Package schrodinger :: Package trajectory :: Package prody :: Module nma :: Class NMA

Class NMA

object --+
         |
        NMA

A class for handling Normal Mode Analysis (NMA) data.

Instance Methods

[hide private]

__init__(self, title='Unknown')
x.__init__(...) initializes x; see help(type(x)) for signature

__len__(self)

__getitem__(self, index)
A list or tuple of integers can be used for indexing.

__iter__(self)

__repr__(self)
repr(x)

__str__(self)
str(x)

_reset(self)

_getMode(self, index)

_getTrace(self)
Return trace, and emit a warning message if trace is calculated using eigenvalues of a subset of variances (eigenvalues or inverse eigenvalues).

getModel(self)
Return self.

is3d(self)
Return **True** if 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 model.

setTitle(self, title)
Set title of the model.

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.

getCovariance(self)
Return covariance matrix.

calcModes(self)

addEigenpair(self, vector, value=None)
Add eigen *vector* and eigen *value* pair(s) to the instance.

setEigens(self, vectors, values=None)
Set eigen *vectors* and eigen *values*.

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, title='Unknown')
(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`, :class:`.GNM`, and :class:`.RTB`, 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`, :class:`.GNM`, and :class:`.RTB`, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

getCovariance(self)

Return covariance matrix. If covariance matrix is not set or yet calculated, it will be calculated using available modes.

addEigenpair(self, vector, value=None)

Add eigen *vector* and eigen *value* pair(s) to the instance. If eigen *value* is omitted, it will be set to 1. Inverse eigenvalues are set as variances.

setEigens(self, vectors, values=None)

Set eigen *vectors* and eigen *values*. If eigen *values* are omitted, they will be set to 1. Inverse eigenvalues are set as variances.

Class NMA

__init__(self, title='Unknown') (Constructor)

__repr__(self) (Representation operator)

__str__(self) (Informal representation operator)

getEigvals(self)

getVariances(self)

getCovariance(self)

addEigenpair(self, vector, value=None)

setEigens(self, vectors, values=None)

init(self, title='Unknown')
(Constructor)

repr(self)
(Representation operator)

str(self)
(Informal representation operator)