schrodinger.trajectory.analysis.

Class _PBCMeasureMananger

object --+ | _PBCMeasureMananger

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

Instance Methods

__init__(self, frame)
x.__init__(...) initializes x; see help(type(x)) for signature

__call__(self, 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.

_getPosition(self, atom)

_distance(self, atom1, atom2)

calcDistance(self, pos1, pos2)

_angle(self, atom1, atom2, atom3)

calcAngle(self, pos1, pos2, pos3)

_dihedral(self, atom1, atom2, atom3, atom4)

calcDihedral(self, pos1, pos2, pos3, pos4)

_planarAngle(self, atom1, atom2, atom3, atom4, atom5, atom6)

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

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

Properties

[hide private]

Inherited from object: __class__

init(self, frame)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

frame (_DesmondFrame instance) - The trajectory frame on which the measurement will be performed.

Overrides: object.__init__

call(self, atom1, atom2, atom3=None, atom4=None, atom5=None, atom6=None, minangle=False)
(Call operator)

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.

Class _PBCMeasureMananger

__init__(self, frame) (Constructor)

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

init(self, frame)
(Constructor)

call(self, atom1, atom2, atom3=None, atom4=None, atom5=None, atom6=None, minangle=False)
(Call operator)