pylift.reader
=============

.. py:module:: pylift.reader

.. autoapi-nested-parse::

   pylift.reader module

   License: The MIT License (MIT)

   Copyright (c) 2024 Brandon C. Tapia

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.



Functions
---------

.. autoapisummary::

   pylift.reader.read_mol2
   pylift.reader.read_topo
   pylift.reader.read_gaff2
   pylift.reader.read_frcmod


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

.. py:function:: read_mol2(mol2_in: str, out_json: Optional[str] = None) -> dict

   pylift.reader.read_mol2

   Extracts all information from a provided mol2 file

   :param mol2_in: mol2 input file
   :type mol2_in: str
   :param out_json: JSON file with mol2 information in PyLIFT-parsable dictionary
   :type out_json: str

   :returns: mol2 information in PyLIFT-parsable dictionary
   :rtype: dict


.. py:function:: read_topo(topo_in: str = 'topo.tmp.lmps', linker_identifier: Optional[str] = 'L', pseudoatoms: str = None, out_json: Optional[str] = None) -> dict

   pylift.reader.read_topo

   Extracts information from a skeleton LAMMPS output file provided from the TopoTools program

   :param topo_in: input LAMMPS file from TopoTools
   :type topo_in: str
   :param linker_identifier: same as linker_identifier previously defined in builder.assign_linkers()
                             Otherwise, set linker_identifier = None
   :param Pseudoatoms: Determines wether there is the hydrogen count appended to the atoms type.
                       If builder.convert_to_pseudo() was used, pseudoatoms = True
                       Otherwise, pseudoatoms = False
   :param out_json: JSON file with information from TopoTools file in PyLIFT-parsable dictionary
   :type out_json: str

   :returns: TopoTools information in PyLIFT-parsable dictionary
   :rtype: dict


.. py:function:: read_gaff2(gaff2_in: Optional[str] = 'gaff2.dat', default_loc=True, out_json: Optional[str] = None, verbose: Optional[bool] = True) -> dict

   pylift.reader.read_gaff2

   Read in a GAFF2 molecule file.

   :param gaff2_in: gaff2 filename if default_loc=True, or gaff2 filepath otherwise
   :type gaff2_in: str
   :param default_loc: if GAFF2 file can be found in default Amber location:
                       ~/amber24/dat/leap/parm/
   :type default_loc: bool
   :param out_json: name of the GAFF2 information translated to a PyLIFT-readable JSON file
   :type out_json: str
   :param verbose: Print out optional information
   :type verbose: bool

   :returns: GAFF2 information translated to a PyLIFT-readable dictionary
   :rtype: dict


.. py:function:: read_frcmod(frcmod_file: str, out_json: Optional[str] = None) -> dict

   pylift.reader.read_frcmod

   Read in a FRCMOD file from the AmberTools prmchk or prmchk2 utilities.

   :param frcmod_file: name of the FRCMOD file
   :type frcmod_file: str
   :param out_json: name of the FRCMOD information translated to a PyLIFT-readable JSON file
   :type out_json: str

   :returns: FRCMOD file contents in a PyLIFT-readable dictionary
   :rtype: dict