pygromos.files.gromos_system package

Submodules

pygromos.files.gromos_system.gromos_system module

File: gromos_system.py Warnings: this class is WIP!

Description:

This is a super class for the collection of all Gromos files used inside a project. Bundle files with the system’s topology, coordinates, input parameters, etc. and start your simulations from here.

Author: Marc Lehner, Benjamin Ries, Felix Pultar test

class pygromos.files.gromos_system.gromos_system.Gromos_System(work_folder: str, system_name: str, rdkitMol: typing.Optional[rdkit.Chem.rdchem.Mol] = None, in_mol2_file: typing.Optional[str] = None, readIn: bool = True, forcefield: pygromos.files.forcefield._generic_force_field._generic_force_field = <pygromos.files.forcefield._generic_force_field._generic_force_field object>, auto_convert: bool = False, adapt_imd_automatically: bool = True, verbose: bool = False, in_smiles: typing.Optional[str] = None, in_residue_list: typing.Optional[typing.List] = None, in_top_path: typing.Optional[str] = None, in_cnf_path: typing.Optional[str] = None, in_imd_path: typing.Optional[str] = None, in_disres_path: typing.Optional[str] = None, in_ptp_path: typing.Optional[str] = None, in_posres_path: typing.Optional[str] = None, in_refpos_path: typing.Optional[str] = None, in_qmmm_path: typing.Optional[str] = None, in_gromosXX_bin_dir: typing.Optional[str] = None, in_gromosPP_bin_dir: typing.Optional[str] = None)

Bases: object

__init__(work_folder: str, system_name: str, rdkitMol: typing.Optional[rdkit.Chem.rdchem.Mol] = None, in_mol2_file: typing.Optional[str] = None, readIn: bool = True, forcefield: pygromos.files.forcefield._generic_force_field._generic_force_field = <pygromos.files.forcefield._generic_force_field._generic_force_field object>, auto_convert: bool = False, adapt_imd_automatically: bool = True, verbose: bool = False, in_smiles: typing.Optional[str] = None, in_residue_list: typing.Optional[typing.List] = None, in_top_path: typing.Optional[str] = None, in_cnf_path: typing.Optional[str] = None, in_imd_path: typing.Optional[str] = None, in_disres_path: typing.Optional[str] = None, in_ptp_path: typing.Optional[str] = None, in_posres_path: typing.Optional[str] = None, in_refpos_path: typing.Optional[str] = None, in_qmmm_path: typing.Optional[str] = None, in_gromosXX_bin_dir: typing.Optional[str] = None, in_gromosPP_bin_dir: typing.Optional[str] = None)

The Gromos_System class is the central unit of PyGromosTools for files and states. With this class all files can be read-in or the files can be automatically generated from smiles. Additionally to that can all gromos++ functions be used from the Gromos System, so system generation can be easily accomplished.

if you want to remove all binary checks, do the following: >>> from pygromos.files.gromos_system.gromos_system import Gromos_System >>> Gromos_System._gromos_noBinary_checks = True >>> sys = Gromos_System()

Parameters

• work_folder (str) – This gives the initial working folder for the system.

• system_name (str) – the name of the system, also used as file prefix

• in_smiles (str, optional) – Molecule input SMILES for file generation, by default None

• in_top_path (str, optional) – input Gromos topology path (.top), by default None

• in_cnf_path (str, optional) – input Gromos coordinate path (.cnf), by default None

• in_imd_path (str, optional) – input Gromos simulation parameters path (.imd), by default None

• in_disres_path (str, optional) – input Gromos distance restraint path (.disres), by default None

• in_ptp_path (str, optional) – input pertubation file for free energy calculations (.ptp), by default None

• in_posres_path (str, optional) – input position restraints file (.por), by default None

• in_qmmm_path (str, optional) – qmmm parameter file (.qmmm), by default None

• in_refpos_path (str, optional) – input reference position file (.rpf), by default None

• in_gromosXX_bin_dir (str, optional) – path to the binary dir of GromosXX, by default None -> uses the set binaries in the PATH variable

• in_gromosPP_bin_dir (str, optional) – path to the binary dir of GromosPP, by default None -> uses the set binaries in the PATH variable

• rdkitMol (Chem.rdchem.Mol, optional) – input rdkit Molecule, by default None

• in_mol2_file (str, optional) – path to input mol2 file, by default None

• readIn (bool, optional) – readIn all provided files?, by default True

• Forcefield (forcefield_system, optional) – input PyGromos - forcefield Class , by default forcefield_system()

• auto_convert (bool, optional) – automatically convert rdkit MOL and smiles to gromos files, by default False

• adapt_imd_automatically (bool, optional) – adjust the input imd file to the GromosSystem, by default True

• verbose (bool, optional) – Stay a while and listen!, by default False

Raises

Warning – Rises warning if files are not present.

adapt_imd(not_ligand_residues: List[str] = [])

property all_file_paths: Dict[str, str]

property all_files: Dict[str, pygromos.files._basics._general_gromos_file._general_gromos_file]

auto_convert()

property cnf: pygromos.files.coord.cnf.Cnf

copy()

property disres: pygromos.files.topology.disres.Disres

generate_posres(residues: typing.List = [<class 'int'>], keep_residues: bool = True, verbose: bool = False)

get_file_paths() → Dict[str, str]

get the paths of the files in a dict.

Returns

returns alle file paths, with attribute file name as key.

Return type

Dict[str, str]

get_script_generation_command(var_name: Optional[str] = None, var_prefixes: str = '') → str

property gromosPP: pygromos.gromos.gromosPP.GromosPP

property gromosPP_bin_dir: str

property gromosXX: pygromos.gromos.gromosXX.GromosXX

property gromosXX_bin_dir: str

property imd: pygromos.files.simulation_parameters.imd.Imd

classmethod load(path: Optional[Union[str, _io.FileIO]] = None) → object

This method stores the Class as binary obj to a given path or fileBuffer.

property name: str

non_ligand_info: pygromos.files.coord.cnf.ligands_info

optional_files = {'disres': <class 'pygromos.files.topology.disres.Disres'>, 'posres': <class 'pygromos.files.coord.posres.Position_Restraints'>, 'ptp': <class 'pygromos.files.topology.ptp.Pertubation_topology'>, 'qmmm': <class 'pygromos.files.qmmm.qmmm.QMMM'>, 'refpos': <class 'pygromos.files.coord.refpos.Reference_Position'>}

parse_attribute_files(file_mapping: Dict[str, str], readIn: bool = True, verbose: bool = False)

This function sets dynamically builds the output folder, the file objs of this class and checks their dependencies.

Parameters

file_mapping (Dict[str, Union[str, None]]) – attribute name: input path

property posres: pygromos.files.coord.posres.Position_Restraints

prepare_for_simulation(not_ligand_residues: List[str] = [])

protein_info: pygromos.files.coord.cnf.protein_info

property ptp: pygromos.files.topology.ptp.Pertubation_topology

property qmmm: pygromos.files.qmmm.qmmm.QMMM

rdkit2Gromos()

rdkit2GromosName() → str

rdkitImport(inputMol: rdkit.Chem.rdchem.Mol)

read_files(verbose: bool = False)

rebase_files()

property refpos: pygromos.files.coord.refpos.Reference_Position

required_files = {'cnf': <class 'pygromos.files.coord.cnf.Cnf'>, 'imd': <class 'pygromos.files.simulation_parameters.imd.Imd'>, 'top': <class 'pygromos.files.topology.top.Top'>}

residue_list: Dict

save(path: Optional[Union[str, _io.FileIO]] = None, safe: bool = True) → str

This method stores the Class as binary obj to a given path or fileBuffer.

solute_info: pygromos.files.coord.cnf.solute_info

solvent_info: pygromos.files.coord.cnf.solvent_info

property top: pygromos.files.topology.top.Top

traj_files = {'trc': <class 'pygromos.files.trajectory.trc.Trc'>, 'tre': <class 'pygromos.files.trajectory.tre.Tre'>}

property trc: pygromos.files.trajectory.trc.Trc

property tre: pygromos.files.trajectory.tre.Tre

property work_folder: str

work_folder_no_update(work_folder: str)

write_files(cnf: bool = False, imd: bool = False, top: bool = False, ptp: bool = False, disres: bool = False, posres: bool = False, refpos: bool = False, qmmm: bool = False, mol: bool = False, all: bool = True, verbose: bool = False)

Module contents