def _visualize(self, obj, **kwargs):
views = []
cls = type(obj)
# For now handle both types of SetOfTiltSeries together
if issubclass(cls, schrodingerScipion.objects.SchrodingerAtomStruct) or \
issubclass(cls, schrodingerScipion.objects.SchrodingerBindingSites) or \
issubclass(cls, schrodingerScipion.objects.SchrodingerPoses):
pwutils.runJob(None,
Plugin.getHome('maestro'),
obj.getFileName(),
env=Plugin.getEnviron())
return views
def preparationStep(self):
if isinstance(self.inputStructure.get(), AtomStruct):
fnIn = self._getExtraPath("atomStructIn.pdb")
aStruct1 = AtomicStructHandler(
self.inputStructure.get().getFileName())
aStruct1.write(fnIn)
fnIn = 'extra/atomStructIn.pdb'
self.runJob(schrodinger_plugin.getHome('maestro'),
"-b %s" % fnIn,
cwd=self._getPath())
else:
fnIn = self._getExtraPath(
"atomStructIn") + self.inputStructure.get().getExtension()
createLink(self.inputStructure.get().getFileName(), fnIn)
fnIn = os.path.join('extra', os.path.split(fnIn)[1])
self.runJob(schrodinger_plugin.getHome('maestro'),
"-m %s" % fnIn,
cwd=self._getPath())
def prepareGrid(self, fnSite, fnTarget):
n = fnSite.split('@')[0]
args = schrodinger_plugin.getPluginHome('utils/schrodingerUtils.py') + " centroid %s %s" % \
(fnSite, self._getTmpPath("centroid.txt"))
schrodinger_plugin.runSchrodinger(self, "python3", args)
fh = open(self._getTmpPath("centroid.txt"))
line = fh.readline()
fh.close()
x, y, z = line.split()
fnGridDir = "grid-%s" % n
makePath(self._getPath(fnGridDir))
fnTargetLocal = self._getPath("%s/%s.maegz" % (fnGridDir, fnGridDir))
createLink(fnTarget, fnTargetLocal)
fnJob = self._getPath('%s/%s.inp' % (fnGridDir, fnGridDir))
fh = open(fnJob, 'w')
fh.write("GRIDFILE %s.zip\n" % fnGridDir)
fh.write("OUTPUTDIR %s\n" % fnGridDir)
fh.write("RECEP_FILE %s.maegz\n" % fnGridDir)
fh.write("REC_MAECHARGES True\n")
fh.write("HBOND_DONOR_AROMH %s\n" % self.HbondDonorAromH.get())
if self.HbondDonorAromH.get():
fh.write("HBOND_DONOR_AROMH_CHARGE %f\n" %
self.HbondDonorAromHCharge.get())
fh.write("HBOND_ACCEP_HALO %s\n" % self.HbondAcceptHalo.get())
fh.write("HBOND_DONOR_HALO %s\n" % self.HbondDonorHalo.get())
fh.write("INNERBOX %d,%d,%d\n" %
(self.innerX.get(), self.innerY.get(), self.innerZ.get()))
fh.write("ACTXRANGE %d\n" % self.outerX.get())
fh.write("ACTYRANGE %d\n" % self.outerY.get())
fh.write("ACTZRANGE %d\n" % self.outerZ.get())
fh.write("OUTERBOX %d,%d,%d\n" %
(self.outerX.get(), self.outerY.get(), self.outerZ.get()))
fh.write("GRID_CENTER %s,%s,%s\n" % (x, y, z))
fh.close()
args = "-WAIT -LOCAL -NJOBS %d %s.inp" % (self.numberOfThreads.get(),
fnGridDir)
self.runJob(schrodinger_plugin.getHome('glide'),
args,
cwd=self._getPath(fnGridDir))
def sitemapStep(self):
prog = Plugin.getHome('sitemap')
fnIn = self._getExtraPath(
"atomStructIn") + self.inputStructure.get().getExtension()
createLink(self.inputStructure.get().getFileName(), fnIn)
fnIn = os.path.join('extra', os.path.split(fnIn)[1])
args = '-WAIT -prot %s -j job -keeplogs -keepeval' % fnIn
args += " -maxsites %d" % self.maxsites.get()
self.runJob(prog, args, cwd=self._getPath())
def preparationStep(self):
if isinstance(self.inputStructure.get(),AtomStruct):
fnIn = self._getExtraPath("atomStructIn.pdb")
aStruct1 = AtomicStructHandler(self.inputStructure.get().getFileName())
aStruct1.write(fnIn)
fnIn='extra/atomStructIn.pdb'
else:
fnIn = self._getExtraPath("atomStructIn.mae")
createLink(self.inputStructure.get().getFileName(),fnIn)
fnIn='extra/atomStructIn.mae'
self.runJob(schrodinger_plugin.getHome('maestro'), "-b %s"%fnIn, cwd=self._getPath())
def _viewResults(self, e=None):
views = []
i = self.pose.get()
fnPose = None
for small in self.protocol.outputSmallMolecules:
if small.getObjId() == i:
fnPose = small.poseFile.get()
break
if fnPose:
i = int(fnPose.split('@')[0])
fnPv = self.protocol.outputPoses.getFileName()
fnPose = self.protocol._getTmpPath('posei.maegz')
pwutils.runJob(None, schrodinger_plugin.getHome('utilities/maesubset'),
"-n %d:%d %s -o %s" % (i, i, fnPv, fnPose))
fnStruct = self.protocol.inputGrid.get().structureFile.get()
fnBoth = self.protocol._getTmpPath('pv.maegz')
pwutils.runJob(None, schrodinger_plugin.getHome('utilities/structcat'),
"-imae %s -imae %s -o %s" % (fnPose,fnStruct,fnBoth))
pwutils.runJob(None, schrodinger_plugin.getHome('maestro'), fnBoth,
env=schrodinger_plugin.getEnviron())
return views
def convertStep(self):
progStructConvert = Plugin.getHome('utilities/structconvert')
if self.inputType == 0:
outputSmallMolecules = SetOfSmallMolecules().create(
path=self._getPath(), suffix='SmallMols')
for mol in self.inputSmallMols.get():
fnSmall = mol.smallMoleculeFile.get()
fnRoot = os.path.splitext(os.path.split(fnSmall)[1])[0]
args = inputArg(fnSmall)
fnOut, argout = outputArg(fnRoot, self.outputFormatSmall.get(),
self)
args += argout
self.runJob(progStructConvert, args)
if self.outputFormatSmall.get() == 2:
putMol2Title(fnOut)
smallMolecule = SmallMolecule(smallMolFilename=fnOut)
outputSmallMolecules.append(smallMolecule)
if len(outputSmallMolecules) > 0:
self._defineOutputs(outputSmallMols=outputSmallMolecules)
self._defineSourceRelation(self.inputSmallMols,
outputSmallMolecules)
else:
fnStructure = self.inputStructure.get().getFileName()
args = inputArg(fnStructure)
fnRoot = os.path.splitext(os.path.split(fnStructure)[1])[0]
fnOut, argout = outputArg(fnRoot, self.outputFormatTarget.get())
args += argout
self.runJob(progStructConvert, args)
if fnOut.endswith('.maegz'):
target = SchrodingerAtomStruct(filename=fnOut)
else:
target = AtomStruct(filename=fnOut)
self._defineOutputs(outputStructure=target)
self._defineSourceRelation(self.inputStructure, target)
def primeStep(self):
prog=Plugin.getHome('prime')
fnInputStructure = self.inputStructure.get().getFileName()
fnIn=self._getPath("atomStructIn")+self.inputStructure.get().getExtension()
createLink(fnInputStructure,fnIn)
fnIn=os.path.split(fnIn)[1]
fhJob = open(self._getPath('job.inp'),'w')
fhJob.write("STRUCT_FILE %s\n" % fnIn)
if self.operation.get()==0:
# Side chain prediction
fhJob.write("PRIME_TYPE SIDE_PRED\n")
fhJob.write("SELECT pick\n")
i=0
for residue in self.residueList.get().split(','):
fhJob.write("RESIDUE_%d %s\n"%(i,residue.strip()))
i+=1
elif self.operation.get()==1:
# Minimization of all hydrogens
fhJob.write("PRIME_TYPE REAL_MIN\n")
fhJob.write("SELECT asl = (atom.ele H)\n")
elif self.operation.get()==2:
# Loop prediction
fhJob.write("PRIME_TYPE LOOP_BLD\n")
fhJob.write("LOOP_0_RES_0 %s\n"%self.residueFirst.get())
fhJob.write("LOOP_0_RES_1 %s\n"%self.residueLast.get())
fhJob.write("RES_SPHERE %f\n"%self.resSphere.get())
fhJob.write("MIN_OVERLAP %f\n"%self.minOverlap.get())
fhJob.write("USE_CRYSTAL_SYMMETRY no\n")
fhJob.write("USE_RANDOM_SEED no\n")
fhJob.write("SEED 0\n")
fhJob.write("EXT_DIEL 80.00\n")
fhJob.write("USE_MEMBRANE no\n")
fhJob.close()
args='-WAIT -LOCAL job.inp'
self.runJob(prog,args,cwd=self._getPath())
def splitStep(self):
args = Plugin.getMMshareDir('python/common/split_structure.py')
if self.splitMode.get() == 0:
args += " -m chain"
if self.mergeLigands.get():
args += " -merge_ligands_with_chain"
if self.mergeWaters.get():
args += " -merge_waters_with_chain"
elif self.splitMode.get() == 1:
args += " -m molecule"
elif self.splitMode.get() == 2:
args += " -m residue"
elif self.splitMode.get() == 3:
args += " -m ligand"
elif self.splitMode.get() == 4:
args += " -m pdb"
if self.positiveASL.get() != "":
args += ' -positive_ion_asl "%s"' % self.positiveASL.get()
if self.negativeASL.get() != "":
args += ' -negative_ion_asl "%s"' % self.negativeASL.get()
if self.keepProperties.get():
args += " --keep_properties"
if self.splitMode.get() != 4 and self.groupWaters.get():
args += " -groupwaters"
if self.splitAll.get():
args += " -splitall"
if self.ligandASL.get() != "":
args += ' -ligand_asl "%s"' % self.ligandASL.get()
if self.cofactorASL.get() != "":
args += ' -cofactor_asl "%s"' % self.cofactorASL.get()
args += " -many_files %s %s" % (self.inputStructure.get().getFileName(
), self._getExtraPath('output.maegz'))
self.runJob(Plugin.getHome('run'), args)
def getNumber(fn, suffix):
fnBase = os.path.splitext(os.path.split(fn)[1])[0]
tokens = fnBase.split(suffix)
return tokens[1]
for fn in glob.glob(self._getExtraPath("output*")):
if "_receptor" in fn:
target = SchrodingerAtomStruct(filename=fn)
number = getNumber(fn, "_receptor")
outputDict = {'outputStructure%s' % number: target}
self._defineOutputs(**outputDict)
self._defineSourceRelation(self.inputStructure, target)
elif "_ligand" in fn:
ligand = SmallMolecule(smallMolFilename=fn)
number = getNumber(fn, "_ligand")
outputDict = {'outputLigand%s' % number: ligand}
self._defineOutputs(**outputDict)
self._defineSourceRelation(self.inputStructure, ligand)
elif "_cof_ion" in fn:
cof = SchrodingerAtomStruct(filename=fn)
number = getNumber(fn, "_cof_ion")
outputDict = {'outputCofactors%s' % number: cof}
self._defineOutputs(**outputDict)
self._defineSourceRelation(self.inputStructure, cof)
else:
print("Scipion: I don't know how to handle %s" % fn)
def prepareStep(self):
def addParam(headerLine, lineToPrint, lineNo, param, value=None):
if value is None:
if hasattr(mol, param):
value = getattr(mol, param).get()
if value is not None:
if lineNo == 0:
if headerLine != "":
headerLine += "; "
headerLine += param
if lineToPrint != "":
lineToPrint += "; "
lineToPrint += str(value)
return headerLine, lineToPrint
def getGridRun(mol):
fn = mol.poseFile.get()
return fn.split('Runs/')[1][0:6]
progStructConvert = Plugin.getHome('utilities/structconvert')
progMaeSubset = Plugin.getHome('utilities/maesubset')
grids = {}
gridNo = 1
for mol in self.inputSmallMols.get():
gridRun = getGridRun(mol)
if not gridRun in grids:
grids[gridRun] = gridNo
gridNo += 1
fh = open(self._getExtraPath("smallMolecules.csv"), 'w')
lineNo = 0
headerLine = ""
for mol in self.inputSmallMols.get():
fnSmall = mol.smallMoleculeFile.get()
fnMol = os.path.split(fnSmall)[1]
fnRoot = os.path.splitext(fnMol)[0]
if "-" in fnRoot:
fnRoot = fnRoot.split('-')[0]
lineToPrint = ""
headerLine, lineToPrint = addParam(headerLine, lineToPrint, lineNo,
"smallMolecule", fnRoot)
if fnRoot.startswith("ZINC"):
headerLine, lineToPrint = addParam(
headerLine, lineToPrint, lineNo, "url",
"https://zinc15.docking.org/substances/%s" % fnRoot)
headerLine, lineToPrint = addParam(headerLine, lineToPrint, lineNo,
"bindingSiteScore")
headerLine, lineToPrint = addParam(headerLine, lineToPrint, lineNo,
"dockingScore")
headerLine, lineToPrint = addParam(headerLine, lineToPrint, lineNo,
"ligandEfficiency")
headerLine, lineToPrint = addParam(headerLine, lineToPrint, lineNo,
"gridNumber",
grids[getGridRun(mol)])
fnOut = self._getExtraPath("pose_%d.pdb" % lineNo)
if not os.path.exists(fnOut):
fnAux = self._getTmpPath("tmp.mae")
n, fnRaw = mol.poseFile.get().split('@')
args = "-n %s %s -o %s" % (n, fnRaw, fnAux)
self.runJob(progMaeSubset, args)
args = "-imae %s -opdb %s" % (fnAux, fnOut)
self.runJob(progStructConvert, args)
headerLine, lineToPrint = addParam(headerLine, lineToPrint, lineNo,
"poseFile",
os.path.split(fnOut)[1])
if lineNo == 0:
fh.write(headerLine + "\n")
fh.write(lineToPrint + "\n")
lineNo += 1
fh.close()
def __init__(self, inputFile, **kwargs):
pwviewer.CommandView.__init__(self,
"%s %s &" %
(Plugin.getHome('maestro'), inputFile),
env=Plugin.getEnviron(),
**kwargs)
def ligPrepStep(self):
progLigPrep = Plugin.getHome('ligprep')
progStructConvert = Plugin.getHome('utilities/structconvert')
outputSmallMolecules = SetOfSmallMolecules().create(
path=self._getPath(), suffix='SmallMols')
outputSmallMoleculesDropped = SetOfSmallMolecules().create(
path=self._getPath(), suffix='SmallMolsDropped')
for mol in self.inputSmallMols.get():
fnSmall = mol.smallMoleculeFile.get()
fnMol = os.path.split(fnSmall)[1]
fnRoot = os.path.splitext(fnMol)[0]
existingFiles = glob.glob(self._getExtraPath(fnRoot + "*"))
if len(existingFiles) == 0:
fnSmallExtra = self._getTmpPath(fnMol)
copyFile(fnSmall, fnSmallExtra)
args = '-WAIT -LOCAL'
if self.ionization.get() != 0:
if self.ionization.get() == 1:
args += " -epik"
if self.emb.get():
args += " -epik_metal_binding"
else:
args += " -i %d" % self.ionization.get() - 2
args += " -ph %f -pht %f" % (self.pH.get(),
self.pHrange.get())
if self.stereoisomers.get():
args += " -g"
else:
args += " -ac -s %d" % self.Niso.get()
if self.optimization.get() == 1:
args += " -bff 14"
elif self.optimization.get() == 2:
args += " -bff 16"
if fnMol.endswith('.smi'):
args += " -ismi tmp/%s" % (fnMol)
elif fnMol.endswith('.mae') or fnMol.endswith('.maegz'):
args += " -imae tmp/%s" % (fnMol)
elif fnMol.endswith('.sdf'):
args += " -isd tmp/%s" % (fnMol)
else:
print("Skipping %s" % fnSmall)
continue
fnMae = "extra/%s.maegz" % fnRoot
if not os.path.exists(fnMae):
args += " -omae %s" % fnMae
self.runJob(progLigPrep, args, cwd=self._getPath())
if os.path.exists(self._getPath(fnMae)):
fnOmae = "extra/o%s.maegz" % fnRoot
args = "-imae %s -omae %s -split-nstructures 1" % (fnMae,
fnOmae)
self.runJob(progStructConvert, args, cwd=self._getPath())
for fn in glob.glob(
self._getExtraPath("o%s*.maegz" % fnRoot)):
fnDir, fnOut = os.path.split(fn)
fnOut = self._getExtraPath(fnOut[1:])
moveFile(fn, fnOut)
smallMolecule = SmallMolecule(smallMolFilename=fnOut)
outputSmallMolecules.append(smallMolecule)
if len(glob.glob(self._getExtraPath(
"%s-*.maegz" % fnRoot))) > 0:
cleanPath(self._getPath(fnMae))
else:
smallMolecule = SmallMolecule(smallMolFilename=fnSmall)
outputSmallMoleculesDropped.append(smallMolecule)
else:
for fn in glob.glob(self._getExtraPath("%s*.maegz" % fnRoot)):
print("Reading %s" % fn)
smallMolecule = SmallMolecule(smallMolFilename=fn)
outputSmallMolecules.append(smallMolecule)
if len(outputSmallMolecules) > 0:
self._defineOutputs(outputSmallMols=outputSmallMolecules)
self._defineSourceRelation(self.inputSmallMols,
outputSmallMolecules)
if len(outputSmallMoleculesDropped) > 0:
self._defineOutputs(
outputSmallMolsDropped=outputSmallMoleculesDropped)
self._defineSourceRelation(self.inputSmallMols,
outputSmallMoleculesDropped)
def dockingStep(self):
def makeLocal(fn):
return fn.replace(self._getPath()+'/','')
glideProg = schrodinger_plugin.getHome('glide')
structConvertProg = schrodinger_plugin.getHome('utilities/structconvert')
structCatProg = schrodinger_plugin.getHome('utilities/structcat')
propListerProg = schrodinger_plugin.getHome('utilities/proplister')
fnGrid = self._getExtraPath("grid.zip")
if not os.path.exists(fnGrid): # Prepared to resume
createLink(self.inputGrid.get().getFileName(),fnGrid)
fnLigands = self._getPath('ligands')
if not os.path.exists(fnLigands):
makePath(fnLigands)
fnIn = self._getPath('job.inp')
if not os.path.exists(fnIn): # Prepared to resume
fhIn = open(fnIn,'w')
fhIn.write("GRIDFILE %s\n"%makeLocal(fnGrid))
if self.dockingMethod.get()==0:
fhIn.write("DOCKING_METHOD confgen\n")
fhIn.write("FLEXTORS True\n")
elif self.dockingMethod.get()==1:
fhIn.write("DOCKING_METHOD rigid\n")
elif self.dockingMethod.get()==2:
fhIn.write("DOCKING_METHOD mininplace\n")
elif self.dockingMethod.get()==3:
fhIn.write("DOCKING_METHOD inplace\n")
if self.dockingPrecision.get()==0:
fhIn.write("PRECISION HTVS\n")
elif self.dockingPrecision.get()==1:
fhIn.write("PRECISION SP\n")
elif self.dockingPrecision.get()==2:
fhIn.write("PRECISION XP\n")
fhIn.write("WRITE_XP_DESC True\n")
fhIn.write("POSTDOCK_NPOSE 10\n")
fhIn.write("SAMPLE_N_INVERSIONS %s\n"%self.sampleNinversions.get())
fhIn.write("SAMPLE_RINGS %s\n"%self.sampleRings.get())
fhIn.write("EPIK_PENALTIES %s\n"%self.sampleNinversions.get())
fhIn.write("SKIP_EPIK_METAL_ONLY %s\n"%self.skipMetalEpik.get())
fhIn.write("EXPANDED_SAMPLING %s\n"%self.expandedSampling.get())
fhIn.write("REWARD_INTRA_HBONDS %s\n"%self.rewardIntraHBonds.get())
fhIn.write("HBOND_DONOR_AROMH %s\n"%self.HbondDonorAromH.get())
if self.HbondDonorAromH.get():
fhIn.write("HBOND_DONOR_AROMH_CHARGE %f\n" % self.HbondDonorAromHCharge.get())
fhIn.write("HBOND_ACCEP_HALO %s\n"%self.HbondAcceptHalo.get())
fhIn.write("HBOND_DONOR_HALO %s\n"%self.HbondDonorHalo.get())
fhIn.write("MAXKEEP %d\n"%self.maxkeep.get())
fhIn.write("SCORING_CUTOFF %f\n"%self.scoreCutoff.get())
if self.maxref.get()>0:
fhIn.write("MAXREF %d\n" % self.maxref.get())
else:
if self.dockingPrecision.get()==2:
fhIn.write("MAXREF %d\n" % 800)
else:
fhIn.write("MAXREF %d\n" % 400)
fhIn.write("POSES_PER_LIG %d\n"%self.posesPerLig.get())
fh=open(self._getTmpPath("allLigands.mol2"),'w')
for small in self.inputLibrary.get():
fnSmall = small.getFileName()
fnBase = os.path.splitext(os.path.split(fnSmall)[1])[0]
if not fnSmall.endswith('.mol2'):
args = inputArg(fnSmall)
fnSmall = self._getTmpPath('ligand.mol2')
args += " -omol2 %s"%fnSmall
self.runJob(structConvertProg, args)
putMol2Title(fnSmall,fnBase)
fhLigand = open(fnSmall)
for line in fhLigand:
fh.write(line)
fhLigand.close()
fh.close()
fhIn.write("LIGANDFILE tmp/allLigands.mol2\n")
fhIn.close()
args = "-WAIT -NJOBS %d -RESTART -LOCAL job.inp"%(self.numberOfThreads.get())
self.runJob(glideProg, args, cwd=self._getPath())
self.runJob(propListerProg,
'-p "title" -p "docking score" -p "glide ligand efficiency" -p "glide ligand efficiency sa" -p "glide ligand efficiency ln" -c -o %s %s'%\
(self._getPath("job_pv.csv"), self._getPath("job_pv.maegz")))
def preparationStep(self):
prog = Plugin.getHome('utilities/prepwizard')
if isinstance(self.inputStructure.get(), AtomStruct):
fnIn = self._getExtraPath("atomStructIn.pdb")
aStruct1 = AtomicStructHandler(
self.inputStructure.get().getFileName())
aStruct1.write(fnIn)
fnIn = 'extra/atomStructIn.pdb'
else:
fnIn = self._getExtraPath("atomStructIn.mae")
createLink(self.inputStructure.get().getFileName(), fnIn)
fnIn = 'extra/atomStructIn.mae'
args = '-WAIT'
if self.stage1.get():
if self.fillSideChains.get():
args += ' -fillsidechains'
if self.fillLoops.get():
args += ' -fillloops'
if self.disulfides.get():
args += ' -disulfides'
if self.mse.get():
args += ' -mse'
if self.hydrogens.get() == 0:
args += " -nohtreat"
elif self.hydrogens.get() == 1:
args += " -rehtreat"
if self.glycosylation.get():
args += " -glycosylation"
if self.palmitoylation.get():
args += " -palmitoylation"
if self.captermini.get():
args += " -captermini"
if self.keepFarWat.get():
args += " -keepfarwat -watdist %f" % self.watdist.get()
if not self.treatMetals.get():
args += " -nometaltreat"
if self.stage2.get():
if self.sampleWaters.get():
args += " -samplewater"
if self.xtal.get():
args += " -xtal"
if self.propKa.get():
args += " -propka_pH %f" % self.propKapH.get()
else:
args += " -nopropka"
if self.minadjh.get():
args += " -minimize_adj_h"
else:
args += " -noprotassign"
if self.stage3.get():
args += " -rmsd %f" % self.rmsdD.get()
if self.fix.get():
args += " -fix"
if self.force.get() == 0:
args += " -f 2005"
else:
args += " -f 3"
else:
args += " -noimpref"
if self.stage4.get():
if self.ms.get():
args += " -ms %d" % self.msN.get()
args += " -epik_pH %f" % self.epikPh.get()
args += " -epik_pHt %f" % self.epikPht.get()
else:
args += " -noepik"
args += ' %s atomStructOut.maegz' % fnIn
self.runJob(prog, args, cwd=self._getPath())