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 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 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 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)