a_new.xyz.put_as_list(mtx.do_to_array(a.xyz.get_as_list()))
r_aa.push_atom(a_new)
""" Adjust the position of P to be exactly identical """
if args.flg_Pexact:
aaP = Coord()
nP = 0
for a in r_aa.atoms:
if a.name.strip() in ("P", "OP1", "OP2", "O1P", "O2P"):
aaP = aaP + a.xyz
nP += 1
if nP != 3:
print('Error: nP != 3, ir=,', ir)
f_log.write('Error: nP != 3, ir=%i' % ir)
sys.exit(2)
aaP = aaP / float(3)
trans = xyzP2 - aaP.get_as_ndarray()
mtx.reset()
mtx.translation(trans[0], trans[1], trans[2])
for a in r_aa.atoms:
a.xyz.put_as_list(mtx.do_to_array(a.xyz.get_as_list()))
c_aa.push_residue(r_aa)
""" The last residue """
if not args.circ:
xyzSPSB_ref = np.array(
[xyzs_S[-2], xyzs_P[-1], xyzs_S[-1], xyzs_B[-1]])
best_rmsd = 9999.9
best_lib = 0
best_mtx = None
for ilib in range(nlib):
p = PdbFile('%s/%06i_%s.pdb' % (LIBPDBCG, ilib + 1, seq[-1]))
