Options of mk_prepare_ligand.py
===============================

Input/Output Options
~~~~~~~~~~~~~~~~~~~~

.. option:: -i, --mol <input_molecule_filename>

   The input molecule file, in formats such as MOL2, SDF, etc. This option is required.

.. option:: --name_from_prop <property_name>

   Set the molecule name using a specified RDKit or SDF property.

.. option:: -o, --out <output_pdbqt_filename>

   Specify the output PDBQT filename. Only compatible with single-molecule input.

.. option:: --multimol_outdir <output_directory>

   Specify the directory to write PDBQT output files for multi-molecule inputs. Incompatible with `-o/--out` and `-`/`--`.

.. option:: --multimol_prefix <prefix>

   Replace the internal molecule name in multi-molecule input with the specified prefix. Incompatible with `-o/--out` and `-`/`--`.

.. option:: -z, --multimol_targz

   (Flag) Compress output files into a `.tar.gz` archive.

.. option:: --multimol_targz_size <size>

   Define the number of PDBQT files per `.tar.gz` archive. Default is 10000.

.. option:: -, --

   (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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. option:: -c, --config_file <config_file>

   Configure `MoleculePreparation` from a JSON file. Command-line arguments will override settings in the file.

.. option:: --rigid_macrocycles

   (Flag) Keep macrocycles rigid in their input conformation.

.. option:: --macrocycle_allow_A

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

.. option:: --keep_chorded_rings

   (Flag) Retain all rings from exhaustive ring perception.

.. option:: --keep_equivalent_rings

   (Flag) Retain rings with equivalent sizes and neighboring atoms.

.. option:: --min_ring_size <size>

   Define the minimum number of atoms required in a ring for it to be considered for opening.

.. option:: -w, --hydrate

   (Flag) Add water molecules to the structure for hydrated docking.

.. option:: --merge_these_atom_types <types> [*]

   Specify a list of atom types to merge. The default is `"H"`.

.. option:: -r, --rigidify_bonds_smarts <SMARTS>

   Provide SMARTS patterns to rigidify specific bonds in the molecule.

.. option:: -b, --rigidify_bonds_indices <i j>

   Specify the indices of two atoms that define a bond in the SMARTS pattern (starting from 1).

.. option:: -a, --flexible_amides

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

.. option:: -p, --load_atom_params <JSON_FILENAME>

   Specify SMARTS-based atom typing in JSON format.

.. option:: -aa, --add_atom_types <JSON>

   Specify additional atom types to assign in JSON format, with SMARTS patterns and atom type names.

.. option:: --double_bond_penalty <penalty>

   Set a penalty value; values greater than 100 prevent breaking double bonds.

.. option:: --charge_model <model>

   Choose the charge model: `gasteiger`, `espaloma`, or `zero`. Default is `gasteiger`; `zero` sets all charges to zero.

.. option:: --bad_charge_ok

   (Flag) Allow NaN and Inf charges in the PDBQT output.

.. option:: --add_index_map

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

.. option:: --remove_smiles

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

Reactive Docking Options
~~~~~~~~~~~~~~~~~~~~~~~~

.. option:: --reactive_smarts <SMARTS>

   Provide a SMARTS pattern for defining the reactive group.

.. option:: --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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. option:: --receptor <filename>

   Specify the receptor file. Supported formats depend on ProDy availability, such as `.pdb` and `.mmcif`.

.. option:: --rec_residue <residue>

   Specify the residue in the receptor for attachment, e.g., `A:LYS:204`.

.. option:: --tether_smarts <SMARTS>

   Provide a SMARTS pattern defining the ligand atoms used for attachment to the receptor.

.. option:: --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`).