pylift.amber
============

.. py:module:: pylift.amber

.. autoapi-nested-parse::

   pylift.amber module

   License: The MIT License (MIT)

   Copyright (c) 2024 Brandon C. Tapia



Attributes
----------

.. autoapisummary::

   pylift.amber.ANTECHAMBER_EXEC


Functions
---------

.. autoapisummary::

   pylift.amber.test_antechamber_exec
   pylift.amber.antechamber


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

.. py:data:: ANTECHAMBER_EXEC

.. py:function:: test_antechamber_exec()

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

   :returns: bool for success/fail


.. py:function:: antechamber(mol2_in: str, mol2_out: str, forcefield: str, charge_method: Optional[str] = None, missing_search: Optional[str] = 'parmchk2', verbose: Optional[bool] = True)

   Calls Antechamber from AmberTools to apply a forcefield and find missing parameters

   :param mol2_in: mol2 input file
   :type mol2_in: str
   :param mol2_out: mol2 output file with forcefield applied
   :type mol2_out: str
   :param forcefield: which forcefield to use
   :param charge_method: charge method to use, default is None
                         Recommended to use QM calculations rather than rely on Antechamber for charges
   :type charge_method: str
   :param missing_search: program used to find missing parameters, default is 'parmchk2'
                          Old versions of AmberTools might require 'parmchk' instead of 'parmchk2'
   :type missing_search: str
   :param verbose: prints stderr and stdout from Antechamber, default is verbose
   :type verbose: bool