ReceptorToolbox

Overview

ReceptorToolbox is a utility program for receptors that can do the following

  • List information about the receptor
  • Set the name of the receptor and/or bound ligand
  • Extract molecules from the receptor
  • Setup a scoring cache for FRED, HYBRID or ScorePose.
  • Enable/Disable existing constraints.

Example Commands

Setup a receptor cache for fred

This example illustrates setting up a receptor cache for FRED.

Input files

  • receptor.oeb.gz : A file containing a receptor.

Command line

prompt> receptor_toolbox -receptor receptor.oeb.gz -prepare_score_cache fred

Output files

  • receptor.oeb.gz : Receptor with score cache for FRED (overwrites input file).

Command Line Help

A description of the command line interface can be obtained by executing ReceptorToolbox with the --help option.

> receptor_toolbox --help

will generate the following output:

Help functions:
  receptor_toolbox --help simple      : Get a list of simple parameters
  receptor_toolbox --help all         : Get a complete list of parameters
  receptor_toolbox --help defaults    : List the defaults for all parameters
  receptor_toolbox --help <parameter> : Get detailed help on a parameter
  receptor_toolbox --help html        : Create an html help file for this program
  receptor_toolbox --help versions    : List the toolkits and versions used in the application

Required Parameters

Receptor File to Operate On

-receptor <receptor file>

ReceptorToolbox reads this receptor file, and if the receptor is edited in any way the modified receptor will be output to this file (overwriting the original).

[ Aliases : -rec ]

Optional Parameters

Molecule Titles

-set_receptor_title <title> [No Default]

If this flag is specified the title of the receptor will be set to the specified value.

[ Aliases : -receptor_title ]

-set_bound_ligand_title <title> [No Default]

If this flag is set the title of the bound ligand will be set to the specified value.

[ Aliases : -set_ligand_title, -ligand_title ]

Score Caching

-prepare_score_cache <fred, scorepose or hybrid> [No Default]

Caches scoring setup for the specified program on the receptor. This is not required, however doing so will improve the initial speed of the program by not requiring it to do as much scoring setup.

A receptor can only have a score cache for one program at a time (previous score caches will be erased when this flag is used).

Note

Creating a score cache will substantially increase the size of the receptor file, typically on the order of 100 MBytes.

[ Aliases -prepare ]

-clear_score_cache [Default: false]

If this flag is set to true any scoring cache on the receptor will be removed.

[ Aliases : -clear_cache ]

Extract Molecules

-extract_bound_ligand <filename> [No Default]

Extracts the receptor’s bound ligand to the specified file.

[ Aliases : -extract_ligand, -bound_ligand, -ligand ]

-extract_protein <filename> [No Default]

Extracts the receptor’s protein structure to the specified file.

[ Aliases : -protein ]

-extract_extra_molecules <filename> [No Default]

Extracts the receptor’s extra molecules to the specified file.

[ Aliases : -extra_molecules, -extra ]

Inner Contour

-turn_inner_contour <on or off> [No Default]

If this flag is set the inner contour will be turned on or off, as specified. See Receptor Theory Section for an explanation of the inner contour.

[ Aliases : -inner_contour, -inner ]

Protein Constraints

-enable_protein_constraint <name> [<name> ...] [No Default]

Enables the specified protein constraints. The name can be either the name of the constraint or the name of the atom that the constraint is associated with.

[ Aliases : -enable_protein_constraints ]

-disable_protein_constraint <name> [<name> ...] [No Default]

Disables the specified protein constraints. The name can be either the name of the constraint or the name of the atom that the constraint is associated with.

[ Aliases : -disable_protein_constraints ]

-enable_all_protein_constraints [Default: false]

Enables all protein constraints.

[ Aliases : -enableallproteinconstraints ]

-disable_all_protein_constraints [Default: false]

Disables all protein constraints.

[ Aliases : -disableallproteinconstraints ]

Custom Constraints

-extract_custom_constraints <filename> [No Default]

Extracts the receptors custom constraint’s to this specified file.

-set_custom_constraints <filename> [No Default]

Sets the receptors custom constraints to be those in the specified file.

The format of the constraint file is a text file with lines of one of the two following forms

SPHERE <ID> <RAD> <X> <Y> <Z>
SMARTS <ID> <SMARTS Pattern>
  • SPHERE creates a sphere associated with a given constraint

    • ID is an integer that uniquely identifies a constraint
    • RAD is the radius of the sphere
    • X, Y and Z is the sphere center
  • SMARTS Creates a SMARTS pattern associated with the specified sphere.

    • ID is an integer that uniquely identifies a constraint
    • SMARTS Pattern is the SMARTS pattern to associate with the constraint.

The following example file

SPHERE 1 4.0 1.0 1.0 1.0
SMARTS 1 F
SPHERE 2 4.5 3.0 2.5 -1.0

Creates two constraints. Constraint 1 has one sphere centered at (1.0, 1.0, 1.0) with radius 4.0 and can only be satisfied by a fluorine atom on the ligand. Constraint 2 has one sphere centered at (3.0, 2.5, -1,0) with radius 4.5 and can be satisfied by any heavy atom on the ligand since the constraint as no associated smarts patterns.

See Receptor Theory Section for more information about constraints.

-enable_custom_constraint <constraint> [<constraint> ...] [No Default]

Enables the specified custom constraints.

[ Aliases : -enable_custom_constraint, -enable_custom_constraints ]

-disable_custom_constraint <constraint> [<constraint> ...] [No Default]

Disables the specified custom constraints.

[ Aliases : -disable_custom_constraints ]

-enable_all_custom_constraints [Default: false]

If this flag is set to true all custom constraints on the receptor are enabled.

-disable_all_custom_constraints [Default: false]

If this flag is set to true all custom constraints on the receptor are disabled.