Blastermaster CLI
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Command line arguments for Blastermaster.
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/tskobilka/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/tskobilka/code/DOCK/proteins/defaults)
--filterParams=FILTERPARAMS
input filter parameters, for binding site (default: /
raid4/people/tskobilka/code/DOCK/proteins/defaults/fil
t.params)
--filterProgram=FILTERPROGRAM
input filter program, for binding site (default: /rai
d4/people/tskobilka/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/tsko
bilka/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/tsko
bilka/code/DOCK/proteins/sphgen/bin/sphgen)
--sphgenOutput=SPHGENOUTPUT
sphere generation output (default: all_spheres.sph)
--pdbsphProgram=PDBSPHPROGRAM
pdb to sphere program (default: /raid4/people/tskobilk
a/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/ts
kobilka/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/tskobilka/code/DOCK/proteins/makespheres1/make
spheres1.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/tskobilk
a/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/tskobilka/code/DOCK/proteins/makespheres3/makesphere
s3.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/tskobilka/code/DOCK/proteins/makebox/mak
ebox.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/tskobil
ka/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/tskobilka/cod
e/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/tsk
obilka/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)