def ligand_comp_org(file_in,
file_init_geo,
catoms_arr,
flag_deleteH=True,
flag_loose=False,
flag_lbd=True,
debug=False,
depth=3,
BondedOct=False):
liglist, liglist_init, flag_match = match_lig_list(file_in,
file_init_geo,
catoms_arr,
flag_loose,
flag_lbd,
debug=debug,
depth=depth,
BondedOct=BondedOct)
if debug:
print(('lig_list:', liglist, len(liglist)))
print(('lig_list_init:', liglist_init, len(liglist_init)))
if flag_lbd:
mymol_xyz = 'mymol_trunc_tmp.xyz'
initmol_xyz = 'init_trunc_tmp.xyz'
else:
mymol_xyz = file_in
initmol_xyz = file_init_geo
if flag_match:
rmsd_arr, max_atom_dist_arr = [], []
for idx, lig in enumerate(liglist):
lig_init = liglist_init[idx]
if debug:
print(('----This is %d th piece of ligand.' % (idx + 1)))
print(('ligand is:', lig, lig_init))
posi_shift = 2
# Create mol3D without a tmp file.
_start = time.clock()
with open(mymol_xyz, 'r') as fo:
foo = []
for ii, line in enumerate(fo):
if (ii - posi_shift) in lig:
if debug:
print(('line is', line))
foo.append(line)
tmp_mol = mol3D()
tmp_mol = readfromtxt(tmp_mol, foo)
with open(initmol_xyz, 'r') as fo:
foo = []
for ii, line in enumerate(fo):
if (ii - posi_shift) in lig_init:
if debug:
print(('line is', line))
foo.append(line)
tmp_org_mol = mol3D()
tmp_org_mol = readfromtxt(tmp_org_mol, foo)
_elapsed = (time.clock() - _start)
# print('-reading txt:', _elapsed)
if debug:
print(('# atoms: %d, init: %d' %
(tmp_mol.natoms, tmp_org_mol.natoms)))
print(('!!!!atoms:', [x.symbol() for x in tmp_mol.getAtoms()],
[x.symbol() for x in tmp_org_mol.getAtoms()]))
if flag_deleteH:
tmp_mol.deleteHs()
tmp_org_mol.deleteHs()
mol0, U, d0, d1 = kabsch(tmp_org_mol, tmp_mol)
rmsd = tmp_mol.rmsd(tmp_org_mol)
rmsd_arr.append(rmsd)
atom_dist_max = tmp_mol.maxatomdist(tmp_org_mol)
max_atom_dist_arr.append(atom_dist_max)
if debug:
print(('rmsd:', rmsd))
print(('atom_dist_max', atom_dist_max))
rmsd_max = max(rmsd_arr)
atom_dist_max = max(max_atom_dist_arr)
else:
rmsd_max, atom_dist_max = 'lig_mismatch', 'lig_mismatch'
return rmsd_max, atom_dist_max
def ligand_comp_org(file_in, file_init_geo, catoms_arr, flag_deleteH=True, flag_loose=False,
flag_lbd=True, debug=False, depth=3, BondedOct=False):
liglist, liglist_init, flag_match = match_lig_list(file_in, file_init_geo,
catoms_arr,
flag_loose, flag_lbd,
debug=debug, depth=depth,
BondedOct=BondedOct)
if debug:
print('lig_list:', liglist, len(liglist))
print('lig_list_init:', liglist_init, len(liglist_init))
if flag_lbd:
mymol_xyz = 'mymol_trunc_tmp.xyz'
initmol_xyz = 'init_trunc_tmp.xyz'
else:
mymol_xyz = file_in
initmol_xyz = file_init_geo
if flag_match:
rmsd_arr, max_atom_dist_arr = [], []
for idx, lig in enumerate(liglist):
lig_init = liglist_init[idx]
if debug:
print('----This is %d th piece of ligand.' % (idx + 1))
print('ligand is:', lig, lig_init)
posi_shift = 2
## Create mol3D without a tmp file.
_start = time.clock()
with open(mymol_xyz, 'r') as fo:
foo = []
for ii, line in enumerate(fo):
if (ii - posi_shift) in lig:
if debug:
print('line is', line)
foo.append(line)
tmp_mol = mol3D()
tmp_mol = readfromtxt(tmp_mol, foo)
with open(initmol_xyz, 'r') as fo:
foo = []
for ii, line in enumerate(fo):
if (ii - posi_shift) in lig_init:
if debug:
print('line is', line)
foo.append(line)
tmp_org_mol = mol3D()
tmp_org_mol = readfromtxt(tmp_org_mol, foo)
_elapsed = (time.clock() - _start)
# print('-reading txt:', _elapsed)
if debug:
print('# atoms: %d, init: %d' % (tmp_mol.natoms, tmp_org_mol.natoms))
print('!!!!atoms:', [x.symbol() for x in tmp_mol.getAtoms()],
[x.symbol() for x in tmp_org_mol.getAtoms()])
if flag_deleteH:
tmp_mol.deleteHs()
tmp_org_mol.deleteHs()
mol0, U, d0, d1 = kabsch(tmp_org_mol, tmp_mol)
rmsd = tmp_mol.rmsd(tmp_org_mol)
rmsd_arr.append(rmsd)
atom_dist_max = tmp_mol.maxatomdist(tmp_org_mol)
max_atom_dist_arr.append(atom_dist_max)
if debug:
print('rmsd:', rmsd)
print('atom_dist_max', atom_dist_max)
rmsd_max = max(rmsd_arr)
atom_dist_max = max(max_atom_dist_arr)
else:
rmsd_max, atom_dist_max = 'lig_mismatch', 'lig_mismatch'
return rmsd_max, atom_dist_max