def get_sequence(self, chain_name=None):
"""
Returns a dictionary with chains as keys and sequence string as values
"""
if chain_name is not None:
return {chain_name: ProteinSequence("".join( [ ProteinSequence.get_aminoacid_code_3to1(self.chains[chain_name][x].get_residue_type()) for x in self._get_sorted_residues(chain_name=chain_name)] ), sequenceID=self.name+"_"+chain_name)}
else:
if len(self.chains)>1:
print "ALERT: Trying to get the sequence from a PDB with more than a single chain."
chains = self.chains.keys()
return dict( [(chain_name, ProteinSequence("".join( [ ProteinSequence.get_aminoacid_code_3to1(self.chains[chain_name][x].get_residue_type()) for x in self._get_sorted_residues(chain_name=chain_name)] ), sequenceID=self.name+"_"+chain_name)) for chain_name in chains ] )
def _parse_dssp_results(self, fp):
# relative_accessibilities = [ None for x in self.]
# accessibilities = []
# ss = []
surface = {'A': 115,
'C': 149,
'D': 170,
'E': 207,
'F': 230,
'G': 86,
'H': 206,
'I': 187,
'K': 222,
'L': 192,
'M': 210,
'N': 184,
'P': 140,
'Q': 208,
'R': 263,
'S': 140,
'T': 164,
'V': 161,
'W': 269,
'Y': 257}
start_regex = re.compile(" # RESIDUE AA STRUCTURE BP1 BP2")
in_results = None
temp_seq = []
for line in fp:
if in_results is None:
if re.search(start_regex,line):
in_results = 1
continue
#Skipping chain breaks?
if line[13]=="!":
continue
temp_seq.append(line[13])
acc = int(line[35:38])
#accessibilities.append(acc)
chain = line[11]
res_num = int(line[5:10].strip())
res_type = line[13]
residue_object = self.chains[chain][res_num]
residue_object.dssp_accessibility = acc
if ProteinSequence.get_aminoacid_code_3to1(residue_object.get_residue_type())!=res_type and res_type!="X":
print ProteinSequence.get_aminoacid_code_3to1(residue_object.get_residue_type())
print res_type
sys.stderr.write("DSSP LINE: %s" %line)
raise ValueError("Discordance between PDB and DSSP")
#if( float(acc)*100/surface[line[13]] > 100 ):
# print "How can be a percentage greater than 100? residue: %s. Accessible area: %s, total surface: %s" %(line[13],acc,surface[line[13]])
try:
residue_object.dssp_rel_accessibility = float(acc)*100/surface[line[13]]
#relative_accessibilities.append(float(acc)*100/surface[line[13]])
except:
print "The code arrives here? if yes... why??"
pass
#print line
#traceback.print_exc()
#relative_accessibilities.append(0) #Added becuase if not it produces an error
if line[16]==' ':
residue_object.dssp_ss = 'N'
#ss.append('N')
else:
residue_object.dssp_ss = line[16]
