pylift package

Submodules

pylift.builder module

pylift.builder

License: The MIT License (MIT)

Copyright 2025 Brandon C. Tapia

pylift.builder.add_ff_params(lammps_dict: dict, ff_dict: dict, missing_ff_params: dict, pseudoatoms: bool, approx_match: bool = True, user_match: dict[str] | None = None, verbose: bool | None = True)[source]

Adds forcefield parameters from a specified forcefield to pair, bond, angle, dihedral, and improper topology information

Parameters:

  • lammps_dict (dict) – contains skeleton topology for molecule

  • ff_dict (dict) – contains forcefield to apply

  • missing_ff_params (dict) – contains FRCMOD information

  • pseudoatoms (bool) – whether the simulation is all-atom (False) or united-atom (True)

  • approx_match (bool) – whether only exact matches to forcefield types should be found (e.g., if approx_match = True then c3-c3-ca-c3 would first look for parameters for c3-c3-ca-c3 and if not found, then X-c3-ca-X)

  • user_match (dict[str]) – contains a dictionary of current atoms (key) to atom to search for instead (value) (e.g., if {‘c3’, ‘cy’} is specified then X-c3-cy-X would first look for parameters for X-c3-cy-X and if not found, then X-c3-c3-X)

Returns:

lammps_dict like dictionary with forcefield parameters

Return type:

dict

pylift.builder.adjust_charges(monomer_dict: dict, xmer_dict: dict, monomer_atoms: list[int], xmer_atoms: list[int], charge_distribution=None, forced_charge: float | None = 0.0, verbose: bool | None = True) → dict[source]
Adjust charge on atoms involved/near to linkers by using an xmer (e.g., dimer) for some charges

(e.g., adjust the charges on the heavy atoms involved in polymerization as well as the hydrogens attached)

Any charge discrpency is uniformly distributed across all atoms

such that overall_charge = forced_charge

Parameters:

  • monomer_dict (dict) – monomer read in through reader.read_mol2

  • xmer_dict (dict) – xmer read in through reader.read_mol2

  • monomer_atoms (list[int]) – atoms where charge will be adjusted in monomer_dict

  • dimer_atoms (list[int]) – atoms where charge will be read from in xmer_dict

  • forced_charge (float) – overall monomer charge after adjusting polymer charges. Charge is uniformly distributed across all atoms including monomer_atoms If forced_charge=None, forced_charge is the overall_charge existing prior to adjustments

Returns:

monomer_dict similar dictionary

pylift.builder.assign_linkers(mol2_dict: dict, linker_atoms: list[int], linker_identifier: str = 'L')[source]

Adds an identifier to specific atoms to prepare them for linking in Polymatic

Parameters:

  • mol2_dict (dict) – contains molecule information generated with PyLIFT.reader.read_mol2

  • linker_atoms (list[int]) – id of atoms to assign identifier to

  • linker_identifier (str) – what the identifier is

Returns:

mol2_dict similar dictionary

pylift.builder.convert_to_pseudo(mol2_dict: dict, h_identifiers: list[str] | None = ['h', 'H']) → dict[source]

Converts all-atom molecules type names to be able to identify united-atom molecules. Atom types are updated by appending the number of hydrogens onto the end (e.g., a c3 gaff2 type is retyped as c33 if it is connected to three hydrogens)

Parameters:

  • mol2_dict (dict) – contains molecule information generated with PyLIFT.reader.read_mol2

  • h_identifiers (list[str]) – contains all identifiers hydrogen atoms may be referenced as

Returns:

mol2_dict similar dictionary

pylift.builder.distribute_charges(monomer_dict)[source]
pylift.builder.remove_h(mol2_dict: dict, specific_atoms: list[int] | None = None, num_delete: list[int] | None = None, charge_distribution: str | None = 'heavy', h_identifiers: list[str] = ['h', 'H'])[source]

Removes hydrogen atoms. If specific_atoms is not specified, all hydrogens are removed. If specific_atoms is specified:

num_delete[i] amount of hydrogens removed from specific_atoms[i] len(num_delete) therefore must equal len(specific_atoms)

Parameters:

  • mol2_dict (dict) – contains molecule information generated with PyLIFT.reader.read_mol2

  • specific_atoms (list[int]) – if specified, heavy atoms to remove hydrogens from. If None, all hydrogens removed

  • charge_distribution (str) –

    method to distribute the charge of removed hydrogens Options: ‘heavy’, ‘uniform’, None ‘heavy’: Charge from removed hydrogens is consolidated into the corresponding heavy atom

    recommended if specific_atoms = None or if adjust_polymer_charges will be used

    ’uniform’: Charge from removed hydrogens is distributed across all remaining atoms

    recommended if specific_atoms != None and adjust_polymer_charges will not be used

    None: charge is not adjusted (will lead to a molecule with a different overall charge)

    not recommended

  • h_identifiers (list[str]) – contains all identifiers hydrogen atom types may start with

  • num_delete (list[int]) – if specific_atoms is specified, num_delete specifies the number of hydrogens to remove from each specified atom

Returns:

mol2_dict similar dictionary

pylift.builder.remove_h_old(mol2_dict: dict, specific_atoms: list[int] | None = None, num_delete: list[int] | None = None, charge_distribution: str | None = 'heavy', h_identifiers: list[str] = ['h', 'H'])[source]

pylift.builder.remove_h

Removes hydrogen atoms. If specific_atoms is not specified, all hydrogens are removed. If specific_atoms is specified:

num_delete[i] amount of hydrogens removed from specific_atoms[i] len(num_delete) therefore must equal len(specific_atoms)

Parameters:

  • mol2_dict (dict) – contains molecule information generated with PyLIFT.reader.read_mol2

  • specific_atoms (list[int]) – if specified, heavy atoms to remove hydrogens from. If None, all hydrogens removed

  • charge_distribution (str) –

    method to distribute the charge of removed hydrogens Options: ‘heavy’, ‘uniform’, None ‘heavy’: Charge from removed hydrogens is consolidated into the corresponding heavy atom

    recommended if specific_atoms = None or if adjust_polymer_charges will be used

    ’uniform’: Charge from removed hydrogens is distributed across all remaining atoms

    recommended if specific_atoms != None and adjust_polymer_charges will not be used

    None: charge is not adjusted (will lead to a molecule with a different overall charge)

    not recommended

  • h_identifiers (list[str]) – contains all identifiers hydrogen atom types may start with

  • num_delete (list[int]) – if specific_atoms is specified, num_delete specifies the number of hydrogens to remove from each specified atom

Returns:

mol2_dict similar dictionary

pylift.builder.types_to_names(mol2_dict: dict) → dict[source]

Mol2 files have unique columns for atom types and atom names. This function copies the forcefield descriptive atom types to the atom names as TopoTools uses atom names to generate LAMMPS skeleton files.

Parameters:

mol2_dict (dict) – contains molecule information generated with PyLIFT.reader.read_mol2

Returns:

mol2_dict similar dictionary

pylift.reader module

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.

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

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

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

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_mol2(mol2_in: str, out_json: str | None = None) → dict[source]

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]

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.utilities module

pylift.utilities module

License: The MIT License (MIT)

Copyright (c) 2024 Brandon C. Tapia

pylift.utilities.cleanup_pylift(user_files: list[str] = None, temp: bool = True, antechamber: bool = True, verbose: bool = True) → dict[source]

Cleans up temporary files generated during program execution.

Parameters:

  • user_files (list[str]) – List of additional file paths to be removed. Default is None.

  • temp (bool) – Removes all files with tmp in their name

  • antechamber (bool) – Removes all extraneous files generated with Antechamber

Returns:

information regarding the success/failure of deletion

Return type:

dict

pylift.utilities.read_json(in_json)[source]

Reads a json file from pylift/ff_data directory

pylift.utilities.write_json(dict_loc: dict, out_json: str) → None[source]

pylift.vmd module

pylift.vmd module

License: The MIT License (MIT)

Copyright 2025 Brandon C. Tapia

pylift.vmd.run_vmd_commands(commands: str, verbose: bool | None = True) → tuple[str, str, int][source]

Send and run commands in VMD.

Parameters:

  • commands (str) – Commands to run in VMD

  • verbose (bool) – Print out additional information to screen

Returns:

process output, prcess error, process returncode

Return type:

tuple

pylift.vmd.test_vmd_exec()[source]

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

Returns:

bool for success/fail

pylift.vmd.topo_write(molecule_in: str, lammps_out: str, bonds: bool | None = True, angles: bool | None = True, dihedrals: bool | None = True, impropers: bool | None = True, verbose: bool | None = True) → None[source]

pylift.vmd.writelammpsdata

Writes a skeleton LAMMPS file using TopoTools in VMD.

Parameters:

  • molecule_in (str) – filename of molecule to be read into VMD

  • lammps_out (str) – filename of skelton LAMMPS file to be created

  • bonds (bool) – if TopoTools should include bond section

  • angles (bool) – if TopoTools should include angles section

  • dihedrals (bool) – if TopoTools should include dihedrals section

  • impropers (bool) – if TopoTools should include impropers section

  • verbose (bool) – if additional information should be printed to screen

Returns:

None

pylift.writer module

pylift.writer

License: The MIT License (MIT)

Copyright 2025 Brandon C. Tapia

pylift.writer.write_lammps(lammps_dict, lammps_out, comment_style=None)[source]

Writes out a LAMMPS file from PyLIFT-readable dictionaries

Parameters:

  • lammps_dict (dict) – LAMMPS information stored from pylift.reader.read_lammps()

  • lammps_out (str) – name of output LAMMPS file

  • comment_style (str) – if/how parameter types are appended as comments after parameters (e.g., comment_style = ‘,’ may append # c3,c3 to a c3-c3 bonding parameter) comment_style = ‘,’ is especially useful if using pysimm

Returns:

None

pylift.writer.write_mol2(mol2_dict: dict, mol2_out: dict) → None[source]

Writes out a MOL2 file from PyLIFT-readable dictionaries

Parameters:

  • mol2_dict (dict) – MOL2 information stored from pylift.reader.read_mol2()

  • mol2_out (str) – name of output mol2 file

Returns:

None

Module contents

pylift.__init__ 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.

pylift.pylift_help()[source]

Prints location of resources

Parameters:

None

Returns:

None