def __init__(self, PERMISSIVE=1, get_header=0, LayoutDatabase=False):
self._PERMISSIVE = PERMISSIVE
#If LayoutDatabase, I'll load the classes about database. Otherwise, I'll not load them.
self._pdbFileLayout = PDBFileLayout()
self._dicResidue = {}
self._dicSeqRes = {}
#self._structure_builder=StructureBuilder()
self._structure_builder = FcfrpStructureBuilder()
class FcfrpPDBParser():
def __init__(self, PERMISSIVE=1, get_header=0, LayoutDatabase=False):
self._PERMISSIVE = PERMISSIVE
#If LayoutDatabase, I'll load the classes about database. Otherwise, I'll not load them.
self._pdbFileLayout = PDBFileLayout()
self._dicResidue = {}
self._dicSeqRes = {}
#self._structure_builder=StructureBuilder()
self._structure_builder = FcfrpStructureBuilder()
def _loadAtomsfromFile(self, id, dicAtom):
i_a = 0 #atom index
#Create reference variables
reference_chain = None
reference_residue = None
reference_resName = None
reference_model = None
inserted_model0 = False
while i_a < dicAtom.__len__():
resname = dicAtom[i_a].getResName()
resseq = dicAtom[i_a].getResSeq()
icode = dicAtom[i_a].getIcode()
residueId = ("", resseq, icode)
#Model
if reference_model != dicAtom[i_a].getModel() or dicAtom[i_a].getModel() == None:
if dicAtom[i_a].getModel() == None: #Cristalografy
reference_model = 0
if inserted_model0 == False:
self._structure_builder.init_model(reference_model)
inserted_model0 = True
else:
reference_model = dicAtom[i_a].getModel()
self._structure_builder.init_model(reference_model)
reference_chain = None
reference_residue = None
reference_resName = None
#Segid
self._structure_builder.init_seg("")
#Chain and Residue
if reference_chain != dicAtom[i_a].getChainId():
reference_chain = dicAtom[i_a].getChainId()
self._structure_builder.init_chain(reference_chain)
#Because changed chain, it's necessary start a new residue in structure
reference_residue = residueId
reference_resName = resname
self._structure_builder.init_residue(resname, "", resseq, icode)
elif reference_resName != resname or reference_residue != residueId:
reference_resName = resname
reference_residue = residueId
self._structure_builder.init_residue(resname, "", resseq, icode)
#Atom
self._structure_builder.init_atom(dicAtom[i_a].get_id(), dicAtom[i_a].get_coord(), dicAtom[i_a].get_bfactor(), dicAtom[i_a].get_occupancy() , dicAtom[i_a].get_altloc(), dicAtom[i_a].get_fullname(), dicAtom[i_a].get_serial_number())
i_a = i_a + 1
def _loadSeqResfromFile(self, id):
self._structure_builder.init_SeqRes(id)
self._structure_builder.structure.add_SeqRes(self._pdbFileLayout.getSeqRes(), self._pdbFileLayout.getRes())
def _loadSSBondsfromfile(self,id):
self._structure_builder.init_SSBonds(id)
self._structure_builder.structure.add_SSBonds(self._pdbFileLayout.getSSBonds())
def _loadErrorsfromFile(self, id, structure, pathfileName, chainId ):
self._structure_builder.init_ErrorStructure(id)
errors, vs = hasErrorFileStructure(structure,pathfileName , chainId)
if len(errors) > 0:
standard = FcfrpStandardizationPDBErrorDetails()
self._pdbFileLayout.setStructureErrors(errors, vs, standard)
self._structure_builder.structure.add_StructureErrors(self._pdbFileLayout.getStructureErrors())
def loadStructureFromFile(self, id, pathfileName, chainId=None):
dir, fileName = os.path.split(pathfileName)
filePDB = FcfrpFile(dir, fileName)
#Define Model value
currentModel = None
#Start the Structure
self._structure_builder.init_structure(id)
#Here the PDB file will read and separate in dictionaries.
for line in filePDB.readLines():
record = line.split()
if record[0] == "SEQRES":
if self.checkChain(record[2], chainId) == True:
self._pdbFileLayout.setRes(record)
self._pdbFileLayout.setSeqRes(record)
elif record[0] == "SSBOND":
if self.checkChain(line[15:16], chainId) == True:
self._pdbFileLayout.setSSBonds(line)
elif record[0] == "MODEL":
#The MODEL line is MODEL 1
# So, when split command is used, the result'll be ['MODEL', '1']
#Therefore, the currentModel represents the Model. If there isn't model, its value'll be always zero.
currentModel = int(record[1])
elif record[0] == "ATOM":
if self.checkChain(line[21:22], chainId) == True:
self._pdbFileLayout.setAtom(currentModel,line)
#Here the dictionaries have been created by for command above, they will be used in specific methods. These methods
# represent each PDB file section.
self._loadSeqResfromFile(id)
self._loadSSBondsfromfile(id)
self._loadAtomsfromFile(id, self._pdbFileLayout.getAtoms())
structure = self._structure_builder.get_structure()
self._loadErrorsfromFile(id, structure, pathfileName, chainId)
#print "Comentado checagem de erro qdo arquvivo PDB"
return structure
def checkChain(self, chainIdFile, chainIdSelected):
cont = False
if chainIdSelected == None:
cont = True
elif chainIdFile == chainIdSelected:
cont = True
else:
cont = False
return cont
