schrodinger.trajectory.pbc_manager module

class schrodinger.trajectory.pbc_manager.PBCMeasureMananger(frame)

Bases: object

A class to measure distance, angle, dihedral and planar angle under periodic boundary conditions.

__init__(frame)

Parameters:frame (_DesmondFrame instance) – The trajectory frame on which the measurement will be performed.

__call__(atom1, atom2, atom3=None, atom4=None, atom5=None, atom6=None, minangle=False)

Measure the distance, angle, dihedral angle, or angle between planes of the provided atoms under periodic boundary condition.

If atom1 and atom2 are provided, return the distance between them.

If atom1, atom2, and atom3 are provided, return the angle between them.

If atoms 1-4 are provided, return the dihedral angle between them.

If atoms 1-6 are provided, return the angle between the planes defined by atoms 1-3 and atoms 4-6.

Each of the atom arguments can be integer atom indices or structure._StructureAtom objects.

Parameters

Parameters:minangle (bool) – This applies to the planar angle calculation and if True restricts the angle to <= 90.0 degrees. That is, it treats the order of atoms defining a plane as unimportant, and the directionality of the plane normals is ignored.

calcDistance(pos1, pos2)

calcAngle(pos1, pos2, pos3)

calcDihedral(pos1, pos2, pos3, pos4)

calcPlanarAngle(pos1, pos2, pos3, pos4, pos5, pos6, minangle=False)

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.trajectory.pbc_manager', '__doc__': '\n A class to measure distance, angle, dihedral and planar angle under\n periodic boundary conditions.\n ', '__init__': <function PBCMeasureMananger.__init__>, '__call__': <function PBCMeasureMananger.__call__>, '_getPosition': <function PBCMeasureMananger._getPosition>, '_distance': <function PBCMeasureMananger._distance>, 'calcDistance': <function PBCMeasureMananger.calcDistance>, '_angle': <function PBCMeasureMananger._angle>, 'calcAngle': <function PBCMeasureMananger.calcAngle>, '_dihedral': <function PBCMeasureMananger._dihedral>, 'calcDihedral': <function PBCMeasureMananger.calcDihedral>, '_planarAngle': <function PBCMeasureMananger._planarAngle>, 'calcPlanarAngle': <function PBCMeasureMananger.calcPlanarAngle>, '__dict__': <attribute '__dict__' of 'PBCMeasureMananger' objects>, '__weakref__': <attribute '__weakref__' of 'PBCMeasureMananger' 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.pbc_manager'

__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).

__weakref__

list of weak references to the object (if defined)