def calculates(self, np):
if (self.__isLocalSearch):
np = self.__LocalSearch.initLocalProcess(np, self.__Ligand)
auxLigand = copy.deepcopy(self.__Ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + np.x),
(self.__newSpaceCenter[1] + np.y),
(self.__newSpaceCenter[2] + np.z)])
auxLigand.rotateByVector(
Methods.spherePoint(1, np.sph_theta, np.sph_phi), np.theta)
for r in xrange(len(self.__rotateAtoms)):
auxLigand.rotateSegment(r, np.rotateAtoms[r])
self.__ScoreFx.traceScoring(auxLigand, np.score)
else:
auxLigand = copy.deepcopy(self.__Ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + np.x),
(self.__newSpaceCenter[1] + np.y),
(self.__newSpaceCenter[2] + np.z)])
auxLigand.rotateByVector(
Methods.spherePoint(1, np.sph_theta, np.sph_phi), np.theta)
for r in xrange(len(self.__rotateAtoms)):
auxLigand.rotateSegment(r, np.rotateAtoms[r])
'Score'
auxPose = rosetta.core.pose.Pose()
auxPose.assign(self.__pose_ligand)
for atom in xrange(
auxPose.residue(auxPose.total_residue()).natoms()):
atomV = rosetta.numeric.xyzVector_Real()
atomV.x = round(auxLigand.x[atom], 3)
atomV.y = round(auxLigand.y[atom], 3)
atomV.z = round(auxLigand.z[atom], 3)
auxPose.residue(auxPose.total_residue()).set_xyz(
auxLigand.atom[atom], atomV)
np.score = self.__ScoreFx.generateScoringByPose(auxPose, auxLigand)
return np
def calculates(self, np):
if(self.__isLocalSearch):
np = self.__LocalSearch.initLocalProcess(np, self.__Ligand)
auxLigand = copy.deepcopy(self.__Ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + np.x),
(self.__newSpaceCenter[1] + np.y),
(self.__newSpaceCenter[2] + np.z)])
auxLigand.rotateByVector(Methods.spherePoint(1, np.sph_theta, np.sph_phi), np.theta)
for r in xrange(len(self.__rotateAtoms)):
auxLigand.rotateSegment(r, np.rotateAtoms[r])
self.__ScoreFx.traceScoring(auxLigand,np.score)
else:
auxLigand = copy.deepcopy(self.__Ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + np.x),
(self.__newSpaceCenter[1] + np.y),
(self.__newSpaceCenter[2] + np.z)])
auxLigand.rotateByVector(Methods.spherePoint(1, np.sph_theta, np.sph_phi), np.theta)
for r in xrange(len(self.__rotateAtoms)):
auxLigand.rotateSegment(r, np.rotateAtoms[r])
'Score'
auxPose = rosetta.core.pose.Pose()
auxPose.assign(self.__pose_ligand)
for atom in xrange(auxPose.residue(auxPose.total_residue()).natoms()):
atomV = rosetta.numeric.xyzVector_Real()
atomV.x = round(auxLigand.x[atom],3)
atomV.y = round(auxLigand.y[atom],3)
atomV.z = round(auxLigand.z[atom],3)
auxPose.residue(auxPose.total_residue()).set_xyz(auxLigand.atom[atom], atomV)
np.score = self.__ScoreFx.generateScoringByPose(auxPose, auxLigand)
return np
def recalculate(self, selectedPop, changeId=False):
if(len(selectedPop)>0):
for j in xrange(len(selectedPop)):
auxLigand = copy.deepcopy(self.__ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + selectedPop[j].x),
(self.__newSpaceCenter[1] + selectedPop[j].y),
(self.__newSpaceCenter[2] + selectedPop[j].z)])
auxLigand.rotateByVector(Methods.spherePoint(1, selectedPop[j].sph_theta, selectedPop[j].sph_phi), selectedPop[j].theta)
for r in xrange(len(self.__rotateAtoms)):
auxLigand.rotateSegment(r, selectedPop[j].rotateAtoms[r])
'Score'
auxPose = rosetta.core.pose.Pose()
auxPose.assign(self.__pose_ligand)
for atom in xrange(auxPose.residue(auxPose.total_residue()).natoms()):
atomV = rosetta.numeric.xyzVector_Real()
atomV.x = round(auxLigand.x[atom],3)
atomV.y = round(auxLigand.y[atom],3)
atomV.z = round(auxLigand.z[atom],3)
auxPose.residue(auxPose.total_residue()).set_xyz(auxLigand.atom[atom], atomV)
selectedPop[j].score = self.__scoreFx.generateScoringByPose(auxPose, auxLigand)
selectedPop.sort(key=lambda x: x.score, reverse=False)
if(changeId):
for k in xrange(len(selectedPop)):
selectedPop[k].id = k
return selectedPop
def getScoring(self, solution):
auxLigand = copy.deepcopy(self.__ligand)
auxLigand.traslateToPoint([(self.__spaceCenter[0] + solution.x),
(self.__spaceCenter[1] + solution.y),
(self.__spaceCenter[2] + solution.z)])
auxLigand.rotateByVector(
Methods.spherePoint(1, solution.sph_theta, solution.sph_phi),
solution.theta)
for r in range(len(self.__ligand.rotationsPoints)):
auxLigand.rotateSegment(r, solution.rotateAtoms[r])
'Score'
auxPose = rosetta.core.pose.Pose()
auxPose.assign(self.__pose_ligand)
for atom in xrange(auxPose.residue(auxPose.total_residue()).natoms()):
atomV = rosetta.numeric.xyzVector_Real()
atomV.x = round(auxLigand.x[atom], 3)
atomV.y = round(auxLigand.y[atom], 3)
atomV.z = round(auxLigand.z[atom], 3)
auxPose.residue(auxPose.total_residue()).set_xyz(
auxLigand.atom[atom], atomV)
result = self.__scoreFx.generateScoringByPose(auxPose, auxLigand,
False)
return result
def applyChanges(self, solution):
auxLigand = copy.deepcopy(self.__Ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + solution.x),
(self.__newSpaceCenter[1] + solution.y),
(self.__newSpaceCenter[2] + solution.z)])
auxLigand.rotateByVector(Methods.spherePoint(1, solution.sph_theta, solution.sph_phi), solution.theta)
for r in xrange(len(self.__Ligand.rotationsPoints)):
auxLigand.rotateSegment(r, solution.rotateAtoms[r])
return auxLigand
def applyChanges(self, solution):
auxLigand = copy.deepcopy(self.__Ligand)
auxLigand.traslateToPoint([(self.__newSpaceCenter[0] + solution.x),
(self.__newSpaceCenter[1] + solution.y),
(self.__newSpaceCenter[2] + solution.z)])
auxLigand.rotateByVector(
Methods.spherePoint(1, solution.sph_theta, solution.sph_phi),
solution.theta)
for r in xrange(len(self.__Ligand.rotationsPoints)):
auxLigand.rotateSegment(r, solution.rotateAtoms[r])
return auxLigand
def getScoring(self, solution):
auxLigand = copy.deepcopy(self.__ligand)
auxLigand.traslateToPoint([(self.__spaceCenter[0] + solution.x),
(self.__spaceCenter[1] + solution.y),
(self.__spaceCenter[2] + solution.z)])
auxLigand.rotateByVector(Methods.spherePoint(1, solution.sph_theta, solution.sph_phi), solution.theta)
for r in range(len(self.__ligand.rotationsPoints)):
auxLigand.rotateSegment(r, solution.rotateAtoms[r])
'Score'
auxPose = rosetta.core.pose.Pose()
auxPose.assign(self.__pose_ligand)
for atom in xrange(auxPose.residue(auxPose.total_residue()).natoms()):
atomV = rosetta.numeric.xyzVector_Real()
atomV.x = round(auxLigand.x[atom],3)
atomV.y = round(auxLigand.y[atom],3)
atomV.z = round(auxLigand.z[atom],3)
auxPose.residue(auxPose.total_residue()).set_xyz(auxLigand.atom[atom], atomV)
result = self.__scoreFx.generateScoringByPose(auxPose, auxLigand, False)
return result
def recalculate(self, selectedPop, changeId=False):
if (len(selectedPop) > 0):
for j in xrange(len(selectedPop)):
auxLigand = copy.deepcopy(self.__ligand)
auxLigand.traslateToPoint([
(self.__newSpaceCenter[0] + selectedPop[j].x),
(self.__newSpaceCenter[1] + selectedPop[j].y),
(self.__newSpaceCenter[2] + selectedPop[j].z)
])
auxLigand.rotateByVector(
Methods.spherePoint(1, selectedPop[j].sph_theta,
selectedPop[j].sph_phi),
selectedPop[j].theta)
for r in xrange(len(self.__rotateAtoms)):
auxLigand.rotateSegment(r, selectedPop[j].rotateAtoms[r])
'Score'
auxPose = rosetta.core.pose.Pose()
auxPose.assign(self.__pose_ligand)
for atom in xrange(
auxPose.residue(auxPose.total_residue()).natoms()):
atomV = rosetta.numeric.xyzVector_Real()
atomV.x = round(auxLigand.x[atom], 3)
atomV.y = round(auxLigand.y[atom], 3)
atomV.z = round(auxLigand.z[atom], 3)
auxPose.residue(auxPose.total_residue()).set_xyz(
auxLigand.atom[atom], atomV)
selectedPop[j].score = self.__scoreFx.generateScoringByPose(
auxPose, auxLigand)
selectedPop.sort(key=lambda x: x.score, reverse=False)
if (changeId):
for k in xrange(len(selectedPop)):
selectedPop[k].id = k
return selectedPop
'Original Molecule'
if (__onlyLigand):
IO.writePDB("Ligand_" + ligandName + ".pdb", ligandOri, resultPath)
else:
IO.writeAllPDB(ligandName, protein, ligandOri, resultPath, True)
'Log'
log = ""
'Generate Files'
for i in range(len(listaGenes)):
auxLigand = None
auxLigand = copy.deepcopy(ligand)
#auxLigand.traslateToPoint([listaGenes[i].x, listaGenes[i].y, listaGenes[i].z])
auxLigand.rotateByVector(
Methods.spherePoint(1, listaGenes[i].sph_theta, listaGenes[i].sph_phi),
listaGenes[i].theta)
for l in range(len(ligand.rotationsPoints)):
auxLigand.rotateSegment(l, listaGenes[i].rotateAtoms[l])
#if( len(ligand.rotationsPoints) > 0):
# auxLigand.traslateToPoint(ligandPoint)
'RMSD'
IO.writeAllPDB("result_aux.pdb", protein, auxLigand, resultPath)
rmsd = scoringFx.getRMSD("original_" + __MoleculeName + ".pdb",
"result_aux.pdb", tempPath, resultPath)
'Create Result'
ligandOri.x = auxLigand.x[:]
ligandOri.y = auxLigand.y[:]
'Original Molecule'
if(__onlyLigand):
IO.writePDB("Ligand_"+ligandName +".pdb",ligandOri,resultPath)
else:
IO.writeAllPDB(ligandName, protein, ligandOri, resultPath, True)
'Log'
log = ""
'Generate Files'
for i in range(len(listaGenes)):
auxLigand = None
auxLigand = copy.deepcopy(ligand)
#auxLigand.traslateToPoint([listaGenes[i].x, listaGenes[i].y, listaGenes[i].z])
auxLigand.rotateByVector(Methods.spherePoint(1, listaGenes[i].sph_theta, listaGenes[i].sph_phi), listaGenes[i].theta)
for l in range(len(ligand.rotationsPoints)):
auxLigand.rotateSegment(l, listaGenes[i].rotateAtoms[l])
#if( len(ligand.rotationsPoints) > 0):
# auxLigand.traslateToPoint(ligandPoint)
'RMSD'
IO.writeAllPDB("result_aux.pdb", protein, auxLigand, resultPath)
rmsd = scoringFx.getRMSD("original_" + __MoleculeName + ".pdb", "result_aux.pdb", tempPath, resultPath)
'Create Result'
ligandOri.x = auxLigand.x[:]
ligandOri.y = auxLigand.y[:]
ligandOri.z = auxLigand.z[:]