def create_and_add_MBR_residue(pdb, memb_chain, highest_atom_number):
rsd = MyPDB.Residue('MBR', 1, memb_chain)
X, Y, Z = [25, -25, -25, 25, 25, -25, -25,
25], [25, 25, -25, -25, 25, 25, -25,
-25], [15, 15, 15, 15, -15, -15, -15, -15]
for i, x, y, z in zip(range(1, 9), X, Y, Z):
rsd.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + i,
name='C%i' % i,
res_type_3='MBR',
chain=memb_chain,
res_seq_num=1,
x=x,
y=y,
z=z,
element='O' if z == 15 else 'N',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
chn = MyPDB.Chain(memb_chain, {1: rsd})
chn.add_residue(rsd)
pdb.add_chain(chn)
def pdb2interface(pdb_name: str, chain: str):
"""
:param pdb: a pdb name
:param chain: a chain
:return: creates a list of residues for any interface of chain with other chains with seq isentity < 0.95
"""
results = {}
pdb_path = find_pdb(pdb_name)
pdb = mp.parse_PDB(file_in=pdb_path, name=pdb_name, with_non_residue=False)
if len(list(pdb.seqs.keys())) < 2:
return None
wanted_seq = pdb.seqs[chain]
for ch_id, ch_seq in pdb.seqs.items():
if ch_id != chain:
score = wanted_seq.align(ch_seq)
if wanted_seq.aligned_identity(ch_seq) < 0.95:
interface = mp.interface_residues(pdb[chain], pdb[ch_id])
results[ch_id] = sorted([a.res_num for a in interface])
out_path = '/'.join(pdb_path.split('/')[:-1])+'/'+pdb_name+'_'+chain+'_result.txt'
with open(out_path, 'w+') as fout:
fout.write('name %s\n' % pdb_name)
fout.write('chain %s\n' % chain)
for ch, inter in results.items():
fout.write('%s %s\n' % (ch, ' '.join([str(a) for a in inter])))
fout.write('seq %s %s\n' % (ch, pdb.seqs[ch].get_seq()))
def pdb2interface(pdb_name: str, chain: str):
"""
:param pdb: a pdb name
:param chain: a chain
:return: creates a list of residues for any interface of chain with other chains with seq isentity < 0.95
"""
results = {}
pdb_path = find_pdb(pdb_name)
pdb = mp.parse_PDB(file_in=pdb_path, name=pdb_name, with_non_residue=False)
if len(list(pdb.seqs.keys())) < 2:
return None
wanted_seq = pdb.seqs[chain]
for ch_id, ch_seq in pdb.seqs.items():
if ch_id != chain:
score = wanted_seq.align(ch_seq)
if wanted_seq.aligned_identity(ch_seq) < 0.95:
interface = mp.interface_residues(pdb[chain], pdb[ch_id])
results[ch_id] = sorted([a.res_num for a in interface])
out_path = '/'.join(pdb_path.split('/')
[:-1]) + '/' + pdb_name + '_' + chain + '_result.txt'
with open(out_path, 'w+') as fout:
fout.write('name %s\n' % pdb_name)
fout.write('chain %s\n' % chain)
for ch, inter in results.items():
fout.write('%s %s\n' % (ch, ' '.join([str(a) for a in inter])))
fout.write('seq %s %s\n' % (ch, pdb.seqs[ch].get_seq()))
def main():
pdb_name = sys.argv[1]
output_file = pdb_name.split('.pdb')[0] + '_MBR.pdb'
pdb = MyPDB.parse_PDB(pdb_name)
memb_chain = determine_membrane_chain(pdb)
highet_atom_number = determine_highest_serial_num(pdb)
create_and_add_MBR_residue(pdb, memb_chain, highet_atom_number)
MyPDB.write_PDB(output_file, pdb)
def main():
pdb_name = sys.argv[1]
output_file = pdb_name.split('.pdb')[0] + '_MBR.pdb'
pdb = MyPDB.parse_PDB(pdb_name)
memb_chain = determine_membrane_chain(pdb)
highet_atom_number = determine_highest_serial_num(pdb)
create_and_add_MBR_residue(pdb, memb_chain, highet_atom_number)
MyPDB.write_PDB(output_file, pdb)
append_CONECT_to_PDB(output_file, highet_atom_number)
def main():
pdb_name = sys.argv[1]
chain = sys.argv[2]
start, end = sys.argv[3], sys.argv[4]
pdb = MyPDB.parse_PDB(pdb_name)
for rid, r in pdb[chain]:
if rid > 1:
print(rid, r.phi(pdb[chain][rid - 1]))
if rid < len(pdb[chain]):
print(rid, r.psi(pdb[chain][rid + 1]))
MyPDB.draw_ramachadran(pdb)
def main():
pdb_name = sys.argv[1]
chain = sys.argv[2]
start, end = sys.argv[3], sys.argv[4]
pdb = MyPDB.parse_PDB(pdb_name)
for rid, r in pdb[chain]:
if rid > 1:
print(rid, r.phi(pdb[chain][rid-1]))
if rid < len(pdb[chain]):
print(rid, r.psi(pdb[chain][rid+1]))
MyPDB.draw_ramachadran(pdb)
def parse_residues_file(self) -> dict:
pdb = mp.parse_PDB(
'/home/labs/fleishman/jonathaw/temp_residue_data/RKDS.txt')
for res in pdb['A'].values():
mpf.translate_and_rotate_res_to_xy_plane(
res, self.main_residue_atoms[res.res_type])
self.residues[res.res_type] = res
def draw_hbonds_profiles():
parser = argparse.ArgumentParser()
parser.add_argument('-pdb')
parser.add_argument('-stage', type=int)
args = vars(parser.parse_args())
pdb = my.parse_PDB(args['pdb'])
if args['stage'] == 1:
seq_length = pdb.seq_length()
command = "for i in `seq 1 %i`;do ~/bin/fleish_sub_general.sh /home/labs/fleishman/jonathaw/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol ~/elazaridis/protocols/scan_hbonds.xml -s %s -mp:scoring:hbond -corrections::beta_nov15 -score:elec_memb_sig_die -score:memb_fa_sol -overwrite -out:prefix ${i}_ -script_vars energy_function=beta_nov15_elazaridis res_num=${i} s1=%i e1=%i ori1=%s s2=%i e2=%i ori2=%s ;done" % (seq_length, args['pdb'], 1, 24, 'out2in', 25, 48, 'out2in')
print('issuing command\n%s' % command)
os.system(command)
if args['stage'] == 2:
os.system("head -2 1_score.sc|tail -1 > all_score.sc")
os.system("grep SCORE: *_score.sc|grep -v des >> all_score.sc")
z_dict = {id: res.memb_z for id, res in pdb.res_items()}
pos_dict = {v: k for k, v in z_dict.items()}
sc_df = Rf.score_file2df('all_score.sc')
zs, scs = [], []
for d, sc in zip(sc_df['description'].values, sc_df['a_e_res']):
zs.append(z_dict[ int( d.split('_')[0] ) ])
scs.append(sc)
plt.scatter(zs, scs)
for z, sc in zip(zs, scs):
if z is not None:
plt.annotate(pos_dict[z], xy=(z, sc), xytext=(-20, 20),
textcoords = 'offset points', ha = 'right', va = 'bottom',
bbox = dict(boxstyle = 'round,pad=0.5', fc = 'yellow', alpha = 0.5),
arrowprops = dict(arrowstyle = '->', connectionstyle = 'arc3,rad=0'))
plt.show()
def by_xyz(args):
print(args['xyz'])
i = args['num']
j = args['res_num']
for l in open(args['xyz'], 'r'):
s = l.rstrip().split()
a = MyPDB.Atom('HETATM',
i,
args['name'],
"",
args['res_name'],
args['chain'],
j,
float(s[0]),
float(s[1]),
float(s[2]),
"",
charge=0,
element="O",
si="",
occupancy=1,
temp=0)
print(a)
i += 1
j += 1
def by_file(args):
atoms = []
for l in open(args['f'], 'r'):
s = l.rstrip().split()
header = s[1]
num = int(s[2])
name = s[3]
res_name = s[4]
chain = s[5]
res_num = int(s[6])
x = float(s[7])
y = float(s[8])
z = float(s[9])
a = MyPDB.Atom(header,
num,
name,
"",
res_name,
chain,
res_num,
x,
y,
z,
"",
charge=0,
element="O",
si="",
occupancy=1,
temp=0)
print(a)
def test_symm_axis_interface(e: Entry, ch: str) -> bool:
print(e)
inter_resi = e.interface[ch]
print(e.symm_segs)
symm_resi = [a for seg in e.symm_segs for a in range(seg[0], seg[1]+1)]
print('symm_resi', symm_resi)
print(inter_resi)
pdb = mp.parse_PDB(find_pdb(e.pdb), with_non_residue=False)
symm_com = mp.com_residues(chain=pdb[e.chain], residues=symm_resi)
print(symm_resi, symm_com)
pdb.translate_xyz(mp.XYZ(0, 0, 0)-symm_com)
print('pdb translated')
print('writing pdb %s_%s_translated.pdb' % (e.pdb, e.chain))
mp.write_PDB('%s_%s_translated.pdb' % (e.pdb, e.chain), pdb)
print('now symm com is at', mp.com_residues(chain=pdb[e.chain], residues=symm_resi))
print('symm axis XYZ %r' % (e.symm_axis))
print_pymol_select(e)
def parse_symm_db(args):
"""
:param args:
:return: list of Entry instances that are significant in the CE database
"""
results = []
with open(work_dir + 'ce_symm.xml', 'r') as fin:
xml = fin.read().split('data')
ABC = 'QWERTYUIOPASDFGHJKLZXCVBNM'
for data in xml:
axis = {}
significant = False
for l in data.split('\n'):
if 'isSig' in l:
significant = l.split('>')[1].split('<')[0] == 'true'
if not significant:
break
if '<x>' in l:
axis['x'] = float(l.split('>')[1].split('<')[0])
if '<y>' in l:
axis['y'] = float(l.split('>')[1].split('<')[0])
if '<z>' in l:
axis['z'] = float(l.split('>')[1].split('<')[0])
if 'protodomain' in l:
try:
s = l.split('>')[1].split('<')[0].split(',')
pdb = s[0][:4]
chain = s[0][5]
if len(s) < 2:
continue
segs = []
for s_ in s:
if '_-' not in s_:
start = int(''.join([
a for a in s_.split('_')[1].split('-')[0]
if a not in ABC
]))
end = int(''.join([
a for a in s_.split('_')[1].split('-')[1]
if a not in ABC
]))
if '_-' in s_:
start = int(''.join([
a for a in s_.split('_-')[1].split('-')[0]
if a not in ABC
]))
end = int(''.join([
a for a in s_.split('_-')[1].split('-')[1]
if a not in ABC
]))
segs.append((start, end))
results.append(
Entry(pdb, chain, segs,
mp.XYZ(axis['x'], axis['y'], axis['z'])))
except:
print('SKIPPING', s)
return results
def create_pdb_AA_AA_d_z(aa1: str, aa2: str, d: float, z: float, res_maker, path: str = "./") -> None:
"""
create a pdb with residues aa1 and aa2 at the XY plane at Z=z and distance d
"""
res1 = res_maker.get_residue(aa1)
res2 = res_maker.get_residue(aa2)
res1.change_chain_name("A")
res2.change_chain_name("B")
# rotate around Z to oppose
axis_z = mp.XYZ(0, 0, 1)
res2.dot_matrix_me(mpf.rotation_matrix_around_vec(axis_z, np.pi))
# translate to get d distance
move_d = mp.XYZ(
0,
res1[res_maker.main_residue_atoms[res1.res_type][1]].xyz.y
- res2[res_maker.main_residue_atoms[res2.res_type][1]].xyz.y
+ d,
0,
)
res2.translate_xyz(move_d)
# translate all to z
move_z = mp.XYZ(0, 0, z)
res1.translate_xyz(move_z)
res2.translate_xyz(move_z)
# setup in a MyPDB instance, and renumber and write
pdb = mp.MyPDB()
for res in [res1, res2]:
for a in res.values():
pdb.add_atom(a)
pdb.renumber()
mp.write_PDB("%s/%s_%s_%.2f_%.2f.pdb" % (path, res1.res_type, res2.res_type, d, z), pdb)
def translate_and_rotate_res_to_xy_plane(res: mp.Residue,
atom_list: list) -> mp.Residue:
xyz = copy.deepcopy(res[atom_list[0]].xyz)
xyz = xyz.scalar_multi(-1)
res.translate_xyz(xyz)
# rotate a1 to xy plane
proj_a2_xy = copy.deepcopy(res[atom_list[1]].xyz)
proj_a2_xy.z = 0
a2_copy = copy.deepcopy(res[atom_list[1]].xyz)
ang_a2_xy = np.arccos(a2_copy.unit().dot(proj_a2_xy.unit()))
axis_a2_xy = a2_copy.unit().cross(proj_a2_xy.unit()).unit()
rotation_matrix = rotation_matrix_around_vec(axis_a2_xy, ang_a2_xy)
res.dot_matrix_me(rotation_matrix)
# rotate a2 to xy plane
proj_a2_xy = copy.deepcopy(res[atom_list[2]].xyz)
proj_a2_xy.z = 0
a2_copy = copy.deepcopy(res[atom_list[2]].xyz)
ang_a2_xy = np.arccos(a2_copy.unit().dot(proj_a2_xy.unit()))
closest_point = point_on_normed_vec_closest_to_point(
proj_a2_xy.as_nparray(), res[atom_list[1]].xyz.unit().as_nparray())
ang_a2_xy = angle_between_3_XYZs(a2_copy, closest_point, proj_a2_xy)
axis = copy.deepcopy(res[atom_list[1]].xyz)
rotation_matrix = rotation_matrix_around_vec(axis, -ang_a2_xy)
res.dot_matrix_me(rotation_matrix)
# rotate so that a2 and 3 are on both sides of the Y axis
a1_copy = res[atom_list[0]].xyz
a2_copy = res[atom_list[1]].xyz
a3_copy = res[atom_list[2]].xyz
ang_312 = angle_between_3_XYZs(a3_copy, a1_copy, a2_copy)
ang_y12 = angle_between_3_XYZs(mp.XYZ(0, 1, 0), a1_copy, a2_copy)
axis = mp.XYZ(0, 0, 1)
rotation_matrix = rotation_matrix_around_vec(axis,
-(ang_y12 + 0.5 * ang_312))
res.dot_matrix_me(rotation_matrix)
def main():
pdb_name = sys.argv[1]
residue_num = int(sys.argv[2])
pdb = MyPDB.parse_PDB(pdb_name)
res = pdb['A'][residue_num]
CO = np.array([res['C'].xyz.x, res['C'].xyz.y, res['C'].xyz.z])
CA = np.array([res['CA'].xyz.x, res['CA'].xyz.y, res['CA'].xyz.z])
CB = np.array([res['CB'].xyz.x, res['CB'].xyz.y, res['CB'].xyz.z])
N = np.array([res['N'].xyz.x, res['N'].xyz.y, res['N'].xyz.z])
# HA = np.array([res['HA'].xyz.x, res['HA'].xyz.y, res['HA'].xyz.z])
v1 = N - CO
v2 = CA - CO
cp = np.cross(v1, v2)
# HA_infront = cp.dot(HA-CA) > 0
CB_infront = cp.dot(CB-CA) > 0
print('residue %r, is %s ' % (res, res.D_or_L()))
def main():
pdb_name = sys.argv[1]
residue_num = int(sys.argv[2])
pdb = MyPDB.parse_PDB(pdb_name)
res = pdb['A'][residue_num]
CO = np.array([res['C'].xyz.x, res['C'].xyz.y, res['C'].xyz.z])
CA = np.array([res['CA'].xyz.x, res['CA'].xyz.y, res['CA'].xyz.z])
CB = np.array([res['CB'].xyz.x, res['CB'].xyz.y, res['CB'].xyz.z])
N = np.array([res['N'].xyz.x, res['N'].xyz.y, res['N'].xyz.z])
# HA = np.array([res['HA'].xyz.x, res['HA'].xyz.y, res['HA'].xyz.z])
v1 = N - CO
v2 = CA - CO
cp = np.cross(v1, v2)
# HA_infront = cp.dot(HA-CA) > 0
CB_infront = cp.dot(CB - CA) > 0
print('residue %r, is %s ' % (res, res.D_or_L()))
def test_symm_axis_interface(e: Entry, ch: str) -> bool:
print(e)
inter_resi = e.interface[ch]
print(e.symm_segs)
symm_resi = [a for seg in e.symm_segs for a in range(seg[0], seg[1] + 1)]
print('symm_resi', symm_resi)
print(inter_resi)
pdb = mp.parse_PDB(find_pdb(e.pdb), with_non_residue=False)
symm_com = mp.com_residues(chain=pdb[e.chain], residues=symm_resi)
print(symm_resi, symm_com)
pdb.translate_xyz(mp.XYZ(0, 0, 0) - symm_com)
print('pdb translated')
print('writing pdb %s_%s_translated.pdb' % (e.pdb, e.chain))
mp.write_PDB('%s_%s_translated.pdb' % (e.pdb, e.chain), pdb)
print('now symm com is at',
mp.com_residues(chain=pdb[e.chain], residues=symm_resi))
print('symm axis XYZ %r' % (e.symm_axis))
print_pymol_select(e)
def create_pdb_AA_AA_d_z(aa1: str,
aa2: str,
d: float,
z: float,
res_maker,
path: str = './') -> None:
"""
create a pdb with residues aa1 and aa2 at the XY plane at Z=z and distance d
"""
res1 = res_maker.get_residue(aa1)
res2 = res_maker.get_residue(aa2)
res1.change_chain_name('A')
res2.change_chain_name('B')
# rotate around Z to oppose
axis_z = mp.XYZ(0, 0, 1)
res2.dot_matrix_me(mpf.rotation_matrix_around_vec(axis_z, np.pi))
# translate to get d distance
move_d = mp.XYZ(
0, res1[res_maker.main_residue_atoms[res1.res_type][1]].xyz.y -
res2[res_maker.main_residue_atoms[res2.res_type][1]].xyz.y + d, 0)
res2.translate_xyz(move_d)
# translate all to z
move_z = mp.XYZ(0, 0, z)
res1.translate_xyz(move_z)
res2.translate_xyz(move_z)
# setup in a MyPDB instance, and renumber and write
pdb = mp.MyPDB()
for res in [res1, res2]:
for a in res.values():
pdb.add_atom(a)
pdb.renumber()
mp.write_PDB(
'%s/%s_%s_%.2f_%.2f.pdb' % (path, res1.res_type, res2.res_type, d, z),
pdb)
def point_on_normed_vec_closest_to_point(p: np.array, v: np.array) -> mp.XYZ:
vec = v * np.dot(p, v)
return mp.XYZ(vec[0], vec[1], vec[2])
#!/usr/bin/env python3.5
__author__ = 'jonathan'
from AASeq import compare_2_seqs
import seq_funcs as sf
import MyPDB
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-mode',
type=str,
default='pdbs',
help='different running modes.\npdbs=from two pdbs')
parser.add_argument('-1', type=str, help='first entry')
parser.add_argument('-2', type=str, help='second entry')
args = vars(parser.parse_args())
if args['mode'] == 'pdbs':
pdb_1 = MyPDB.parse_PDB(args['1'], args['1'])
pdb_2 = MyPDB.parse_PDB(args['2'], args['2'])
seq_1 = MyPDB.extract_seq(pdb_1)
seq_2 = MyPDB.extract_seq(pdb_2)
start = 0
sorted_keys = sorted(seq_1.keys())
for k in sorted_keys:
compare_2_seqs(seq_1[k], seq_2[k], start=start)
start += len(seq_1[k])
print(start, len(seq_1[k]))
def create_and_add_MBR_residue(pdb, memb_chain, highest_atom_number):
inn = MyPDB.Residue('INN', 1, memb_chain)
atom_num = 1
i = 1
for x in range(-30, 30):
for y in range(-30, 30):
inn.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + atom_num,
name='%i' % i,
res_type_3='INN',
chain=memb_chain,
res_seq_num=1,
x=x,
y=y,
z=-15,
element='N',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
atom_num += 1
i += 1
out = MyPDB.Residue('OUT', 2, memb_chain)
i = 1
for x in range(-30, 30):
for y in range(-30, 30):
out.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + atom_num,
name='%i' % i,
res_type_3='MID',
chain=memb_chain,
res_seq_num=2,
x=x,
y=y,
z=15,
element='O',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
atom_num += 1
i += 1
mid = MyPDB.Residue('MID', 3, memb_chain)
i = 1
for x in range(-30, 30):
for y in range(-30, 30):
mid.add_atom(
MyPDB.Atom(serial_num=highest_atom_number + atom_num,
name='%i' % i,
res_type_3='MID',
chain=memb_chain,
res_seq_num=3,
x=x,
y=y,
z=0,
element='C',
charge='',
occupancy=1,
temp=1,
header='HETATM',
alternate='',
achar='',
si=''))
atom_num += 1
i += 1
chn = MyPDB.Chain(memb_chain, {1: inn, 2: out, 3: mid})
chn.add_residue(inn)
chn.add_residue(out)
chn.add_residue(mid)
pdb.add_chain(chn)
def parse_residues_file(self) -> dict:
pdb = mp.parse_PDB("/home/labs/fleishman/jonathaw/temp_residue_data/RKDS.txt")
for res in pdb["A"].values():
mpf.translate_and_rotate_res_to_xy_plane(res, self.main_residue_atoms[res.res_type])
self.residues[res.res_type] = res
#!/usr/bin/env python3.5
__author__ = 'jonathan'
from AASeq import compare_2_seqs
import seq_funcs as sf
import MyPDB
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-mode', type=str, default='pdbs', help='different running modes.\npdbs=from two pdbs')
parser.add_argument('-1', type=str, help='first entry')
parser.add_argument('-2', type=str, help='second entry')
args = vars(parser.parse_args())
if args['mode'] == 'pdbs':
pdb_1 = MyPDB.parse_PDB(args['1'], args['1'])
pdb_2 = MyPDB.parse_PDB(args['2'], args['2'])
seq_1 = MyPDB.extract_seq(pdb_1)
seq_2 = MyPDB.extract_seq(pdb_2)
start = 0
sorted_keys = sorted(seq_1.keys())
for k in sorted_keys:
compare_2_seqs(seq_1[k], seq_2[k], start=start)
start += len(seq_1[k])
print(start, len(seq_1[k]))