Package schrodinger :: Package trajectory :: Package prody :: Module mode :: Class Mode

Class Mode

object --+    
         |    
VectorBase --+
             |
            Mode

A class to provide access to and operations on mode data.

Instance Methods

[hide private]

__init__(self, model, index)
Initialize mode object as part of an NMA model.

__len__(self)

__repr__(self)
repr(x)

__str__(self)
str(x)

__int__(self)

__float__(self)

is3d(self)
Return **True** if mode instance is from a 3-dimensional model.

numAtoms(self)
Return number of atoms.

numDOF(self)
Return number of degrees of freedom (three times the number of atoms).

getTitle(self)
A descriptive title for the mode instance.

getIndex(self)
Return the index of the mode.

getModel(self)
Return the model that the mode instance belongs to.

getArray(self)
Return a copy of the normal mode array (eigenvector).

getEigvec(self)
Return a copy of the normal mode array (eigenvector).

_getArray(self)
Return a copy of the normal mode array (eigenvector).

getEigval(self)
Return normal mode eigenvalue.

getVariance(self)
Return variance along the mode.

Inherited from VectorBase: __abs__, __add__, __div__, __iadd__, __idiv__, __imul__, __isub__, __mul__, __neg__, __pow__, __radd__, __rmul__, __rsub__, __sub__, getArrayNx3, numModes

Inherited from VectorBase (private): _getArrayNx3

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

Properties

[hide private]

_index

_model

Inherited from object: __class__

Method Details

[hide private]

init(self, model, index)
(Constructor)

Initialize mode object as part of an NMA model.

:arg model: a normal mode analysis instance :type model: :class:`.NMA`, :class:`.GNM`, or :class:`.PCA` :arg index: index of the mode :type index: int

Overrides: object.__init__

repr(self)
(Representation operator)

repr(x)

Overrides: object.__repr__: (inherited documentation)

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

is3d(self)

Return **True** if mode instance is from a 3-dimensional model.

Overrides: VectorBase.is3d

numAtoms(self)

Return number of atoms.

Overrides: VectorBase.numAtoms

getIndex(self)

Return the index of the mode. Note that mode indices are zero-based.

getArray(self)

Return a copy of the normal mode array (eigenvector).

Overrides: VectorBase.getArray

_getArray(self)

Return a copy of the normal mode array (eigenvector).

Overrides: VectorBase._getArray

getEigval(self)

Return normal mode eigenvalue. 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.

getVariance(self)

Return variance along the mode. 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 Mode

__init__(self, model, index) (Constructor)

__repr__(self) (Representation operator)

__str__(self) (Informal representation operator)

is3d(self)

numAtoms(self)

getIndex(self)

getArray(self)

_getArray(self)

getEigval(self)

getVariance(self)

init(self, model, index)
(Constructor)

repr(self)
(Representation operator)

str(self)
(Informal representation operator)