def calc_span_dg(pdb: MyPDB, start: int, end: int, rosetta_splines: dict) -> float:
"""
calculate a span's dG from structure
"""
dg = 0.0
for i in range(start, end+1):
dg += interpolate.splev( pdb.get_res(i).memb_z, rosetta_splines[ pdb.get_res(i).res_type ], der=0 )
return dg
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 find_spans_pdb(pdb: MyPDB) -> list:
memb_vec = []
for res in pdb.iter_all_res():
memb_vec.append( res.memb_z is not None )
spans = []
chain, start, end, ori = pdb.get_res(1).chain, -1, -1, 'fwd'
tm_open = False
for i in range(len(memb_vec)):
if pdb.get_res(i+1).chain != chain and tm_open:
end = i
ori = 'fwd' if pdb.get_res(start).memb_z < 0 and pdb.get_res(end) > 0 else 'rev'
spans.append([start, end, ori])
tm_open = False
if memb_vec[i] and not tm_open:
start = i + 1
tm_open = True
if not memb_vec[i] and tm_open:
end = i-1
ori = 'fwd' if pdb.get_res(start).memb_z < 0 and pdb.get_res(end) > 0 else 'rev'
spans.append([start, end, ori])
tm_open = False
chain = pdb.get_res(i+1).chain
if tm_open:
spans.append([start, i+1, ori])
return spans
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 find_helix_vector(pdb: MyPDB, start: int, end: int):
xs, ys, zs = [], [], []
for i in range(start, end+1):
res_i = pdb.get_res(i)
for bb_atom in res_i.iter_bb():
xs.append(bb_atom.xyz.x)
ys.append(bb_atom.xyz.y)
zs.append(bb_atom.xyz.z)
xs_ = np.array(xs)
ys_ = np.array(ys)
zs_ = np.array(zs)
dist = np.sqrt((xs[-1]-xs[0])**2 + (ys[-1]-ys[0])**2 + (zs[-1]-zs[0])**2 )
data = np.concatenate((xs_[:, np.newaxis], ys_[:, np.newaxis], zs_[:, np.newaxis]), axis=1)
datamean = data.mean(axis=0)
uu, dd, vv = np.linalg.svd(data - datamean)
linepts = vv[0] * np.mgrid[-dist/2:dist/2:2j][:, np.newaxis]
linepts += datamean
return linepts, data
def find_helix_vector(pdb: MyPDB, start: int, end: int):
xs, ys, zs = [], [], []
for i in range(start, end + 1):
res_i = pdb.get_res(i)
for bb_atom in res_i.iter_bb():
xs.append(bb_atom.xyz.x)
ys.append(bb_atom.xyz.y)
zs.append(bb_atom.xyz.z)
xs_ = np.array(xs)
ys_ = np.array(ys)
zs_ = np.array(zs)
dist = np.sqrt((xs[-1] - xs[0])**2 + (ys[-1] - ys[0])**2 +
(zs[-1] - zs[0])**2)
data = np.concatenate(
(xs_[:, np.newaxis], ys_[:, np.newaxis], zs_[:, np.newaxis]), axis=1)
datamean = data.mean(axis=0)
uu, dd, vv = np.linalg.svd(data - datamean)
linepts = vv[0] * np.mgrid[-dist / 2:dist / 2:2j][:, np.newaxis]
linepts += datamean
return linepts, data