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.

property align_molecules_using_mcs

After determining the maximum common substructure (MCS), use it to align the coordinates of the second molecule to the first.

Returns:

default (False)

Return type:

bool

property allow_disjoint_components

Defines whether there might be multiple superimposed areas that are separated by alchemical region.

Returns:

default (False)

Return type:

bool

property ambertools_antechamber

Antechamber path based on the .ambertools_home

Returns:

property ambertools_home

Ambertools HOME path. If not configured, the env variable AMBERHOME as AMBER_PREFIX will be checked.

Returns:

ambertools path

property ambertools_parmchk2

Parmchk2 path based on the .ambertools_home :return:

property ambertools_tleap

Tleap path based on the .ambertools_home :return:

property antechamber_dr

Whether to use -dr setting when calling antechamber.

Returns:

property atom_pair_q_atol

It defines the maximum difference in charge between any two superimposed atoms a1 and a2. If the two atoms differ in charge more than this value, they will be unmatched and added to the alchemical regions.

Returns:

default (0.1e)

Return type:

float

property complex_tleap_in

The tleap input file for the complex.

Returns:

Default ‘leap_complex.in’

Type:

string

property coordinates_file

A file from which coordinate can be taken.

Returns:

static get_element_map()

Returns:

get_serializable()

Get a JSON serializable structure of the config.

pathlib.Path is not JSON serializable, so replace it with str

todo - consider capturing all information about the system here, including each suptop.get_serializable() so that you can record specific information such as the charge changes etc.

Returns:

Dictionary {key:value} with the settings

Return type:

Dictionary

property ignore_charges_completely

Ignore the charges during the superimposition. Useful for debugging. :return: default (False) :rtype: bool

property lig_acprep_dir

Directory location where the .ac charges are converted into the .mol2 format.

Returns:

Default (workdir/prep/acprep_to_mol2)

property lig_dir

Directory location with the .mol2 files.

Returns:

Default (workdir/mol2)

property lig_frcmod_dir

Directory location with the .frcmod created for each ligand.

Returns:

Default (workdir/prep/ligand_frcmods)

property lig_unique_atom_names_dir

Directory location for files with unique atom names.

Returns:

Default (workdir/prep/unique_atom_names)

property ligand_ff

The forcefield for the ligand.

property ligand_ff_name

Either GAFF or GAFF2

Returns:

property ligand_files

A list of ligand filenames. :return:

property ligand_net_charge

The ligand charge. If not provided, neutral charge is assumed. The charge is necessary for calling antechamber (-nc).

Returns:

property ligand_tleap_in

The name of the tleap input file for ambertools for the ligand.

Returns:

Default (‘leap_ligand.in’)

Return type:

string

property ligands_contain_q

If not provided, it tries to deduce whether charges are provided. If all charges are set to 0, then it assumes that charges are not provided.

If set to False explicitly, charges are ignored and computed again.

Returns:

default (None)

Return type:

bool

property manually_matched_atom_pairs

Either a list of pairs or a file with a list of pairs of atoms that should be superimposed/matched.

Returns:

property manually_mismatched_pairs

A path to a file with a list of a pairs that should be mismatched.

property md_engine

The MD engine, with the supported values NAMD2.13, NAMD2.14, NAMD3 and OpenMM

Returns:

NAMD2.13, NAMD2.14, NAMD3 and OpenMM

Return type:

string

property net_charge_threshold

Defines how much the superimposed regions can, in total, differ in charge. If the total exceeds the thresholds, atom pairs will be unmatched until the threshold is met.

Returns:

default (0.1e)

Return type:

float

property pair_morphfrcmods_dir

Path to the .frcmod files for the morph.

Returns:

Default (workdir/prep/morph_frcmods)

property pair_morphfrmocs_tests_dir

Path to the location where a test is carried out with .frcmod

Returns:

Default (workdir/prep/morph_frcmods/tests)

property pair_unique_atom_names_dir

Location of the morph files with unique filenames.

Returns:

Default (workdir/prep/morph_unique_atom_names)

property prep_dir

Path to the prep directory. Currently in the workdir

Returns:

Default (workdir/prep)

property protein

Path to the protein

Returns:

Protein filename

Return type:

str

property protein_ff

The protein forcefield to be used by ambertools for the protein parameterisation.

Returns:

default (leaprc.ff19SB)

Return type:

string

property redistribute_q_over_unmatched

The superimposed and matched atoms have every slightly different charges. Taking an average charge between any two atoms introduces imbalances in the net charge of the alchemical regions, due to the different charge distribution.

Returns:

default(True)

property superimposition_starting_pair

Set a starting pair for the superimposition to narrow down the MCS search. E.g. “C2-C12”

Return type:

str

property use_element_in_superimposition

Use element rather than the actual atom type for the superimposition during the joint-traversal of the two molecules.

Returns:

default (False)

Return type:

bool

property use_hybrid_single_dual_top

Hybrid single dual topology (experimental). Currently not implemented.

Returns:

default(False).

property use_original_coor

Antechamber when assigning charges can modify the charges slightly. If that’s the case, use the original charges in order to correct this slight divergence in coordinates.

Returns:

default (?)

Return type:

bool

property workdir

Working directory for antechamber calls. If None, a temporary directory in /tmp/ will be used.

Returns:

Work dir

Return type:

str