def GetSequenceFromPdb(self, tmpPath='.', localPdb='', verbose=False):
for i, prot in self.analogs.iterrows():
pdb2name = prot['pdb']
myChain = prot['chain']
if verbose:
print(" reading file " + tmpPath + '/' + pdb2name + '.pdb')
pdb = Pdb()
if not path.isfile(tmpPath + '/' + pdb2name + '.pdb'):
if localPdb == '':
if verbose: print(" downloading file")
pdb.Download(pdbCode=pdb2name, verbose=True, path=tmpPath)
pdb.ReadFile(tmpPath + '/' + pdb2name + '.pdb',
skipNonAminoacid=True)
else:
if verbose:
print(" copying file from local directory " + localPdb)
pdb.TakeLocalFiles(pdbCode=pdb2name,
sourceDir=localPdb,
targetDir=tmpPath)
pdb.ReadFile(tmpPath + '/' + pdb2name + '.pdb',
skipNonAminoacid=True)
else:
pdb.ReadFile(tmpPath + '/' + pdb2name + '.pdb',
skipNonAminoacid=True)
seq = pdb.GetSequence(chain=myChain)
self.analogs.at[i, 'sequence'] = seq
self.analogs.at[i, 'organism_id'] = pdb.GetKey('ORGANISM_TAXID')
self.analogs.at[i, 'organism_scientific'] = pdb.GetKey(
'ORGANISM_SCIENTIFIC')
if len(seq) == 0:
sys.exit("ERROR: Empty sequence for pdb " + pdb2name + myChain)
if verbose:
print(' has read pdb ' + pdb2name + myChain + ' (length=' +
str(len(seq)) + ')')
print(seq)
del pdb
