def main():
pdb = parse_PDB(sys.argv[1])
for name, xyz in zip(['B', 'C', 'X'], [XYZ(7.5, 0, 0), XYZ(0, 7.5, 0), XYZ(7.5, 7.5, 7.5)]):
new_chain = copy.deepcopy(pdb.chains['A'])
new_chain.change_chain_name(name)
new_chain.translate_xyz(xyz)
pdb.add_chain(new_chain)
pdb.renumber()
write_PDB('test.pdb', pdb)
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 main():
pdb = parse_PDB(sys.argv[1])
for name, xyz in zip(
['B', 'C', 'X'],
[XYZ(7.5, 0, 0), XYZ(0, 7.5, 0),
XYZ(7.5, 7.5, 7.5)]):
new_chain = copy.deepcopy(pdb.chains['A'])
new_chain.change_chain_name(name)
new_chain.translate_xyz(xyz)
pdb.add_chain(new_chain)
pdb.renumber()
write_PDB('test.pdb', pdb)
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 repalce_Bfactor(pdb: MyPDB, resnum_occupancy_dict_: dict, args: dict,
new_name: str) -> None:
resnum_occupancy_dict = {}
min_ = min(resnum_occupancy_dict_.values())
max_ = max(resnum_occupancy_dict_.values())
for k, v in resnum_occupancy_dict_.items():
resnum_occupancy_dict[k] = (v - min_) / (max_ - min_) * 50.0
for cid in sorted(pdb.chains.keys()):
for rid in sorted(pdb[cid].residues.keys()):
for aid in sorted(pdb[cid][rid].keys()):
if pdb[cid][rid].res_num in resnum_occupancy_dict.keys():
pdb[cid][rid][aid].set_temp(
resnum_occupancy_dict[pdb[cid][rid].res_num])
else:
pdb[cid][rid][aid].set_temp(0.0)
write_PDB(new_name, pdb)
print('writing the pdb into %s' % new_name)
