def __init__(self, table, pdb):
table = table.reset_index(drop=True)
struct = PDBParser().get_structure(table['pdb_id'][0], pdb)
table = table.fillna('')
alpha_num = sum([1 for x in table['tcr_v_allele'].tolist() if x.find('TRA') != -1])
beta_num = table.shape[0] - alpha_num
table.insert(table.columns.get_loc('tcr_chain'), 'tcr_chain_name', ['alpha'] * alpha_num + ['beta'] * beta_num)
print table
self.__table = table
self.__name = str(struct.get_id())
self.__struct = struct
self.__chains = [chain.get_id() for chain in struct[0]]
self.__regions = table.groupby(['tcr_chain_name', 'tcr_region'])
# Dictionary of regions residues;
# looks like : { ('alpha', 'CDR1') : [residue list],
# ('alpha', 'CDR2') : [residue list], ... }
self.__regions_res = self.__regions.groups
for key in self.__regions_res.keys():
self.__regions_res[key] = []
# Pepdide residue list
self.__peptide = []
# Dictionaries with pairwise region matrices;
# look like : { (('alpha', 'CDR1'), ('alpha', 'CDR2')) : dataframe,
# (('alpha', 'CDR1'), ('alpha', 'CDR3')) : dataframe, ... }
self.__d_matrices = {}
self.__e_matrices = {}
self.verbose = True
if not self.getRegionsResidues():
print 'SOME REGION WAS NOT FOUND IN PDB'
if not self.definePeptideChain():
print 'PEPTIDE WAS NOT FOUND IN PDB'
def download_and_get_chains():
from Bio.PDB import PDBParser, PDBIO
failed = []
pdbs_dict = read_rostdb_entries()
io = PDBIO()
pdbl = PDBList()
for pdb_e, chains in pdbs_dict.items():
for chain_e in chains:
try:
pdbl.retrieve_pdb_file(pdb_e, pdir='./')
pdb = PDBParser().get_structure(pdb_e, 'pdb'+pdb_e.lower()+'.ent')
for chain in pdb.get_chains():
if chain.get_id() == chain_e:
io.set_structure(chain)
io.save(pdb.get_id() + '_' + chain.get_id() + '.pdb')
except:
failed.append((pdb_e, chain_e))
print("failures:", failed)
def download_and_get_chains():
from Bio.PDB import PDBParser, PDBIO
failed = []
pdbs_dict = read_rostdb_entries()
io = PDBIO()
pdbl = PDBList()
for pdb_e, chains in pdbs_dict.items():
for chain_e in chains:
try:
pdbl.retrieve_pdb_file(pdb_e, pdir='./')
pdb = PDBParser().get_structure(pdb_e,
'pdb' + pdb_e.lower() + '.ent')
for chain in pdb.get_chains():
if chain.get_id() == chain_e:
io.set_structure(chain)
io.save(pdb.get_id() + '_' + chain.get_id() + '.pdb')
except:
failed.append((pdb_e, chain_e))
print("failures:", failed)
#
p = Pool(20)
parts = len(list_result_n) // 20
for i in tqdm(range(parts)):
p.map(download, list_result_n[i * 20:i * 20 + 20])
p.map(download, list_result_n[parts * 20:])
result_chains = {}
for i in result:
for i1 in result[i]:
struc = i1.split(";")[0]
chain = i1.split(";")[1].strip()
if struc in result_chains:
result_chains[struc].append(chain)
else:
result_chains[struc] = [chain]
print(result_chains)
for i in tqdm(os.listdir("pdb_m")):
io = PDBIO()
pdb = PDBParser().get_structure(i, "pdb_m/%s" % i)
for chain in pdb.get_chains():
if chain.get_id() in result_chains[i.split("_")[1]]:
io.set_structure(chain)
io.save("pdb_chain/" + pdb.get_id() + "_" + chain.get_id() +
".pdb")
from Bio.PDB import PDBParser from Bio.PDB import PPBuilder from Bio.PDB import Polypeptide item = '2bnr' structure = PDBParser().get_structure(item, '../pdbs/'+item+'.pdb') ppb=PPBuilder() peps = ppb.build_peptides(structure) print structure.get_id() print peps[0] #print peps[0][1:-3] print peps[0][3:9] p = peps[0][3:9] print peps[0][1].get_resname()
from Bio.PDB import PDBParser, PDBIO
from Bio.PDB.Polypeptide import is_aa, three_to_one
import sys
path = sys.argv[1]
code = path[:-4]
io = PDBIO()
pdb = PDBParser().get_structure(code, path)
for chain in pdb.get_chains():
io.set_structure(chain)
io.save(pdb.get_id() + "_" + chain.get_id() + ".pdb")
seq = list()
out = open(code + "_" + chain.get_id() + '.fasta', 'w')
for residue in chain:
if is_aa(residue.get_resname(), standard=True):
seq.append(three_to_one(residue.get_resname()))
else:
seq.append("X")
## This line is used to display the sequence from each chain
print(">Chain_" + chain.get_id() + "\n" + str("".join(seq)), file=out)
out.close()
