def setup_db(args):
rost_db = parse_rost_db()
failed = []
logger = Logger('./db_setup.log')
for k, v in rost_db.items():
# if k != 'q9u6b8': continue
logger.create_header('working on %s' % k)
logger.log('seq: %s' % v['seq'])
logger.log('pdb: %s' % v['pdb'])
logger.log('chain: %s' % v['chain'])
logger.log('ts: %s' % v['ts'])
os.mkdir(k)
os.chdir(k)
# get pdb and extract chain
download_pdb({'name': v['pdb'], 'path': './'})
empty_pdb = MyPDB(name=v['pdb'])
pdb = parse_PDB('pdb%s.ent' % v['pdb'])
chain = pdb.chains[v['chain']]
empty_pdb.add_chain(chain)
write_PDB('%s_%s.pdb' % (k, v['chain']), empty_pdb)
pdb_seq = extract_seq(empty_pdb)
rdb_seq = AASeq(v['seq'])
score, start, end = pdb_seq[v['chain']].align(rdb_seq)
logger.log('pdb seq: %s' % pdb_seq[v['chain']].aligned)
logger.log('rst seq: %s' % rdb_seq.aligned)
# get spans and print xml
spans = find_topo(v['ts'])
new_spans = []
for sp in spans:
start = pdb_seq[v['chain']].aligned_position_at_non_aligned(
sp[0]) + 1
end = pdb_seq[v['chain']].aligned_position_at_non_aligned(
sp[1]) + 1
logger.log('span %i->%i %s moving to %i->%i' %
(sp[0], sp[1], sp[2], start, end))
new_spans.append([start, end, sp[2]])
create_AddMembrane_xml(new_spans, '%s_AddMembrane.xml' % v['pdb'])
# create flags file
with open('embed.flags', 'w+') as fout:
fout.write(
'-parser:protocol /home/labs/fleishman/jonathaw/elazaridis/protocols/embed_in_membrane.xml\n'
)
fout.write('-s %s\n' % '%s_%s.pdb' % (k, v['chain']))
fout.write('-parser:script_vars add_memb_xml=%s\n' %
'%s_AddMembrane.xml' % v['pdb'])
fout.write('-overwrite\n')
fout.write('-score::elec_memb_sig_die\n')
fout.write('-corrections::beta_nov15\n')
fout.write('-score::memb_fa_sol\n')
os.chdir('../')
def setup_db(args):
rost_db = parse_rost_db()
failed = []
logger = Logger('./db_setup.log')
for k, v in rost_db.items():
# if k != 'q9u6b8': continue
logger.create_header('working on %s' % k)
logger.log('seq: %s' % v['seq'])
logger.log('pdb: %s' % v['pdb'])
logger.log('chain: %s' % v['chain'])
logger.log('ts: %s' % v['ts'])
os.mkdir(k)
os.chdir(k)
# get pdb and extract chain
download_pdb({'name': v['pdb'], 'path': './'})
empty_pdb = MyPDB(name=v['pdb'])
pdb = parse_PDB('pdb%s.ent' % v['pdb'])
chain = pdb.chains[v['chain']]
empty_pdb.add_chain(chain)
write_PDB('%s_%s.pdb' % (k, v['chain']), empty_pdb)
pdb_seq = extract_seq(empty_pdb)
rdb_seq = AASeq(v['seq'])
score, start, end = pdb_seq[v['chain']].align(rdb_seq)
logger.log('pdb seq: %s' % pdb_seq[v['chain']].aligned)
logger.log('rst seq: %s' % rdb_seq.aligned)
# get spans and print xml
spans = find_topo(v['ts'])
new_spans = []
for sp in spans:
start = pdb_seq[v['chain']].aligned_position_at_non_aligned(sp[0]) + 1
end = pdb_seq[v['chain']].aligned_position_at_non_aligned(sp[1]) + 1
logger.log('span %i->%i %s moving to %i->%i' %(sp[0], sp[1], sp[2], start, end))
new_spans.append([start, end, sp[2]])
create_AddMembrane_xml(new_spans, '%s_AddMembrane.xml' % v['pdb'])
# create flags file
with open('embed.flags', 'w+') as fout:
fout.write('-parser:protocol /home/labs/fleishman/jonathaw/elazaridis/protocols/embed_in_membrane.xml\n')
fout.write('-s %s\n' % '%s_%s.pdb' % (k, v['chain']))
fout.write('-parser:script_vars add_memb_xml=%s\n' % '%s_AddMembrane.xml' % v['pdb'])
fout.write('-overwrite\n')
fout.write('-score::elec_memb_sig_die\n')
fout.write('-corrections::beta_nov15\n')
fout.write('-score::memb_fa_sol\n')
os.chdir('../')
#!/usr/bin/env python3.5
from MyPDB import parse_PDB, extract_seq
import sys
in_1 = sys.argv[1]
in_2 = sys.argv[2]
pdb_1 = parse_PDB(in_1, in_1.split('.')[0])
pdb_2 = parse_PDB(in_2, in_2.split('.')[0])
seqs_1 = extract_seq(pdb_1)
seqs_2 = extract_seq(pdb_2)
assert seqs_1.keys() == seqs_2.keys(), 'PDBs have different chain names'
seq_1, seq_2 = '', ''
for chain_name in sorted(seqs_1.keys()):
seq_1 += seqs_1[chain_name].get_seq
seq_2 += seqs_2[chain_name].get_seq
assert len(seq_1) == len(seq_2), 'sequences not the same length'
diffs = []
for i in range(len(seq_1)):
if seq_1[i] != seq_2[i]:
print('%s%i%s' % (seq_1[i], i+1, seq_2[i]))
diffs.append(i+1)
print('found %i changes, over %i chains' % (len(diffs), len(seqs_1.keys())))
print('select diffs, resi %s' % '+'.join([str(a) for a in diffs]))
#!/usr/bin/env python3.5
from MyPDB import parse_PDB, extract_seq
import sys
in_1 = sys.argv[1]
in_2 = sys.argv[2]
pdb_1 = parse_PDB(in_1, in_1.split('.')[0])
pdb_2 = parse_PDB(in_2, in_2.split('.')[0])
seqs_1 = extract_seq(pdb_1)
seqs_2 = extract_seq(pdb_2)
assert seqs_1.keys() == seqs_2.keys(), 'PDBs have different chain names'
seq_1, seq_2 = '', ''
for chain_name in sorted(seqs_1.keys()):
seq_1 += seqs_1[chain_name].get_seq
seq_2 += seqs_2[chain_name].get_seq
assert len(seq_1) == len(seq_2), 'sequences not the same length'
diffs = []
for i in range(len(seq_1)):
if seq_1[i] != seq_2[i]:
print('%s%i%s' % (seq_1[i], i + 1, seq_2[i]))
diffs.append(i + 1)
print('found %i changes, over %i chains' % (len(diffs), len(seqs_1.keys())))
print('select diffs, resi %s' % '+'.join([str(a) for a in diffs]))
