pylift.amber

pylift.amber module

License: The MIT License (MIT)

Copyright (c) 2024 Brandon C. Tapia

Attributes

ANTECHAMBER_EXEC

Functions

test_antechamber_exec()	Tests if Antechamber executable can be found and run from the environment variable.
antechamber(mol2_in, mol2_out, forcefield[, ...])	Calls Antechamber from AmberTools to apply a forcefield and find missing parameters

Module Contents

pylift.amber.ANTECHAMBER_EXEC

pylift.amber.test_antechamber_exec()

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

Returns:

bool for success/fail

pylift.amber.antechamber(mol2_in: str, mol2_out: str, forcefield: str, charge_method: str | None = None, missing_search: str | None = 'parmchk2', verbose: bool | None = True)

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

Parameters:

• mol2_in (str) – mol2 input file

• mol2_out (str) – mol2 output file with forcefield applied

• forcefield – which forcefield to use

• charge_method (str) – charge method to use, default is None Recommended to use QM calculations rather than rely on Antechamber for charges

• missing_search (str) – program used to find missing parameters, default is ‘parmchk2’ Old versions of AmberTools might require ‘parmchk’ instead of ‘parmchk2’

• verbose (bool) – prints stderr and stdout from Antechamber, default is verbose