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Written by Ryan Coleman, based on a prototype in the lab (MakeDOCK/startdockblasterN) which was contributed to by many people. | 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 = | |||
<pre> | |||
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) | |||
</pre> |
Revision as of 03:39, 23 February 2014
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)