ReceptorInDU¶
Overview¶
ReceptorInDU is a utility program to make a receptor inside a prepared OEDesignUnit.
Note
While ReceptorInDU is good at automatically setting up receptors, it is recommended that the MakeReceptor GUI be used to examine/modify the receptor created by ReceptorInDU prior to using it with FRED, HYBRID or POSIT. Particularly, if a user wants to define constraints or include specific water molecules in the receptor. This step is not required, however.
See also
The SPRUCE chapter
Example Commands¶
Make receptor version of OEDU file for 5MM6¶
Converts the prepared OEDU file into a receptor containing OEDU file.
Input files
5MM6_HIL__DU__32U_H-311.oedu : OEDU file to convert into a receptor.
Command line
prompt> receptorindu 5MM6_HIL__DU__32U_H-311.oedu rec_5MM6_HIL__DU__32U_H-311.oedu
Output files
rec_5MM6_HIL__DU__32U_H-311.oedu : Receptor version of 5MM6 design unit.
Command Line Help¶
A description of the command line interface can be obtained by executing ReceptorInDU with the –help option.
> receptorindu --help
will generate the following output:
Help functions:
receptorindu --help simple : Get a list of simple parameters
receptorindu --help all : Get a complete list of parameters
receptorindu --help defaults : List the defaults for all parameters
receptorindu --help <parameter> : Get detailed help on a parameter
receptorindu --help html : Create an html help file for this program
receptorindu --help versions : List the toolkits and versions used in the application
Required Parameters¶
-
-in<filename>¶ An OEDesignUnit file generated by Spruce.
[keyless parameter 1]
Optional Parameters¶
Input Options¶
-
-molnames¶ This parameter specifies a text file containing a list of molecule names (one name per line in the file). If this parameter is set then only molecule in the input file(s) (see parameter
-in) with names that match those in the text files will be read in.The general purpose of this flag is to provide an easy mechanism for reading a few specific molecule(s) that are contained in a large database, without having to extract those molecules by hand from the database.
Output Options¶
-
-out<filename>¶ An OEDesignUnit file containing the receptor.
[keyless parameter 2]
-
-prefix¶ Prefix used to name output files.
-
-progress¶ Show progress on screen. Options are ‘none’, ‘dots’, ‘log’ and ‘percent’. The ‘dots’ options will displays dots on screen to show molecules completed. The ‘log’ option will duplicate the log file on screen. The ‘percent’ option will track progress through the input file. [default = none]
Receptor Options¶
-
-targetMask[Default: targetComplexNoSolvent]¶ Design unit components mask defining the subset of design unit components to be used as targets for the receptor. Multiple components can also be combined as a comma separated string to create the input.
Possible values:
cofactors, counter_ions, excipients, lipids, metals, nucleic, other_cofactors, other_ligands, other_nucleics, other_proteins, packing_residues, polymers, post_translational, protein, solvent, sugars
Multi component choices:
targetComplex (protein,nucleic,cofactors,solvent,metals,counter_ions,lipids,other_proteins, other_nucleics,other_ligands,other_cofactors)
targetComplexNoSolvent (protein,nucleic,cofactors,metals,lipids,other_proteins, other_nucleics,other_ligands,other_cofactors)
macroMolComponents (protein,nucleic,other_proteins,other_nucleics)
-
-targetPred¶ Residue-based selection predicate to subset components of the design unit targetMask. The predicate is only enforced on a component of the targetMask if it matches something in that component from the design unit. Input like: “HOH:1024: :A|HOH:567: :A|” with a targetMask that includes the solvent from the designunit, will subset the solvent component to only include these specific water molecules in the receptor generation, however, since this does not match anything in the Protein component of the design unit it will leave that component as is.
-
-negImageType[Default: standard]¶ The type of negative image to create in generating the receptor grid. Choices: large, standard, small
-
-box<box file> [No Default]¶ A file describing a box enclosing the active site. All docked poses will be required to fit within this box.
The box must be in a 3D molecular format. SDF, MOL2, OEBinary and several other common molecular formats are supported.
The box will always be aligned along the X, Y and Z axis of the coordinate system and the edges of the box will be the maximum and minimum X, Y and Z value of any atom in the box file.
Note
The bound ligand is ignored for active site detection, when this flag is specified.