def test_benzene_reflection_should_not_change_bonding():
mol = Molecule(read=benzene_xyz)
mol.reflect('xy')
mol.get_bonds()
assert np.allclose(mol.bonds, benzene_bonds)
mol.reflect('yz')
mol.get_bonds()
assert np.allclose(mol.bonds, benzene_bonds)
mol.reflect('xz')
mol.get_bonds()
assert np.allclose(mol.bonds, benzene_bonds)
for i, (atom, coor) in enumerate(zip(elements, coordinates)):
rm.write('%2i %2s_%3s % 5.4f % 5.4f % 5.4f\n' % (i, atom, code, coor[0], coor[1], coor[2]))
rm.write(
"# Chiral centers Bond BondDipoles Bend UrayBradley InvBend Torsion Imp." +
" Torsion Bond/Bond Stretch/Bend Bend/Bend Bend/Torsion IntraVDW IntraCoulomb\n" +
" 0 %3i 0 0 0 0 0" % len(bonds) +
" 0 0 0 0 0 0 0\n" +
"# Bond stretch: atom n1-n2, type, parameters\n"
)
# Write bonds
for b in bonds:
rm.write("%2i %2i RIGID_BOND\n" % (b[0], b[1]))
rm.write("# Number of config moves\n0\n")
mol_file = os.path.abspath(sys.argv[1])
print('Reading -> %s' % mol_file)
mol = Molecule(read=mol_file)
mol.get_bonds()
if len(sys.argv) > 2:
mol_name = os.path.basename(sys.argv[2]).split('.')[0]
raspa_molecule_file = os.path.abspath(sys.argv[2])
else:
mol_name = os.path.basename(mol_file).split('.')[0]
raspa_molecule_file = os.path.join(os.path.split(mol_file)[0], '%s.def' % mol_name)
print('Writing -> %s' % raspa_molecule_file)
write_raspa_molecule(mol, raspa_molecule_file)