Options of mk_prepare_ligand.py

Contents

Options of mk_prepare_ligand.py#

Input/Output Options#

-i, --mol <input_molecule_filename>#: The input molecule file, in formats such as MOL2, SDF, etc. This option is required.

--name_from_prop <property_name>#: Set the molecule name using a specified RDKit or SDF property.

-o, --out <output_pdbqt_filename>#: Specify the output PDBQT filename. Only compatible with single-molecule input.

--multimol_outdir <output_directory>#: Specify the directory to write PDBQT output files for multi-molecule inputs. Incompatible with -o/–out and -/–.

--multimol_prefix <prefix>#: Replace the internal molecule name in multi-molecule input with the specified prefix. Incompatible with -o/–out and -/–.

-z, --multimol_targz#: (Flag) Compress output files into a .tar.gz archive.

--multimol_targz_size <size>#: Define the number of PDBQT files per .tar.gz archive. Default is 10000.

-, --#: (Flag) Redirect output to standard output (STDOUT) instead of writing a file. Ignored if -o/–out is specified. Only compatible with single-molecule input.

Molecule Preparation Options#

-c, --config_file <config_file>#: Configure MoleculePreparation from a JSON file. Command-line arguments will override settings in the file.

--rigid_macrocycles#: (Flag) Keep macrocycles rigid in their input conformation.

--macrocycle_allow_A#: (Flag) Allow bond break with atom type A, which will be retyped as carbon (C).

--keep_chorded_rings#: (Flag) Retain all rings from exhaustive ring perception.

--keep_equivalent_rings#: (Flag) Retain rings with equivalent sizes and neighboring atoms.

--min_ring_size <size>#: Define the minimum number of atoms required in a ring for it to be considered for opening.

-w, --hydrate#: (Flag) Add water molecules to the structure for hydrated docking.

--merge_these_atom_types <types> [*]#: Specify a list of atom types to merge. The default is “H”.

-r, --rigidify_bonds_smarts <SMARTS>#: Provide SMARTS patterns to rigidify specific bonds in the molecule.

-b, --rigidify_bonds_indices <i j>#: Specify the indices of two atoms that define a bond in the SMARTS pattern (starting from 1).

-a, --flexible_amides#: (Flag) Allow amide bonds to rotate, making them non-planar (not recommended).

-p, --load_atom_params <JSON_FILENAME>#: Specify SMARTS-based atom typing in JSON format.

-aa, --add_atom_types <JSON>#: Specify additional atom types to assign in JSON format, with SMARTS patterns and atom type names.

--double_bond_penalty <penalty>#: Set a penalty value; values greater than 100 prevent breaking double bonds.

--charge_model <model>#: Choose the charge model: gasteiger, espaloma, or zero. Default is gasteiger; zero sets all charges to zero.

--bad_charge_ok#: (Flag) Allow NaN and Inf charges in the PDBQT output.

--add_index_map#: (Flag) Include a map of atom indices from the input to the PDBQT file.

--remove_smiles#: (Flag) Exclude SMILES from being written as a remark in the PDBQT output.

Reactive Docking Options#

--reactive_smarts <SMARTS>#: Provide a SMARTS pattern for defining the reactive group.

--reactive_smarts_idx <index>#: Specify the 1-based index of the reactive atom within the SMARTS pattern provided by –reactive_smarts.

Covalent Docking (Tethered) Options#

--receptor <filename>#: Specify the receptor file. Supported formats depend on ProDy availability, such as .pdb and .mmcif.

--rec_residue <residue>#: Specify the residue in the receptor for attachment, e.g., A:LYS:204.

--tether_smarts <SMARTS>#: Provide a SMARTS pattern defining the ligand atoms used for attachment to the receptor.

--tether_smarts_indices <IDX IDX>#: Specify the 1-based indices of the two atoms in the SMARTS pattern that will be attached (default: 1 2).