectors array.

getEigvecs(self)
Return a copy of eigenvectors array.

_getArray(self)
Return eigenvectors array.

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties

[hide private]

_indices

_model

Inherited from object: __class__

Method Details

[hide private]

init(self, model, indices)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

repr(self)
(Representation operator)

repr(x)

Overrides: object.__repr__: (inherited documentation)

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

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.

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.

Class ModeSet

__init__(self, model, indices) (Constructor)

__repr__(self) (Representation operator)

__str__(self) (Informal representation operator)

getEigvals(self)

getVariances(self)

init(self, model, indices)
(Constructor)

repr(self)
(Representation operator)

str(self)
(Informal representation operator)