def main():
parser = argparse.ArgumentParser()
parser.add_argument('-mode', default='select_memb')
parser.add_argument('-in_file', default=sys.argv[1])
parser.add_argument('-name', default=None)
args = vars(parser.parse_args())
if args['mode'] == 'select_memb_old':
# load pdb
pdb = parse_PDB(args['in_file'], args['name'])
res_in_memb = pymol_select_memb_old(pdb)
print('select membrane_residues, resi %s' % '+'.join([str(a) for a in res_in_memb]))
elif args['mode'] == 'print_num_memb_old':
pdb = parse_PDB(args['in_file'], args['name'])
res_in_memb = pymol_select_memb_old(pdb)
print('num_in_memb %i' % len(res_in_memb))
elif args['mode'] == 'select_memb':
pdb = parse_PDB(args['in_file'], args['name'])
memb_ress = memb_residues(pdb)
print('select membrane_residues, resi %s' % '+'.join([str(r.res_num) for r in memb_ress]))
else:
print('no mode selected')
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-mode', default='select_memb')
parser.add_argument('-in_file', default=sys.argv[1])
parser.add_argument('-name', default=None)
args = vars(parser.parse_args())
if args['mode'] == 'select_memb_old':
# load pdb
pdb = parse_PDB(args['in_file'], args['name'])
res_in_memb = pymol_select_memb_old(pdb)
print('select membrane_residues, resi %s' %
'+'.join([str(a) for a in res_in_memb]))
elif args['mode'] == 'print_num_memb_old':
pdb = parse_PDB(args['in_file'], args['name'])
res_in_memb = pymol_select_memb_old(pdb)
print('num_in_memb %i' % len(res_in_memb))
elif args['mode'] == 'select_memb':
pdb = parse_PDB(args['in_file'], args['name'])
memb_ress = memb_residues(pdb)
print('select membrane_residues, resi %s' %
'+'.join([str(r.res_num) for r in memb_ress]))
else:
print('no mode selected')
def by_two_numbers():
from mpl_toolkits.mplot3d import axes3d
from PDB_Bfactor_by_list import repalce_Bfactor
from MyPDB import parse_PDB
by_6A = parse_atom_count(work_path+'6A.lst')
by_12A = parse_atom_count(work_path+'12A.lst')
results = {}
slope6, intercept6 = 0.05, 30
slope12, intercept12 = 0.05, 350
for k, v6 in by_6A.items():
results[k] = sigmoid(v6, slope6, intercept6) * sigmoid(by_12A[k], intercept12, intercept12)
print(k, v6, by_12A[k], results[k])
pdb = parse_PDB('3o7q.pdb')
repalce_Bfactor(pdb, results, {'pdb': '3o7q.pdb', 'list': '6x12sigs.lst'})
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x = np.arange(0, 400, 1)
y = np.arange(0, 400, 1)
X, Y = np.meshgrid(x, y)
zs = np.array([sigmoid(x, slope=slope6, intercept=intercept6)*
sigmoid(y, slope=slope12, intercept=intercept12)
for x, y in zip(np.ravel(X), np.ravel(Y))])
Z = zs.reshape(X.shape)
ax.plot_surface(X, Y, Z)
ax.set_xlabel('6A')
ax.set_ylabel('12A')
ax.set_zlabel('energy')
plt.show()
def Bfactor_by_list(args):
pdb = parse_PDB(args['pdb'])
resnum_occupancy_dict = parse_Bfactor_list(args['list'])
file_name = args['pdb'].split('.pdb')[0] + '_' + args['list'].split(
'.')[0] + '.pdb'
repalce_Bfactor(pdb, resnum_occupancy_dict, args, new_name=file_name)
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 main():
pdb_file = sys.argv[1]
pdb = parse_PDB(pdb_file)
energy_table = parse_energy_table(pdb_file)
polyval = MakeHydrophobicityGrade()
for res in pdb.iter_all_res():
cnt_6 = pdb.count_atoms_near_res(res, 6)
cnt_12 = pdb.count_atoms_near_res(res, 12)
print(res, burial_sigmoid(cnt_6, cnt_12))
def Bfactor_by_z(args):
pdb = parse_PDB(args['pdb'])
z_Bfactor_dict = {}
for rsd in pdb.iter_all_res():
if -15 <= rsd['CA'].xyz.z <= 15:
z_Bfactor_dict[rsd.res_num] = 50
else:
z_Bfactor_dict[rsd.res_num] = 0
new_file = args['pdb'].split('.pdb')[0] + '_z.pdb'
repalce_Bfactor(pdb, z_Bfactor_dict, args, new_file)
def main():
pdb_file = sys.argv[1]
pdb = parse_PDB(pdb_file)
energy_table = parse_energy_table(pdb_file)
polyval = MakeHydrophobicityGrade()
for res in pdb.iter_all_res():
cnt_6 = pdb.count_atoms_near_res(res, 6)
cnt_12 = pdb.count_atoms_near_res(res, 12)
print(res, burial_sigmoid(cnt_6, cnt_12))
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 main():
global rosetta_splines
rosetta_splines = calc_rosetta_splines()
arg1 = sys.argv[1]
if '.pdb' not in arg1:
seq = arg1
ori = sys.argv[2]
dg = calc_seq_dg(seq, ori, rosetta_splines)
print('%s %s %.2f' % (seq, ori, dg))
else:
pdb = parse_PDB(arg1)
spans = find_spans_pdb(pdb)
for span in spans:
dg = calc_span_dg(pdb, span[0], span[1], rosetta_splines)
print('span %i->%i ∆G=%.2f' % (span[0], span[1], dg))
def main():
global rosetta_splines
rosetta_splines = calc_rosetta_splines()
arg1 = sys.argv[1]
if '.pdb' not in arg1:
seq = arg1
ori = sys.argv[2]
dg = calc_seq_dg(seq, ori, rosetta_splines)
print('%s %s %.2f' % (seq, ori, dg))
else:
pdb = parse_PDB(arg1)
spans = find_spans_pdb(pdb)
for span in spans:
dg = calc_span_dg(pdb, span[0], span[1], rosetta_splines)
print('span %i->%i ∆G=%.2f' % (span[0], span[1], dg))
def main():
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d as m3d
parser = argparse.ArgumentParser()
parser.add_argument('-pdb')
parser.add_argument('-s1', type=int)
parser.add_argument('-e1', type=int)
parser.add_argument('-s2', type=int)
parser.add_argument('-e2', type=int)
args = vars(parser.parse_args())
pdb = parse_PDB(args['pdb'])
l1, data1 = find_helix_vector(pdb, args['s1'], args['e1'])
l2, data2 = find_helix_vector(pdb, args['s2'], args['e2'])
p1, p2 = find_points_of_closest_distance(l1, l2)
cross_angle = calc_dihedral(l1[0], p1, p2, l2[0])
dist = np.linalg.norm(p1-p2)
print('cross angle', cross_angle)
print('dist', dist)
def test_input(args):
if args['seq'] is None:
pdb = parse_PDB(args['native_pdb'])
seq_dict = pdb.get_seq()
args['seq'] = seq_dict[args['chain']]
if args['topo_string'] is None:
args['topo_string'] = 'H' * len(args['seq'])
args['logger'].log('NO TOPO-STRING GIVEN, using helix only, creating file')
with open('%s.ts' % args['name'], 'w+') as fout:
fout.write('>%s\n' % args['name'])
fout.write('%s' % args['topo_string'])
args['logger'].log('NO SEQ GIVEN, using %s, %i AAs' % (args['seq'], len(args['seq'])))
ok = len(args['seq']) == len(args['topo_string'])
if args['mode'] == 'fnd':
args['xml'] = fnd_protocol
elif args['mode'] == 'design':
args['xml'] = design_protocol
else:
sys.exit('mode was neither design nor fnd...')
if not ok:
sys.exit('sequence and topo string not same length')
def by_two_numbers():
from mpl_toolkits.mplot3d import axes3d
from PDB_Bfactor_by_list import repalce_Bfactor
from MyPDB import parse_PDB
by_6A = parse_atom_count(work_path + '6A.lst')
by_12A = parse_atom_count(work_path + '12A.lst')
results = {}
slope6, intercept6 = 0.05, 30
slope12, intercept12 = 0.05, 350
for k, v6 in by_6A.items():
results[k] = sigmoid(v6, slope6, intercept6) * sigmoid(
by_12A[k], intercept12, intercept12)
print(k, v6, by_12A[k], results[k])
pdb = parse_PDB('3o7q.pdb')
repalce_Bfactor(pdb, results, {'pdb': '3o7q.pdb', 'list': '6x12sigs.lst'})
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
x = np.arange(0, 400, 1)
y = np.arange(0, 400, 1)
X, Y = np.meshgrid(x, y)
zs = np.array([
sigmoid(x, slope=slope6, intercept=intercept6) *
sigmoid(y, slope=slope12, intercept=intercept12)
for x, y in zip(np.ravel(X), np.ravel(Y))
])
Z = zs.reshape(X.shape)
ax.plot_surface(X, Y, Z)
ax.set_xlabel('6A')
ax.set_ylabel('12A')
ax.set_zlabel('energy')
plt.show()
#!/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]))
#!/usr/bin/env python3.5
from MyPDB import parse_PDB
from sys import argv
name = argv[1]
pdb = parse_PDB(file_in=name, name=name)
seq = pdb.seqs
if len(argv) > 2:
chains = argv[2:]
for c in chains:
print('>%s.%s' % (name, c))
print(seq[c].get_seq)
else:
for c in sorted(seq.keys()):
if 'non_res' not in c:
print('>%s.%s' % (name, c))
print(seq[c].get_seq)
