pylift.reader

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

read_mol2(→ dict)

pylift.reader.read_mol2

read_topo(→ dict)

pylift.reader.read_topo

read_gaff2(→ dict)

pylift.reader.read_gaff2

read_frcmod(→ dict)

pylift.reader.read_frcmod

Module Contents

pylift.reader.read_mol2(mol2_in: str, out_json: str | None = None) → dict[source]

pylift.reader.read_mol2

Extracts all information from a provided mol2 file

Parameters:

  • mol2_in (str) – mol2 input file

  • out_json (str) – JSON file with mol2 information in PyLIFT-parsable dictionary

Returns:

mol2 information in PyLIFT-parsable dictionary

Return type:

dict

pylift.reader.read_topo(topo_in: str = 'topo.tmp.lmps', linker_identifier: str | None = 'L', pseudoatoms: str = None, out_json: str | None = None) → dict[source]

pylift.reader.read_topo

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

Parameters:

  • topo_in (str) – input LAMMPS file from TopoTools

  • linker_identifier – same as linker_identifier previously defined in builder.assign_linkers() Otherwise, set linker_identifier = None

  • 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

  • out_json (str) – JSON file with information from TopoTools file in PyLIFT-parsable dictionary

Returns:

TopoTools information in PyLIFT-parsable dictionary

Return type:

dict

pylift.reader.read_gaff2(gaff2_in: str | None = 'gaff2.dat', default_loc=True, out_json: str | None = None, verbose: bool | None = True) → dict[source]

pylift.reader.read_gaff2

Read in a GAFF2 molecule file.

Parameters:

  • gaff2_in (str) – gaff2 filename if default_loc=True, or gaff2 filepath otherwise

  • default_loc (bool) – if GAFF2 file can be found in default Amber location: ~/amber24/dat/leap/parm/

  • out_json (str) – name of the GAFF2 information translated to a PyLIFT-readable JSON file

  • verbose (bool) – Print out optional information

Returns:

GAFF2 information translated to a PyLIFT-readable dictionary

Return type:

dict

pylift.reader.read_frcmod(frcmod_file: str, out_json: str | None = None) → dict[source]

pylift.reader.read_frcmod

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

Parameters:

  • frcmod_file (str) – name of the FRCMOD file

  • out_json (str) – name of the FRCMOD information translated to a PyLIFT-readable JSON file

Returns:

FRCMOD file contents in a PyLIFT-readable dictionary

Return type:

dict