pylift.vmd

pylift.vmd module

License: The MIT License (MIT)

Copyright 2025 Brandon C. Tapia

Attributes

Functions

`test_vmd_exec`()	Tests if VMD executable can be found and run from the environment variable.
`run_vmd_commands`(→ tuple[str, str, int])	pylift.vmd.run_vmd_commands
`topo_write`(→ None)	pylift.vmd.writelammpsdata

Module Contents

pylift.vmd.VMD_EXEC[source]

pylift.vmd.test_vmd_exec()[source]

Tests if VMD executable can be found and run from the environment variable.

Returns:: bool for success/fail

pylift.vmd.run_vmd_commands(commands: str, verbose: bool | None = True) → tuple[str, str, int][source]

pylift.vmd.run_vmd_commands

Send and run commands in VMD.

Parameters:

commands (str) – Commands to run in VMD
verbose (bool) – Print out additional information to screen

Returns:

process output, prcess error, process returncode

Return type:

tuple

pylift.vmd.topo_write(molecule_in: str, lammps_out: str, bonds: bool | None = True, angles: bool | None = True, dihedrals: bool | None = True, impropers: bool | None = True, verbose: bool | None = True) → None[source]

pylift.vmd.writelammpsdata

Writes a skeleton LAMMPS file using TopoTools in VMD.

Parameters:

molecule_in (str) – filename of molecule to be read into VMD
lammps_out (str) – filename of skelton LAMMPS file to be created
bonds (bool) – if TopoTools should include bond section
angles (bool) – if TopoTools should include angles section
dihedrals (bool) – if TopoTools should include dihedrals section
impropers (bool) – if TopoTools should include impropers section
verbose (bool) – if additional information should be printed to screen

Returns:

None