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
def __init__(self,
refPdb,
refChain,
tmpPath='.',
localPdb='',
verbose=False):
self.analogs = pd.DataFrame(columns=[
'pdb', 'chain', 'z', 'rmsd', 'lali', 'nres', 'id', 'title',
'sequence', 'aligned', 'organism_id', 'organism_scientific'
])
self.equivalences = pd.DataFrame(
columns=['pdb2', 'chain2', 'from1', 'to1', 'from2', 'to2'])
self.refPdb = refPdb
self.refChain = refChain
self.refSequence = ''
self.refLength = 0
self.analogs['organism_id'] = ''
if verbose: print('Creating Dali object for pdb ' + refPdb + refChain)
pdb = Pdb()
if not path.isdir(tmpPath):
try:
mkdir(tmpPath)
except:
sys.exit('Cannot make dir ' + tmpPath)
if not path.isfile(tmpPath + '/' + refPdb + '.pdb'):
if localPdb == '':
pdb.Download(pdbCode=refPdb, verbose=verbose, path=tmpPath)
else:
pdb.TakeLocalFiles(pdbCode=refPdb,
sourceDir=localPdb,
targetDir=tmpPath)
pdb.ReadFile(tmpPath + '/' + refPdb + '.pdb', skipNonAminoacid=True)
self.refSequence = pdb.GetSequence(chain=refChain)
del pdb
self.refLength = len(self.refSequence)
if verbose:
print('Length of reference sequence is ' + str(self.refLength))
