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.

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schrodinger.application.desmond.packages.pfx.glue(topo, gids, tr)

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)

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)

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