def extractDomains(self, model=0, onlyBackbone=False, verbose=False):
"""1.-query the database to know every pair(pdbID, domainID)
2.-for each domain of the family contained in the pdb, load its segments.
3.-for each domain serialize it with the name domain.pdb
"""
(db, cursor) = queryCDDF.setUpDB(self.__host, self.__user, self.__passwd, self.__db)
self.PDB_Domains = queryCDDF.loadCATHfamilyDomains(self.cathcode, cursor)
for (pdbID, domain) in self.PDB_Domains:
validDomain = True
segments = queryCDDF.loadSegments(domain, cursor)
for segment in segments:
if segment[1] != -1:
self.validSegments.append((pdbID, domain, segment))
else:
self.notValidSegments.append((pdbID, domain, segment))
validDomain = False
if validDomain:
try:
pdb = PDB(self.__composeLocalFileName(self.workingDirectory, pdbID, ".pdb"))
pdb.load_atoms_hetams()
except IOError:
print "%s does not exist" %(self.__composeLocalFileName(self.workingDirectory, pdbID, ".pdb"),)
else:
pdb.serializeSegments(segments, self.__composeLocalFileName(self.workingDirectory, domain, ".pdb"), model, onlyBackbone)
if verbose:
print ("%s domain extracted" % (domain,))
queryCDDF.tearDownDB(db, cursor)
def getFamilyPDBS(self):
""" downloads every pdb that contains a domain of the cath family
(a pdb can contain more than one domain of the same family)"""
(db, cursor) = queryCDDF.setUpDB(self.__host, self.__user, self.__passwd, self.__db)
self.pdbIDs = queryCDDF.loadCATHfamily(self.cathcode, cursor)
queryCDDF.tearDownDB(db, cursor)