Blastermaster

Blastermaster

Written by Ryan Coleman, based on a prototype in the lab (MakeDOCK/startdockblasterN) which was contributed to by many people.

Simple default usage

Create rec.pdb and xtal-lig.mol2 for the receptor and the ligand, and type:

./blastermaster.py -v 

Command line help

unix> ./blastermaster.py --help
Usage: blastermaster.py [options]

Turns pdb files into dockable grids & spheres.Rewrite of MakeDOCK/DOCKblaster
into non-makefile form

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -v, --verbose         lots of debugging output
  --elecapp             lots of electrostatics debugging files
  -r RECEPTOR, --receptor=RECEPTOR
                        receptor input pdb file, (default: rec.pdb)
  -l LIGAND, --ligand=LIGAND
                        crystal ligand input pdb file, (default: xtal-lig.pdb)
  -b DOCKBASE, --dockbase=DOCKBASE
                        DOCKBASE path for finding necessary programs,
                        (default: /raid4/people/mattchu/code/DOCK)
  -w WORKINGDIR, --working=WORKINGDIR
                        working directory for extra files (default: working)
  -o OUTPUTDIR, --output=OUTPUTDIR
                        output directory for DOCK input files (default:
                        dockfiles)
  --vdw=VDWPREFIX       vdw grid output filename prefix (default: vdw)
  --liganddesolv=LIGANDDESOLV
                        ligand desolvation output filename  (default:
                        ligand.desolv)
  --defaultFiles=DEFAULTFILES
                        default files  (default:
                        /raid4/people/mattchu/code/DOCK/proteins/defaults)
  --filterParams=FILTERPARAMS
                        input filter parameters, for binding site  (default: /
                        raid4/people/mattchu/code/DOCK/proteins/defaults/filt.
                        params)
  --filterProgram=FILTERPROGRAM
                        input filter program, for binding site  (default: /rai
                        d4/people/mattchu/code/DOCK/proteins/filt/bin/filt)
  --filterLog=FILTERLOG
                        filter logfile, for binding site  (default:
                        filter.log)
  --bindsiteResidues=BINDSITERESIDUES
                        binding site residues file (default: rec.site)
  --msProgram=MSPROGRAM
                        molecular surface program (default:
                        /raid4/people/mattchu/code/DOCK/proteins/dms/bin/dms)
  --msOutput=MSOUTPUT   molecular surface output (default: rec.ms)
  --msLog=MSLOG         molecular surface logfile (default: dms.log)
  --sphgenProgram=SPHGENPROGRAM
                        sphere generation program (default: /raid4/people/matt
                        chu/code/DOCK/proteins/sphgen/bin/sphgen)
  --sphgenOutput=SPHGENOUTPUT
                        sphere generation output (default: all_spheres.sph)
  --pdbsphProgram=PDBSPHPROGRAM
                        pdb to sphere program (default: /raid4/people/mattchu/
                        code/DOCK/proteins/pdbtosph/bin/pdbtosph)
  --pdbsphOutput=PDBSPHOUTPUT
                        ligand spheres output (default: xtal-lig.match.sph)
  --addhProgram=ADDHYDROGENSPROGRAM
                        add polar hydrogens program (default: /raid4/people/ma
                        ttchu/code/DOCK/proteins/Reduce/reduce)
  --addhDict=ADDHYDROGENSDICT
                        add polar hydrogens heteroatom dictionary (default:
                        reduce_wwPDB_het_dict.txt)
  --addhOptions=ADDHYDROGENSOPTIONS
                        add polar hydrogens heteroatom options (default:  -OH
                        -HIS -ALLALT -NOROTNH3 -Keep -METALBump1.5
                        -NONMETALBump-5.0 )
  --addhFirst           add polar hydrogens before processing (default: True)
  --addhFirstOptions=ADDHYDROGENSFIRSTOPTIONS
                        add first polar hydrogens heteroatom options (default:
                        -OH -HIS -ALLALT -ROTNH3 -Keep )
  --chargedPdbOutput=CHARGEDPDBOUTPUT
                        charged pdb structure name (default: rec.crg.pdb)
  --addhLog=ADDHLOG     add polar hydrogens logfile (default: addh.log)
  --lowdielectricSpheresProgram=LOWDIELECTRICSPHERESPROGRAM
                        create low dielectric spheres program (default: /raid4
                        /people/mattchu/code/DOCK/proteins/makespheres1/makesp
                        heres1.cli.pl)
  --lowdielectricSpheresOutput=LOWDIELECTRICSPHERESOUTPUT
                        low dielectric spheres output name (default:
                        lowdielectric.sph)
  --lowdielectricSpheresLog=LOWDIELECTRICSPHERESLOG
                        low dielectric spheres logfile (default:
                        lowdielectric.spheres.log)
  --minLowdielectricSpheres=MINLOWDIELECTRICSPHERES
                        minimum number of low dielectric spheres (default: 25)
  --sphtopdbProgram=SPHTOPDBPROGRAM
                        sphere to pdb program (default: /raid4/people/mattchu/
                        code/DOCK/proteins/showsphere/doshowsph.csh)
  --lowdielectricPdbOutput=LOWDIELECTRICPDBOUTPUT
                        low dielectric spheres pdb file output name (default:
                        lowdielectric.sph.pdb)
  --lowdielectricPdbLog=LOWDIELECTRICPDBLOG
                        low dielectric pdb logfile (default:
                        lowdielectric.sph.pdb.log)
  --matchingSpheresProgram=MATCHINGSPHERESPROGRAM
                        create matching spheres program (default: /raid4/peopl
                        e/mattchu/code/DOCK/proteins/makespheres3/makespheres3
                        .cli.pl)
  --matchingSpheresOutput=MATCHINGSPHERESOUTPUT
                        matching spheres output name (default:
                        matching_spheres.sph)
  --matchingSpheresLog=MATCHINGSPHERESLOG
                        matching spheres logfile (default:
                        matching_spheres.log)
  --matchingSpheresDist1=MATCHINGSPHERESDIST1
                        matching spheres distance cutoff 1 (default: 1.5)
  --matchingSpheresDist2=MATCHINGSPHERESDIST2
                        matching spheres distance cutoff 2 (default: 0.8)
  --matchingSpheresMax=MATCHINGSPHERESMAX
                        matching spheres maximum number (default: 45)
  --boxProgram=BOXPROGRAM
                        create box surrounding binding site program (default: 
                        /raid4/people/mattchu/code/DOCK/proteins/makebox/makeb
                        ox.smallokay.pl)
  --boxOutput=BOXOUTPUT
                        box output name (default: box)
  --boxLog=BOXLOG       make box logfile (default: makebox.log)
  --receptorLowdielectricOutput=RECEPTORLOWDIELECTRICOUTPUT
                        output name of charged receptor plus low dielectric
                        spheres (default: receptor.crg.lowdielectric.pdb)
  --qnifftProgram=QNIFFTPROGRAM
                        electrostatics program (default: /raid4/people/mattchu
                        /code/DOCK/proteins/qnifft/bin/qnifft22_193_pgf_32)
  --qnifftOut=QNIFFTOUT
                        qnifft output name (default:
                        qnifft.electrostatics.phi)
  --qnifftTrimOut=QNIFFTTRIMOUT
                        qnifft trimmed output name (default:
                        trim.electrostatics.phi)
  --qnifftPdbOut=QNIFFTPDBOUT
                        qnifft pdb logfile with charges and radii (default:
                        qnifft.atm)
  --qnifftLog=QNIFFTLOG
                        qnifft logfile (default: qnifft.log)
  --qnifftGrid=QNIFFTGRID
                        qnifft grid size (default: 193)
  --chargeFile=CHARGEFILE
                        qnifft charge file (default: amb.crg.oxt)
  --radiusFile=RADIUSFILE
                        qnifft radius file (default: vdw.siz)
  --vdwProgram=VDWPROGRAM
                        vdw program name (default: /raid4/people/mattchu/code/
                        DOCK/proteins/chemgrid/bin/chemgrid)
  --vdwLog=VDWLOG       vdw logfile (default: vdw.log)
  --vdwprottable=VDWPROTEINTABLE
                        vdw protein table (default: prot.table.ambcrg.ambH)
  --vdwparameters=VDWPARAMETERS
                        vdw parameters (default: vdw.parms.amb.mindock)
  --solvmapProgram=SOLVMAPPROGRAM
                        ligand desolvation program (default: /raid4/people/mat
                        tchu/code/DOCK/proteins/solvmap/bin/solvmap)
  --solvmapLog=SOLVMAPLOG
                        ligand desolvation logfile (default: solvmap.log)
  --solvmapHydrogenRadius=SOLVMAPHYDROGENRADIUS
                        ligand desolvation hydrogen radius (default: 1.0)
  --solvmapHeavyRadius=SOLVMAPHEAVYRADIUS
                        ligand desolvation heavy atom radius (default: 1.8)
  --solvmapProbeRadius=SOLVMAPPROBERADIUS
                        ligand desolvation probe radius (default: 1.4)
  --solvmapHydrogenName=SOLVMAPHYDROGENNAME
                        ligand desolvation hydrogen suffix (default:
                        .hydrogen)
  --solvmapHeavyName=SOLVMAPHEAVYNAME
                        ligand desolvation heavy atom suffix (default: .heavy)
  -s, --sge             use sge submission for long tasks that can be done in
                        parallel
  -f, --flexibleReceptor
                        flexible receptor grid building, off by default
  --flexibleResidues=FLEXIBLERESIDUES
                        flexible residues in format '55+56,66,87' groups
                        separated by commas, residues separated by +.
  --indockName=INDOCKNAME
                        indock filename (default: INDOCK)
  --flexibleReadme=FLEXIBLEREADME
                        flexible explanation filename (default:
                        flexible.explanation.txt)
  --partReadme=PARTREADME
                        part explanation filename (default:
                        part.explanation.txt)