def save(self,structure,dir,fileName):
filePDB = FcfrpFile(dir, fileName)
filePDB.getAsFile("w")
#Create Remark Section
self._saveRemark(structure, filePDB)
#Create SEQRES Section
self._saveSeqRes(structure, filePDB)
#Create SSBOND Section
self._saveSSBonds(structure, filePDB)
#Create ATOM Section
iModels = 0 #index for Models
iAtom = 0 #index for atom
iRes = 0 #index for Residue
for model in structure:
#Will write Model, if there are more than 1 models.
if self._amountModels > 1:
iModels += 1
filePDB.write(self._MODEL % str(iModels))
iAtom = 0
iRes = 0
for chain in model:
for residue in chain:
iRes += 1
for atom in residue: #Atoms
iAtom += 1
self._saveAtom(iAtom,atom,residue,chain,iRes,filePDB, int(residue.id[1]))
filePDB.write(self._TER)
filePDB.write(self._ENDMDL)
filePDB.close()
def saveFile(self, fileName, conteudo):
f = FcfrpFile(self._pathOut, fileName)
f.getAsFile("w")
f.write(conteudo)
f.close()
class FcfrpStructureChains():
def __init__(self,path, fileNameSet):
self._path = path
self.fileSet = FcfrpFile(path, fileNameSet)
def getPDBIdFromName(self,name):
return str(name).split("_")[0]
def splitPDBChains(self,id):
return getStructureChains(id)
def getDirectory(self,id):
#Check if there isn't the path, it'll create and return it
path = os.path.join(self._path, id)
if os.path.exists(path) == False:
os.mkdir(path)
return path
def getPathFileName(self, name):
id = self.getPDBIdFromName(name)
path = self.getDirectory(id)
FileName = name + ".pdb"
return os.path.join(path,FileName)
def saveStructures(self,dicStructures):
# Save each structure stored in the dicStructures dictionary.
for k,structure in dicStructures.iteritems():
pathFileName = self.getPathFileName(k)
saveStructure(structure,pathFileName)
def buildFileSetProteins(self,id,dicStructures):
f = self.fileSet.getAsFile('a')
f.write(";"+id+"\n")#The main pdb
for k,v in dicStructures.iteritems():
f.write(" "+k+"\n")
def executeTitration(self,dicStructures, table):
for k, structure in dicStructures.iteritems():
id = self.getPDBIdFromName(k)
path = self.getDirectory(id)
FcfrpTitration(3,structure=structure,TableId=table,PDBid=k,path=path,FileName=None).execute(path)
def executeCapacitance(self,dicStructures, table):
for k, structure in dicStructures.iteritems():
id = self.getPDBIdFromName(k)
path = self.getDirectory(id)
FcfrpCapacitance(3,structure=structure,TableId=table,PDBid=k,path=path,FileName=None).execute(path)
