def runTravelDepthCompletely(
pdbFileName, gridSize=1.0, whichSrf="mesh", probeSize=False,
radScaleIn=False, pathToExecs="$TDHOME/bin/", deleteFiles=True,
check2trisPerEdge=True, doTravelDepth=True, gridSizeIncrement=0.2,
doIncrement=True, incrementMax=20):
pathToExecs = os.path.expandvars(pathToExecs)
rootNameTemp = string.replace(pdbFileName, ".pdb", "")
rootName = string.replace(rootNameTemp, ".PDB", "")
#now there are 4 more files
print "running the tst creation code"
gridSizeTry = float(gridSize)
triesLeft = incrementMax
if not doIncrement:
triesLeft = 1 # only do one try
while triesLeft >= 1:
okay = makeTstDoChecks(
pdbFileName, gridSizeTry, pathToExecs, rootName, whichSrf, probeSize,
radScaleIn, check2trisPerEdge=check2trisPerEdge)
if not okay:
triesLeft -= 1
gridSizeTry += float(gridSizeIncrement)
print "changing grid size to", gridSizeTry, "and trying again."
else: # everything was okay
print "that run worked, proceeding"
break
if okay:
tstFileName = rootName + ".tst"
print "repairing nearby points if necessary"
tstTravelDist.repairPointPdbRecord(tstD=None, tstFileName=tstFileName)
phiFileName = rootName + ".phi"
tstCavFileName = rootName + ".cav.tst"
phiCavFileName = rootName + ".cav.phi"
nocavTstFileName = rootName + ".nocav.tst"
nocavPhiFileName = rootName + ".nocav.phi"
print "removing cavities"
cavity.tstCavityRemoval(
tstFileName, nocavTstFileName, phiFileName, nocavPhiFileName)
#now no more cavities
print "running convex hull"
tstConvexHull.tstConvexHull(
pathToExecs + khullExec, nocavTstFileName, pathToExecs + qhullExec)
convexTempFile1 = nocavTstFileName + ".tempQHullFile.output"
convexTempFile2 = nocavTstFileName + ".tempQHullFile"
#now has convex hull data,next step is travel depth
if doTravelDepth: # sometimes just skip for pockets, etc
print "running travel depth"
oldTravelDist.tstTravelDepth(nocavTstFileName, nocavPhiFileName)
#now has travel depth data in it
print "renaming files, deleting temporary files"
os.rename(tstFileName, tstCavFileName) # keep the cavities
os.rename(phiFileName, phiCavFileName)
if deleteFiles: # delete unnecessary debugging files...
os.unlink(convexTempFile1)
os.unlink(convexTempFile2)
os.unlink(rootName + ".tri")
return nocavTstFileName
elif sys.argv[1] == "findholes" and len(sys.argv) > 3:
tstFile, phiFile = sys.argv[2:4]
print tstFile, phiFile
tstTravelFindHoles(tstFile, phiFile, debugOut=False)
elif sys.argv[1] == "findholesdebug" and len(sys.argv) > 3:
tstFile, phiFile = sys.argv[2:4]
print tstFile, phiFile
tstTravelFindHoles(tstFile, phiFile, debugOut=True)
elif sys.argv[1] == "meshsurfin" and len(sys.argv) > 3:
tstFile, phiFile = sys.argv[2:4]
print tstFile, phiFile
tstTravelSurfInsideMesh(tstFile, phiFile)
elif sys.argv[1] == "cavityremove" and len(sys.argv) > 3:
tstFile, tstOut, phiFile, phiOut = sys.argv[2:6]
print tstFile, tstOut, phiFile, phiOut
cavity.tstCavityRemoval(tstFile, tstOut, phiFile, phiOut)
elif sys.argv[1] == "countholes" and len(sys.argv) > 2:
tstFileIn = sys.argv[2]
print tstFileIn,
print tstCountHoles(tstFileIn)
elif sys.argv[1] == "assigncharge" and len(sys.argv) > 2:
tstFile = sys.argv[2]
print tstFile,
if len(sys.argv) > 3:
chargeFile = sys.argv[3]
print chargeFile
chargeD = charge.charge(chargeFile)
else:
chargeD = charge.charge()
tstAssignCharges(tstFile, chargeD)
elif sys.argv[1] == "pocketmap" and len(sys.argv) > 3:
