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: