shnitsel.vis.vmd

Attributes

_tcl_script_path

Functions

traj_to_xyz(traj_atXYZ[, units])

Convert an entire trajectory's worth of geometries to an XYZ string

traj_vmd(atXYZ[, groupby])

Open geometries in the VMD viewer, if installed

Package Contents

traj_to_xyz(traj_atXYZ, units='angstrom')

Convert an entire trajectory’s worth of geometries to an XYZ string

Parameters:

  • traj_atXYZ (shnitsel.core.typedefs.AtXYZ) – Molecular geometries – should have dimensions ‘atom’ and ‘direction’; should also be groupable by ‘time’ (i.e. either have a ‘time’ dimension or a ‘time’ coordinate)

  • units – The units to which to convert before creating the XYZ string

Return type:

The XYZ data as a string, with time indicated in the comment line of each frame

Notes

The units of the outputs will be the same as the array; consider converting to angstrom first, as most tools will expect this.

_tcl_script_path
traj_vmd(atXYZ, groupby='trajid')

Open geometries in the VMD viewer, if installed

Parameters:

  • atXYZ – The geometries to transmit

  • groupby – A set of frames will be grouped into a VMD molecule if they have the same value in this coordinate, by default this is ‘trajid’ so that each trajectory

  • optional – A set of frames will be grouped into a VMD molecule if they have the same value in this coordinate, by default this is ‘trajid’ so that each trajectory