schrodinger.application.desmond.packages.pfx module

Periodic boundary condition related functions. These functions use particle connection maintained by cms.Cms (cms.Cms.glued_topology) for coordinates transformation.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.desmond.packages.pfx.Frame(cms)[source]

Bases: object

This a minimum interface to allow pfx functions for cms.Cms object.

__init__(cms)[source]

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

box: numpy.array = None
pos()[source]
vel()[source]
schrodinger.application.desmond.packages.pfx.glue(topo, gids, tr)[source]

Given topology (topo), glue gids together for each frames of trajectory (tr). :type topo: List[List[int]] :param topo: Lists of particles connected to each of the particles in

trajectory

Parameters

  • gids (List[int]) – List of particle ids to be glued

  • tr (List[traj.Frame]) – Simulation trajectory to be modified

Return type

List

Returns

Modified simulation trajectory

schrodinger.application.desmond.packages.pfx.center(topo, gids, tr, dims=None)[source]

Given topology (topo), center around gids for each frames of trajectory (tr). :type topo: List[List[int]] :param topo: Lists of particles connected to each of the particles in

trajectory

Parameters

  • gids (List[int]) – List of particle ids

  • tr (List[traj.Frame]) – simulation trajectory to be modified

  • dims (Set[int]) – Dimensions to be centered on

Return type

List

Returns

Modified simulation trajectory

schrodinger.application.desmond.packages.pfx.superimpose(topo, gids, tr, ref_pos, weights=None)[source]

Given topology (topo), superimpose gids for each frames of trajectory (tr) to ref_pos. :type topo: List[List[int]] :param topo: Lists of particles connected to each of the particles in

trajectory

Parameters

  • gids (List[int]) – List of particle ids

  • tr (List[traj.Frame]) – Trajectory to be modified

  • ref_pos (numpy.array, 3xlen(gids) matrix) – reference positions

  • weigths (List or None) – weights for each particle in gids

Return type

List

Returns

Modified trajectory