ties.Config

class ties.Config(**kwargs)

The configuration with parameters that can be used to define the entire protocol. The settings can be overridden later in the actual classes.

The settings are stored as properties in the object and can be overwritten.

__init__(**kwargs)

Methods

__init__(**kwargs)
get_element_map()	return:
get_serializable()	Get a JSON serializable structure of the config.
set_configs(**kwargs)

Attributes

align_molecules_using_mcs	After determining the maximum common substructure (MCS), use it to align the coordinates of the second molecule to the first.
allow_disjoint_components	Defines whether there might be multiple superimposed areas that are separated by alchemical region.
ambertools_antechamber	Antechamber path based on the .ambertools_home
ambertools_home	Ambertools HOME path.
ambertools_parmchk2	Parmchk2 path based on the .ambertools_home :return:
ambertools_tleap	Tleap path based on the .ambertools_home :return:
antechamber_charge_type
antechamber_dr	Whether to use -dr setting when calling antechamber.
atom_pair_q_atol	It defines the maximum difference in charge between any two superimposed atoms a1 and a2.
complex_tleap_in	The tleap input file for the complex.
coordinates_file	A file from which coordinate can be taken.
ignore_charges_completely	Ignore the charges during the superimposition.
lambda_rep_dir_tree
lig_acprep_dir	Directory location where the .ac charges are converted into the .mol2 format.
lig_dir	Directory location with the .mol2 files.
lig_frcmod_dir	Directory location with the .frcmod created for each ligand.
lig_unique_atom_names_dir	Directory location for files with unique atom names.
ligand_ff	The forcefield for the ligand.
ligand_ff_name	Either GAFF or GAFF2
ligand_files	A list of ligand filenames.
ligand_net_charge	The ligand charge.
ligand_tleap_in	The name of the tleap input file for ambertools for the ligand.
ligands_contain_q	If not provided, it tries to deduce whether charges are provided.
manually_matched_atom_pairs	Either a list of pairs or a file with a list of pairs of atoms that should be superimposed/matched.
manually_mismatched_pairs	A path to a file with a list of a pairs that should be mismatched.
md_engine	The MD engine, with the supported values NAMD2.13, NAMD2.14, NAMD3 and OpenMM
net_charge_threshold	Defines how much the superimposed regions can, in total, differ in charge.
pair_morphfrcmods_dir	Path to the .frcmod files for the morph.
pair_morphfrmocs_tests_dir	Path to the location where a test is carried out with .frcmod
pair_unique_atom_names_dir	Location of the morph files with unique filenames.
prep_dir	Path to the prep directory.
protein	Path to the protein
protein_ff	The protein forcefield to be used by ambertools for the protein parameterisation.
redistribute_q_over_unmatched	The superimposed and matched atoms have every slightly different charges.
superimposition_starting_pair	Set a starting pair for the superimposition to narrow down the MCS search.
use_element_in_superimposition	Use element rather than the actual atom type for the superimposition during the joint-traversal of the two molecules.
use_hybrid_single_dual_top	Hybrid single dual topology (experimental).
use_original_coor	Antechamber when assigning charges can modify the charges slightly.
workdir	Working directory for antechamber calls.