Options of mk_prepare_receptor.py

Contents

Options of mk_prepare_receptor.py#

Input/Output Options#

--read_pdb <PDB_FILENAME>#: Read a PDB file using the PDB parser in RDKit.

--read_pqr <PQR_FILENAME>#: Read PQR file and does not use ProDy

-i, --read_with_prody <MACROMOL_FILENAME>#: Read a PDB or mmCIF file using ProDy (if installed). ProDy can be installed from PyPI or conda-forge.

-o, --output_basename <basename>#: Specify a default basename for output files created by –write options when no filename is specified.

-p, --write_pdbqt <PDBQT_FILENAME> [*]#: Output PDBQT files with _rigid or _flex suffixes for flexible residues. Defaults to –output_basename if no filename is provided.

-j, --write_json <JSON_FILENAME> [*]#: Save the receptor’s parameterized configuration to JSON format. Defaults to –output_basename if unspecified.

--write_pdb [PDB_FILENAME ...]#
Write prepared receptor to pdb (must specify filename)#

-g, --write_gpf <GPF_FILENAME> [*]#: Output an AutoGrid input file (GPF). Defaults to –output_basename if not specified.

-v, --write_vina_box <VINA_BOX_FILENAME> [*]#: Generate a configuration file for Vina with grid box dimensions. Defaults to –output_basename if not specified.

--write_pdb <PDB_FILENAME> [*]#: Save the prepared receptor in PDB format. Must specify the filename.

--debug_fn DEBUG_FN#
Log debug elvel to filename DEBUG_FN#

Receptor Perception Options#

-n, --set_template <template>#: Assign templates to residues, e.g., A:5,7=CYX,B:17=HID.

-d, --delete_residues <residues>#: Specify residues to delete, e.g., A:350,B:15,16,17.

-b, --blunt_ends <positions>#: Blunt end definitions, e.g., A:123,200=2,A:1=0.

--add_templates <JSON_FILENAME> [*]#: Load additional templates from one or more JSON files.

--cache_templates [CACHE_TEMPLATES]#
Turns on caching of ResidueChemTemplates (default is OFF) by this option and (optionally) a provided JSON filename.#
Default cache filename is: $HOME/.meeko_residue_chem_templates_cached.json) When the caching is ON, the templates#
for polymer construction will be read from the specified cache file and updates may be made to the same file in a#
cumulative manner.#

--config_preset#: Name of packaged configuration (choices: scofu1). Overriden by –config_file and by command line options.

--config_file#: Local json configuration file. Overrides –config_preset option-wise. Overriden by command line options.

-d, --delete_bad_res#: (Flag) Ignore residues with missing atoms instead of raising an error. Replaces previous option -a or –allow_bad_res

--delete_bad_res_from_box_radius#: specify radius from box surface outside of which unmatched residues will be deleted. Requires –box_center or –box_enveloping. Incompatible with –delete_bad_res.

--default_altloc <location>#: Define a default alternate location for residues, overridden by –wanted_altloc.

--wanted_altloc <location>#
Specify alternate locations for particular residues, e.g., `:5=B,B:17=A`.#

--compute_charges#
Flag to request that charges be computed from scratch. Default is to read#
pre-calculated charges from template, which is much faster.#

--charge_model [gasteiger, nagl, espaloma, zero, read]#
Specify charge model to use. Charges will be computed or extracted from template depending#
on the `--compute_charges` flag. Note that computing Nagl or Espaloma charges from scratch#
can be slow.#
Default is gasteiger, 'zero' sets all zeros, 'read' requires --read_pqr#

Grid Box Options#

--box_size <X Y Z>#: Set the size of the grid box in Angstroms (x, y, z).

--box_center <X Y Z>#: Define the center of the grid box in Angstroms (x, y, z).

--box_center_off_reactive_res#: (Flag) Shift the grid box center 5 Å along the CA-CB bond from CB. Applicable only when there is one reactive flexible residue.

--box_enveloping <FILENAME>#: Adjust the grid box to enclose atoms in the specified file. Supported formats: .sdf, .mol, .mol2, .pdb, .pdbqt.

--padding <value>#: Set padding around atoms specified in –box_enveloping (in Å).

Flexible and/or Reactive Options#

-f, --flexres <residues>#: Define flexible residues by chain ID and residue number, e.g., -f “:42,B:23”.

-r, --reactive_flexres <residues>#: Define reactive flexible residues by chain ID and residue number, e.g., -r “:42,B:23”. Maximum of 8 reactive residues.

--reactive_name <residue:atom>#: Specify the reactive atom name for a residue type, e.g., –reactive_name “TRP:NE1”. Can be repeated for multiple assignments.

-s, --reactive_name_specific <residue:atom>#: Specify the reactive atom for an individual residue by residue ID, e.g., -s “A:42=NE2”. The residue becomes reactive.

-t, --rot_terminal_group <residues>#: specify the residues for which to make terminal functional group rotatable by the chain ID and residue number, e.g. -t “:42,B:23” is equivalent to -t “:42” -t “B:23” (leave chain ID empty if omitted in input PDB or mmCIF)’

--r_eq_12 <value>#: Set the equilibrium distance (r_eq) for reactive atoms in 1-2 interactions. Default is 1.8 Å.

--eps_12 <value>#: Set the epsilon value for reactive atoms in 1-2 interactions. Default is 2.5.

--r_eq_13_scaling <factor>#: Scale r_eq for 1-3 interactions across reactive atoms. Default is 0.5.

--r_eq_14_scaling <factor>#: Scale r_eq for 1-4 interactions across reactive atoms. Default is 0.5.