schrodinger.trajectory.prody.mode module

This module defines classes for handling mode data.

class schrodinger.trajectory.prody.mode.VectorBase

Bases: object

A base class for Mode and Vector.

This base class defines some shared methods, such as scalar multiplication or addition of mode instances.

Defined operations are:

  • Absolute value (abs(mode)) returns mode length
  • Additive inverse (-mode)
  • Mode addition (mode1 + mode2)
  • Mode subtraction (mode1 - mode2)
  • Scalar multiplication (x*mode or mode*x)
  • Division by a scalar (mode/x)
  • Dot product (mode1*mode2)
  • Power (mode**x)
__slots__ = []
__abs__()
__neg__()
__div__(other)
__idiv__(other)
__mul__(other)

Return scaled mode or dot product between modes.

__rmul__(other)

Return scaled mode or dot product between modes.

__imul__(other)
__add__(other)
__radd__(other)
__iadd__(other)
__sub__(other)
__rsub__(other)
__isub__(other)
__pow__(other)
getArray()

Return a copy of array.

numAtoms()

Return number of atoms.

is3d()

Return True if vector is 3d.

getArrayNx3()

Return a copy of array with shape (N, 3).

numModes()

Return 1.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__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__

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

__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.mode'
__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

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__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).

class schrodinger.trajectory.prody.mode.Mode(model, index)

Bases: schrodinger.trajectory.prody.mode.VectorBase

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

__slots__ = ['_model', '_index']
__init__(model, index)

Initialize mode object as part of an NMA model.

Parameters:
  • model (NMA, GNM, or PCA) – a normal mode analysis instance
  • index (int) – index of the mode
__len__()
__repr__()

Return repr(self).

__str__()

Return str(self).

__int__()
__float__()
is3d()

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

numAtoms()

Return number of atoms.

numDOF()

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

getTitle()

A descriptive title for the mode instance.

getIndex()

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

getModel()

Return the model that the mode instance belongs to.

getArray()

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

getEigvec()

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

getEigval()

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

getVariance()

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

__abs__()
__add__(other)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__div__(other)
__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).

__iadd__(other)
__idiv__(other)
__imul__(other)
__init_subclass__()

This method is called when a class is subclassed.

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

__isub__(other)
__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.trajectory.prody.mode'
__mul__(other)

Return scaled mode or dot product between modes.

__ne__

Return self!=value.

__neg__()
__new__()

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

__pow__(other)
__radd__(other)
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__rmul__(other)

Return scaled mode or dot product between modes.

__rsub__(other)
__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__sub__(other)
__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).

getArrayNx3()

Return a copy of array with shape (N, 3).

numModes()

Return 1.

class schrodinger.trajectory.prody.mode.Vector(array, title='Unknown', is3d=True)

Bases: schrodinger.trajectory.prody.mode.VectorBase

A class to provide operations on a modified mode array. This class holds only mode array (i.e. eigenvector) data, and has no associations with an NMA instance. Scalar multiplication of Mode instance or addition of two Mode instances results in a Vector instance.

__slots__ = ['_title', '_array', '_is3d']
__init__(array, title='Unknown', is3d=True)

Instantiate with a name, an array, and a 3d flag.

__len__()
__repr__()

Return repr(self).

__str__()

Return str(self).

is3d()

Return True if vector instance describes a 3-dimensional property, such as a deformation for a set of atoms.

getTitle()

Get the descriptive title for the vector instance.

setTitle(title)

Set the descriptive title for the vector instance.

getArray()

Return a copy of array.

getNormed()

Return mode after normalizing it.

numDOF()

Return number of degrees of freedom.

numAtoms()

Return number of atoms. For a 3-dimensional vector, returns length of the vector divided by 3.

__abs__()
__add__(other)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__div__(other)
__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).

__iadd__(other)
__idiv__(other)
__imul__(other)
__init_subclass__()

This method is called when a class is subclassed.

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

__isub__(other)
__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.trajectory.prody.mode'
__mul__(other)

Return scaled mode or dot product between modes.

__ne__

Return self!=value.

__neg__()
__new__()

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

__pow__(other)
__radd__(other)
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__rmul__(other)

Return scaled mode or dot product between modes.

__rsub__(other)
__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__sub__(other)
__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).

getArrayNx3()

Return a copy of array with shape (N, 3).

numModes()

Return 1.