def defineLigandStructure(self, ligandFile, nameLigand, pathfile=""):
self.__ligandName = nameLigand
'Validates path parameters'
if (pathfile == ""):
pathfile = self.__resDir
'Delete Files'
self.deleteRosettaFiles()
'Creates mdl file'
os.system(BABEL_COM + ' -ipdb ' + os.path.join(pathfile, ligandFile) +
' -omdl ' + os.path.join(self.__tmpDir, 'Struct.mdl'))
'Generates param file'
os.system(PYTHON_COM +
os.path.join(self.__molDir, 'molfile_to_params.py') + ' ' +
os.path.join(self.__tmpDir, 'Struct.mdl') + ' -d ' +
self.__tmpDir + ' -n ' + self.__ligandName)
self.__residueSet = rosetta.generate_nonstandard_residue_set(
[os.path.join(self.__tmpDir, self.__ligandName + '.params')])
'Generates Ligand'
self.__ligandFile = IO.readPDB(self.__ligandName + '_0001.pdb',
'HETATM', self.__tmpDir)
IO.writePDB("ligand.pdb", self.__ligandFile, self.__tmpDir)
'Init Function'
self.__scorefxn = rosetta.create_score_function("ligand")
def generateFinalLog(self):
self.__timer.stop()
'Writes Files'
ligand_PDB_name = "Ligand_score_" + "{0:.3f}".format(self.__scoreFx.getBestScore()) + ".pdb"
ligandProtein_PDB_name = "LigandProtein_score_" + "{0:.3f}".format(self.__scoreFx.getBestScore()) + ".pdb"
IO.writePDB(ligand_PDB_name,self.__scoreFx.getBestLigand(),self.__fileDir)
IO.writeAllPDB(ligandProtein_PDB_name, self.__protein, self.__scoreFx.getBestLigand(), self.__fileDir)
initLog = "Molecule Name: " + self.__moleculeName + "\n"
initLog += "Test Pdb: " + self.__testPdb + "\n"
initLog += "Population: " + str(len(self.population)) + "\n"
initLog += "Generations: " + str(self.__generations) + "\n"
initLog += "Time to Stop: " + str(self.__timeStop) + "\n"
initLog += "Space Size: " + str(self.__spaceLen) + "\n"
initLog += "Point: ( " + str(self.__spaceCenter[0]) + " , " + str(self.__spaceCenter[1]) + " , " + str(self.__spaceCenter[2]) + " )\n"
initLog += "Local Search: " + str(self.__localS) + "\n"
initLog += "Rotate Atoms: " + str(self.__rotateAtoms) + "\n"
initLog += "\n- Best Score: " + str(self.__scoreFx.getBestScore()) + "\n"
initLog += "- Reach Best Score: " + str(self.__bestLoop) + "\n"
auxRMSD = str(self.__scoreFx.getRMSD("original_" + self.__moleculeName + ".pdb", ligandProtein_PDB_name, self.__tmpDir, self.__fileDir))
initLog += "- RMSD: " + auxRMSD + "\n"
initLog += "- Timer: " + str(self.__timer.getTimeChronometer()) + "\n" + "\n"
self.__log = initLog + self.__log
'Data Log'
IO.writeLog("iterations.log", self.__log, self.__fileDir)
IO.writeLog("data.log", self.__dataLog, self.__fileDir)
IO.writeHistoricLog("historic.log", str(self.__scoreFx.getBestScore()) + ";" + auxRMSD + ";" + str(self.__bestLoop) + ";" + str(self.__loop) , self.__fileDir)
'Delete files'
Methods.deleteTempFiles(self.__scoreFx.getLigandName(), self.__moleculeName)
def generateFinalLog(self):
self.__timer.stop()
'Writes Files'
ligand_PDB_name = "Ligand_score_" + "{0:.3f}".format(
self.__scoreFx.getBestScore()) + ".pdb"
ligandProtein_PDB_name = "LigandProtein_score_" + "{0:.3f}".format(
self.__scoreFx.getBestScore()) + ".pdb"
IO.writePDB(ligand_PDB_name, self.__scoreFx.getBestLigand(),
self.__fileDir)
IO.writeAllPDB(ligandProtein_PDB_name, self.__protein,
self.__scoreFx.getBestLigand(), self.__fileDir)
initLog = "Molecule Name: " + self.__moleculeName + "\n"
initLog += "Test Pdb: " + self.__testPdb + "\n"
initLog += "Population: " + str(len(self.population)) + "\n"
initLog += "Generations: " + str(self.__generations) + "\n"
initLog += "Time to Stop: " + str(self.__timeStop) + "\n"
initLog += "Space Size: " + str(self.__spaceLen) + "\n"
initLog += "Point: ( " + str(self.__spaceCenter[0]) + " , " + str(
self.__spaceCenter[1]) + " , " + str(
self.__spaceCenter[2]) + " )\n"
initLog += "Local Search: " + str(self.__localS) + "\n"
initLog += "Rotate Atoms: " + str(self.__rotateAtoms) + "\n"
initLog += "\n- Best Score: " + str(
self.__scoreFx.getBestScore()) + "\n"
initLog += "- Reach Best Score: " + str(self.__bestLoop) + "\n"
auxRMSD = str(
self.__scoreFx.getRMSD("original_" + self.__moleculeName + ".pdb",
ligandProtein_PDB_name, self.__tmpDir,
self.__fileDir))
initLog += "- RMSD: " + auxRMSD + "\n"
initLog += "- Timer: " + str(
self.__timer.getTimeChronometer()) + "\n" + "\n"
self.__log = initLog + self.__log
'Data Log'
IO.writeLog("iterations.log", self.__log, self.__fileDir)
IO.writeLog("data.log", self.__dataLog, self.__fileDir)
IO.writeHistoricLog(
"historic.log",
str(self.__scoreFx.getBestScore()) + ";" + auxRMSD + ";" +
str(self.__bestLoop) + ";" + str(self.__loop), self.__fileDir)
'Delete files'
Methods.deleteTempFiles(self.__scoreFx.getLigandName(),
self.__moleculeName)
def generateScoring(self, protein, ligand, traceBest=True):
ligand_p = rosetta.core.pose.Pose()
rosetta.core.import_pose.pose_from_pdbstring(
ligand_p, IO.getPbdStr(protein, ligand, self.__pdbStr))
score = self.__scorefxn(ligand_p)
'Best Values'
if (traceBest):
self.traceScoring(ligand, score)
return score
import copy
'************************** PDB FILES ***************************'
__MoleculeName = '1BV9'
__LigandName = 'XV6'
__pdbLigand = '1BV9_Flexible_2_RMSD_1.400_ligand.pdb'
'****************************************************************'
'Constants'
tempPath = os.path.join(ROOTPATH, 'temp')
pdbPath = os.path.join(ROOTPATH, 'originalPdb')
'Reads data'
newLigand = IO.readPDB(__pdbLigand, 'HETATM', pdbPath)
moleculeList = IO.readAllPDB(__MoleculeName + '.pdb', __LigandName, pdbPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
'Writes a new clean structure'
IO.writePDB("ligand.pdb", ligand, tempPath)
IO.writePDB("protein.pdb", protein, tempPath)
'Gets Connection Matrix'
connectMatrix = ligand.connectMatrix
'Init Scoring Function'
scoringFx = ScoringFunction.ScoringFunction()
scoringFx.defineLigandStructure("ligand.pdb", __LigandName, tempPath)
__initTemperature = 1000
__minTemperature = 1
__alphaTemperature = 0.9
__innerLoop = 1
'Random Seed'
random.seed(2139738276)
'****************************************************************'
'Timer start'
timer = TimeManager()
timer.start()
'Reads data'
moleculeList = IO.readAllPDB(__testPDB, __LigandName)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
'Center Molecule'
originPoint = protein.findCenter()
protein.translate(
[originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
ligand.translate(
[originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
'Traslate search center point'
alterCenterPoint = [
__searchCenterPoint[0] + (originPoint[0] * -1),
__searchCenterPoint[1] + (originPoint[1] * -1),
__searchCenterPoint[2] + (originPoint[2] * -1)
__minTemperature = 1
__alphaTemperature = 0.9
__innerLoop = 1
'Random Seed'
random.seed(2139738276)
'****************************************************************'
'Timer start'
timer = TimeManager()
timer.start()
'Reads data'
moleculeList = IO.readAllPDB(__testPDB, __LigandName)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
'Center Molecule'
originPoint = protein.findCenter()
protein.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
ligand.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
'Traslate search center point'
alterCenterPoint = [__searchCenterPoint[0] + (originPoint[0]*-1),
__searchCenterPoint[1] + (originPoint[1]*-1),
__searchCenterPoint[2] + (originPoint[2]*-1)]
'Writes a new clean structure'
IO.writePDB("ligand.pdb", ligand, os.path.join(ROOTPATH,'temp'))
__MoleculeName = '2UPJ.pdb'
__LigandName = 'U02'
#__MoleculeName = '1BV9.pdb'
#__LigandName = 'XV6'
'****************************************************************'
'Constants'
moleculeName = __MoleculeName.replace(".pdb", "")
resultPath = os.path.join(ROOTPATH, 'results')
pdbPath = os.path.join(ROOTPATH, 'testPdb')
originalPath = os.path.join(ROOTPATH, 'originalPdb')
'Reads data'
moleculeList = IO.readAllPDB(__MoleculeName, __LigandName, originalPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
'Writes a new clean structure'
IO.writePDB(moleculeName + "_ligand.pdb", ligand, resultPath)
IO.writePDB(moleculeName + "_protein.pdb", protein, resultPath)
IO.writeAllPDB(moleculeName + "_clean.pdb", protein, ligand, resultPath, True)
'Print Center'
proteinCenter = protein.findCenter()
ligandCenter = ligand.findCenter()
print "Protein Center [ " + str(proteinCenter[0]) + ", " + str(
proteinCenter[1]) + ", " + str(proteinCenter[2]) + " ]"
print "Ligand Center [ " + str(ligandCenter[0]) + ", " + str(
ligandCenter[1]) + ", " + str(ligandCenter[2]) + " ]"
__SearchSpaceSize = 5
'*********************+*** Other Params *************************'
__onlyLigand = False
__dataLog = True
'****************************************************************'
'Constants'
resultPath = os.path.join(ROOTPATH, 'results')
tempPath = os.path.join(ROOTPATH, 'temp')
pdbPath = os.path.join(ROOTPATH, 'originalPdb')
'Reads data'
moleculeList = IO.readAllPDB(__MoleculeName + '.pdb', __LigandName, pdbPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
ligandOri = copy.deepcopy(moleculeList[1])
'Center Molecule'
originPoint = protein.findCenter()
ligandPoint = ligand.findCenter()
#protein.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
#ligand.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
#ligandOri.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
'Traslate search center point'
alterCenterPoint = [
__SearchCenterPoint[0] + (originPoint[0] * -1),
__SearchCenterPoint[1] + (originPoint[1] * -1),
__MoleculeName = '2UPJ_Flexible_4_RMSD_1.300.pdb' __LigandName = 'U02' '****************************************************************' ligandFile = 'ligand_' + __LigandName + '.pdb' proteinFile = 'protein_' + __LigandName + '.pdb' molFile = 'ligand_' + __LigandName + '.mol' 'Constants' resultPath = os.path.join(ROOTPATH,'results') pdbPath = os.path.join(ROOTPATH,'testPdb') tempPath = os.path.join(ROOTPATH,'temp') originalPath = os.path.join(ROOTPATH,'originalPdb') molPath = os.path.join(ROOTPATH,'others') moleculeList = IO.readAllPDB(__MoleculeName, __LigandName, originalPath) protein = copy.deepcopy(moleculeList[0]) ligand = copy.deepcopy(moleculeList[1]) IO.writePDB(ligandFile, ligand, tempPath) IO.writePDB(proteinFile, protein, tempPath) 'Creates mdl file' os.system(BABEL_COM + ' -ipdb ' + os.path.join(tempPath, ligandFile) + ' -omdl ' + os.path.join(tempPath, molFile)) os.system(DELETE_COM + os.path.join(tempPath, ligandFile)) os.system(DELETE_COM + os.path.join(tempPath, proteinFile))
#__LigandName = 'KNI'
__MoleculeName = '2UPJ.pdb'
__LigandName = 'U02'
#__MoleculeName = '1BV9.pdb'
#__LigandName = 'XV6'
'****************************************************************'
'Constants'
moleculeName = __MoleculeName.replace(".pdb", "")
resultPath = os.path.join(ROOTPATH,'results')
pdbPath = os.path.join(ROOTPATH,'testPdb')
originalPath = os.path.join(ROOTPATH,'originalPdb')
'Reads data'
moleculeList = IO.readAllPDB(__MoleculeName, __LigandName, originalPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
'Writes a new clean structure'
IO.writePDB(moleculeName + "_ligand.pdb", ligand, resultPath)
IO.writePDB(moleculeName + "_protein.pdb", protein, resultPath)
IO.writeAllPDB(moleculeName + "_clean.pdb", protein, ligand, resultPath, True)
'Print Center'
proteinCenter = protein.findCenter()
ligandCenter = ligand.findCenter()
print "Protein Center [ " + str(proteinCenter[0]) + ", " + str(proteinCenter[1]) + ", " + str(proteinCenter[2]) + " ]"
print "Ligand Center [ " + str(ligandCenter[0]) + ", " + str(ligandCenter[1]) + ", " + str(ligandCenter[2]) + " ]"
'************************** PDB FILES ***************************'
__MoleculeName = '1BV9'
__LigandName = 'XV6'
__pdbLigand = '1BV9_Flexible_2_RMSD_1.400_ligand.pdb'
'****************************************************************'
'Constants'
tempPath = os.path.join(ROOTPATH,'temp')
pdbPath = os.path.join(ROOTPATH,'originalPdb')
'Reads data'
newLigand = IO.readPDB(__pdbLigand, 'HETATM', pdbPath)
moleculeList = IO.readAllPDB(__MoleculeName + '.pdb', __LigandName, pdbPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
'Writes a new clean structure'
IO.writePDB("ligand.pdb", ligand, tempPath)
IO.writePDB("protein.pdb", protein, tempPath)
'Gets Connection Matrix'
connectMatrix = ligand.connectMatrix
'Init Scoring Function'
scoringFx = ScoringFunction.ScoringFunction()
scoringFx.defineLigandStructure("ligand.pdb", __LigandName, tempPath)
'*********************+*** Other Params *************************'
__onlyLigand = False
__dataLog = True
'****************************************************************'
'Constants'
resultPath = os.path.join(ROOTPATH,'results')
tempPath = os.path.join(ROOTPATH,'temp')
pdbPath = os.path.join(ROOTPATH,'originalPdb')
'Reads data'
moleculeList = IO.readAllPDB(__MoleculeName + '.pdb', __LigandName, pdbPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
ligandOri = copy.deepcopy(moleculeList[1])
'Center Molecule'
originPoint = protein.findCenter()
ligandPoint = ligand.findCenter()
#protein.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
#ligand.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
#ligandOri.translate([originPoint[0] * -1, originPoint[1] * -1, originPoint[2] * -1])
'Traslate search center point'
alterCenterPoint = [__SearchCenterPoint[0] + (originPoint[0]*-1),
__SearchCenterPoint[1] + (originPoint[1]*-1),
__SearchCenterPoint[2] + (originPoint[2]*-1)]
__MoleculeName = '2UPJ_Flexible_4_RMSD_1.300.pdb'
__LigandName = 'U02'
'****************************************************************'
ligandFile = 'ligand_' + __LigandName + '.pdb'
proteinFile = 'protein_' + __LigandName + '.pdb'
molFile = 'ligand_' + __LigandName + '.mol'
'Constants'
resultPath = os.path.join(ROOTPATH, 'results')
pdbPath = os.path.join(ROOTPATH, 'testPdb')
tempPath = os.path.join(ROOTPATH, 'temp')
originalPath = os.path.join(ROOTPATH, 'originalPdb')
molPath = os.path.join(ROOTPATH, 'others')
moleculeList = IO.readAllPDB(__MoleculeName, __LigandName, originalPath)
protein = copy.deepcopy(moleculeList[0])
ligand = copy.deepcopy(moleculeList[1])
IO.writePDB(ligandFile, ligand, tempPath)
IO.writePDB(proteinFile, protein, tempPath)
'Creates mdl file'
os.system(BABEL_COM + ' -ipdb ' + os.path.join(tempPath, ligandFile) +
' -omdl ' + os.path.join(tempPath, molFile))
os.system(DELETE_COM + os.path.join(tempPath, ligandFile))
os.system(DELETE_COM + os.path.join(tempPath, proteinFile))
def getPoseFromPdbStr(self, protein, ligand):
ligand_p = rosetta.core.pose.Pose()
rosetta.core.import_pose.pose_from_pdbstring(
ligand_p, IO.getPbdStr(protein, ligand, self.__pdbStr))
return ligand_p