mk_prepare_receptor.py CLI Reference

usage: mk_prepare_receptor.py [-h] [--read_pdb PDB_FILENAME]
                              [--read_pqr PQR_FILENAME] [-i MACROMOL_FILENAME]
                              [-o OUTPUT_BASENAME] [-p [PDBQT_FILENAME ...]]
                              [-j [JSON_FILENAME ...]]
                              [--write_pdb [PDB_FILENAME ...]]
                              [-g [GPF_FILENAME ...]]
                              [-v [VINA_BOX_FILENAME ...]] [-n SET_TEMPLATE]
                              [-d DELETE_RESIDUES] [-b BLUNT_ENDS]
                              [--add_templates JSON_FILENAME [JSON_FILENAME ...]]
                              [--cache_templates [CACHE_TEMPLATES]]
                              [--mk_config JSON_FILENAME] [-a]
                              [--default_altloc DEFAULT_ALTLOC]
                              [--wanted_altloc WANTED_ALTLOC] [-f FLEXRES]
                              [--charge_model {gasteiger,espaloma,zero,read}]
                              [--box_size X Y Z] [--box_center X Y Z]
                              [--box_center_off_reactive_res]
                              [--box_enveloping FILENAME] [--padding PADDING]
                              [-r REACTIVE_FLEXRES]
                              [--reactive_name REACTIVE_NAME]
                              [-s REACTIVE_NAME_SPECIFIC] [--r_eq_12 R_EQ_12]
                              [--eps_12 EPS_12]
                              [--r_eq_13_scaling R_EQ_13_SCALING]
                              [--r_eq_14_scaling R_EQ_14_SCALING]

Input/Output

--read_pdb

reads PDB, not PDBQT, and does not use ProDy

--read_pqr

reads PQR and does not use ProDy

-i, --read_with_prody

reads PDB/mmCIF file with Prody

-o, --output_basename

default basename for –write options used without filename

-p, --write_pdbqt

adds _rigid/_flex with flexible residues (filename defaults to –output_basename when not specified)

-j, --write_json

parameterized receptor (filename defaults to –output_basename when not specified)

--write_pdb

prepared receptor (must specify filename)

-g, --write_gpf

autogrid input file (filename defaults to –output_basename when not specified)

-v, --write_vina_box

config file for Vina with box dimensions (filename defaults to –output_basename when not specified_

Receptor perception

-n, --set_template

e.g. A:5,7=CYX,B:17=HID

-d, --delete_residues

e.g. A:350,B:15,16,17

-b, --blunt_ends

e.g. A:123,200=2,A:1=0

--add_templates

[.json]

Default: []

--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.

Default: False

--mk_config

[.json]

-a, --allow_bad_res

delete residues with missing atoms instead of raising error

Default: False

--default_altloc

default alternate location (overridden by –wanted_altloc)

--wanted_altloc

require altloc for specific residues, e.g. :5=B,B:17=A

-f, --flexres

specify the flexible residues by the chain ID and residue number, e.g. -f “:42,B:23” is equivalent to -f “:42” -f “B:23” (leave chain ID empty if omitted in input PDB or mmCIF)

Default: []

--charge_model

Possible choices: gasteiger, espaloma, zero, read

default is gasteiger, ‘zero’ sets all zeros, ‘read’ requires –read_pqr

Size and center of grid box

--box_size

size of grid box (x, y, z) in Angstrom

--box_center

center of grid box (x, y, z) in Angstrom

--box_center_off_reactive_res

project grid box center along CA-CB bond 5 A away from CB (only applicable when there is exactly one reactive flexible residue)

Default: False

--box_enveloping

Box will envelop atoms in this file [.sdf .mol .mol2 .pdb .pdbqt]

--padding

padding around atoms passed to –box_enveloping [A]

Reactive

-r, --reactive_flexres

same as –flexres but for reactive residues (max 8)

Default: []

--reactive_name

set name of reactive atom of a residue type, e.g: –reactive_name ‘TRP:NE1’. Repeat flag for multiple assignments. Overridden by –reactive_name_specific

Default: []

-s, --reactive_name_specific

set name of reactive atom for an individual residue by the residue ID, e.g: -s ‘A:42=NE2’. Residue will be reactive.

Default: []

--r_eq_12

r_eq for reactive atoms (1-2 interaction)

Default: 1.8

--eps_12

epsilon for reactive atoms (1-2 interaction)

Default: 2.5

--r_eq_13_scaling

r_eq scaling for 1-3 interaction across reactive atoms

Default: 0.5

--r_eq_14_scaling

r_eq scaling for 1-4 interaction across reactive atoms

Default: 0.5