pylift.vmd
==========

.. py:module:: pylift.vmd

.. autoapi-nested-parse::

   pylift.vmd module

   License: The MIT License (MIT)

   Copyright 2025 Brandon C. Tapia



Attributes
----------

.. autoapisummary::

   pylift.vmd.VMD_EXEC


Functions
---------

.. autoapisummary::

   pylift.vmd.test_vmd_exec
   pylift.vmd.run_vmd_commands
   pylift.vmd.topo_write


Module Contents
---------------

.. py:data:: VMD_EXEC

.. py:function:: test_vmd_exec()

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

   :returns: bool for success/fail


.. py:function:: run_vmd_commands(commands: str, verbose: Optional[bool] = True) -> tuple[str, str, int]

   pylift.vmd.run_vmd_commands

   Send and run commands in VMD.

   :param commands: Commands to run in VMD
   :type commands: str
   :param verbose: Print out additional information to screen
   :type verbose: bool

   :returns: process output, prcess error, process returncode
   :rtype: tuple


.. py:function:: topo_write(molecule_in: str, lammps_out: str, bonds: Optional[bool] = True, angles: Optional[bool] = True, dihedrals: Optional[bool] = True, impropers: Optional[bool] = True, verbose: Optional[bool] = True) -> None

   pylift.vmd.writelammpsdata

   Writes a skeleton LAMMPS file using TopoTools in VMD.

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

   :returns: None