RECEPTOR_TOOLBOX

Overview

RECEPTOR_TOOLBOX 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.

Input Preparation

No special preparation of the receptor is required.

Parameter List

Receptor File to Operate On

-receptor : Receptor is read from this file, and any modification will be written to this file.

Molecule Titles

-set_receptor_title : Sets the receptor title.

-set_bound_ligand_title : Sets the bound ligands title.

Score Caching

-prepare_score_cache : Adds a score cache to the receptor for a given program.

-clear_score_cache : Clears the score cache on the receptor.

Extract Molecules

-extract_bound_ligand : Extracts the bound ligand into a new file given the specified filename.

-extract_protein : Extracts the protein structure into a new file given the specified filename.

-extract_extra_molecules : Extracts the extra molecules into a new file given the specified filename.

Inner Contour

-turn_inner_contour : Turns the inner contour on or off.

Protein Constraints

-enable_protein_constraint : Enables the specified protein constraint.

-disable_protein_constraint : Disables the specified protein constraint.

-enable_all_protein_constraints : Enables all protein constraints.

-disable_all_protein_constraints : Disables all protein constraints.

Custom Constraints

-extract_custom_constraints : Extracts custom constraints into a new file given the specified filename.

-set_custom_constraints : Sets custom constraints from the specified file.

-enable_custom_constraint : Enables specified custom constraints.

-disable_custom_constraint : Disables specified custom constraints.

-enable_all_custom_constraints : Enables all custom constraints.

-disable_all_custom_constraints : Disables all custom constraints.

Note

Values in parenthesis are defaults.

Parameter Details

Receptor File to Operate On

-receptor <receptor file> [No Default: Required Parameter]

RECEPTOR_TOOLBOX 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 ]

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 on 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 trye all custom constraints on the receptor are disabled.

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).