schrodinger.trajectory.prody.nma module

This module defines a class handling normal mode analysis data.

class schrodinger.trajectory.prody.nma.NMA(title='Unknown')

Bases: object

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

__init__(title='Unknown')

Initialize self. See help(type(self)) for accurate signature.

__len__()

__getitem__(index)

A list or tuple of integers can be used for indexing.

__iter__()

__repr__()

Return repr(self).

__str__()

Return str(self).

getModel()

Return self.

is3d()

Return True if model is 3-dimensional.

numAtoms()

Return number of atoms.

numModes()

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

numDOF()

Return number of degrees of freedom.

getTitle()

Return title of the model.

setTitle(title)

Set title of the model.

getEigvals()

Return eigenvalues. For PCA and EDA models built using coordinate data in Å, unit of eigenvalues is |A2|. For ANM, GNM, and RTB, on the other hand, eigenvalues are in arbitrary or relative units but they correlate with stiffness of the motion along associated eigenvector.

getVariances()

Return variances. For PCA and EDA models built using coordinate data in Å, unit of variance is |A2|. For ANM, GNM, and RTB, on the other hand, variance is the inverse of the eigenvalue, so it has arbitrary or relative units.

getArray()

Return a copy of eigenvectors array.

getEigvecs()

Return a copy of eigenvectors array.

getCovariance()

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

calcModes()

addEigenpair(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(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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.trajectory.prody.nma', '__doc__': 'A class for handling Normal Mode Analysis (NMA) data.', '__init__': <function NMA.__init__>, '__len__': <function NMA.__len__>, '__getitem__': <function NMA.__getitem__>, '__iter__': <function NMA.__iter__>, '__repr__': <function NMA.__repr__>, '__str__': <function NMA.__str__>, '_reset': <function NMA._reset>, '_getMode': <function NMA._getMode>, '_getTrace': <function NMA._getTrace>, 'getModel': <function NMA.getModel>, 'is3d': <function NMA.is3d>, 'numAtoms': <function NMA.numAtoms>, 'numModes': <function NMA.numModes>, 'numDOF': <function NMA.numDOF>, 'getTitle': <function NMA.getTitle>, 'setTitle': <function NMA.setTitle>, 'getEigvals': <function NMA.getEigvals>, 'getVariances': <function NMA.getVariances>, 'getArray': <function NMA.getArray>, 'getEigvecs': <function NMA.getArray>, '_getArray': <function NMA._getArray>, 'getCovariance': <function NMA.getCovariance>, 'calcModes': <function NMA.calcModes>, 'addEigenpair': <function NMA.addEigenpair>, 'setEigens': <function NMA.setEigens>, '__dict__': <attribute '__dict__' of 'NMA' objects>, '__weakref__': <attribute '__weakref__' of 'NMA' objects>})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.trajectory.prody.nma'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)