mk_prepare_ligand.py CLI Reference

mk_prepare_ligand.py CLI Reference#

usage: mk_prepare_ligand.py [-h] [-v] -i INPUT_MOLECULE_FILENAME
                            [--name_from_prop NAME_FROM_PROP]
                            [-o OUTPUT_PDBQT_FILENAME]
                            [--multimol_outdir MULTIMOL_OUTPUT_DIR]
                            [--multimol_prefix MULTIMOL_PREFIX] [-z]
                            [--multimol_targz_size MULTIMOL_TARGZ_SIZE] [-]
                            [-c CONFIG_FILE] [--rigid_macrocycles]
                            [--macrocycle_allow_A] [--keep_chorded_rings]
                            [--keep_equivalent_rings]
                            [--min_ring_size MIN_RING_SIZE] [-w]
                            [--merge_these_atom_types [MERGE_THESE_ATOM_TYPES ...]]
                            [-r SMARTS] [-b i j [i j ...]] [-a]
                            [-p LOAD_ATOM_PARAMS [LOAD_ATOM_PARAMS ...]]
                            [-aa [{'smarts': '<smarts pattern>', 'atype': ',atomtype name>'}, {'smarts': '<smarts pattern>', 'atype': ',atomtype name>'}]]
                            [--double_bond_penalty DOUBLE_BOND_PENALTY]
                            [--charge_model {gasteiger,espaloma,zero,read}]
                            [--charge_atom_prop CHARGE_ATOM_PROP]
                            [--bad_charge_ok] [--add_index_map]
                            [--remove_smiles] [--rename_atoms]
                            [--reactive_smarts REACTIVE_SMARTS]
                            [--reactive_smarts_idx REACTIVE_SMARTS_IDX]
                            [--receptor RECEPTOR] [--rec_residue REC_RESIDUE]
                            [--tether_smarts TETHER_SMARTS]
                            [--tether_smarts_indices IDX IDX]

Named Arguments#

-v, --verbose

print information about molecule setup

Default: False

Input/Output#

-i, --mol

molecule file (MOL2, SDF,…)

--name_from_prop

set molecule name from RDKit/SDF property

-o, --out

output pdbqt filename. Single molecule input only.

--multimol_outdir

folder to write output pdbqt for multi-mol inputs. Incompatible with -o/–out and -/–.

--multimol_prefix

replace internal molecule name in multi-molecule input by specified prefix. Incompatible with -o/–out and -/–.

-z, --multimol_targz

compress output files in .tar.gz

Default: False

--multimol_targz_size

number of PDBQT files per .tar.gz

Default: 10000

-, --

do not write file, redirect output to STDOUT. Argument -o/–out is ignored. Single molecule input only.

Default: False

Molecule preparation#

-c, --config_file

configure MoleculePreparation from JSON file. Overriden by command line args.

--rigid_macrocycles

keep macrocycles rigid in input conformation

Default: False

--macrocycle_allow_A

allow bond break with atom type A, retyped as C

Default: False

--keep_chorded_rings

return all rings from exhaustive perception

Default: False

--keep_equivalent_rings

equivalent rings have the same size and neighbors

Default: False

--min_ring_size

min nr of atoms in ring for opening

-w, --hydrate

add water molecules for hydrated docking

Default: False

--merge_these_atom_types

list of atom types to merge, default is “H”

Default: ['H']

-r, --rigidify_bonds_smarts

SMARTS patterns to rigidify bonds

-b, --rigidify_bonds_indices

indices of two atoms (in the SMARTS) that define a bond (start at 1)

-a, --flexible_amides

allow amide bonds to rotate and be non-planar, which is bad

Default: False

-p, --load_atom_params

filename with SMARTS defined atom types (JSON format)

Default: ['ad4_types']

-aa, --add_atom_types

Additional atom types to assign (JSON formated)

--double_bond_penalty

penalty > 100 prevents breaking double bonds

--charge_model

Possible choices: gasteiger, espaloma, zero, read

default is ‘gasteiger’, ‘zero’ sets all zeros

Default: 'gasteiger'

--charge_atom_prop

set atom partial charges from an RDKit atom property based on the input file. The default is ‘PartialCharge’ for SDF and ‘_TriposPartialCharge’ for MOL2 unless overriden by a user defined property name.

--bad_charge_ok

NaN and Inf charges allowed in PDBQT

Default: False

--add_index_map

write map of atom indices from input to pdbqt

Default: False

--remove_smiles

do not write smiles as remark to pdbqt

Default: False

--rename_atoms

rename atoms: the new name will be the original name and its (1-based) index in MoleculeSetup

Default: False

Reactive docking#

--reactive_smarts

SMARTS pattern for reactive group

--reactive_smarts_idx

index (1-based) of the reactive atom in –reactive_smarts

Covalent docking (tethered)#

--receptor

receptor filename. Supported formats: [pdb/mmcif]

--rec_residue

examples: “A:LYS:204”, “A:HIS:”, “:LYS:”

--tether_smarts

SMARTS pattern to define ligand atoms for receptor attachment

--tether_smarts_indices

indices (1-based) of the SMARTS atoms that will be attached (default: 1 2)

Default: [1, 2]

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