def _generate_minimum_resonance_isomer(mol):
"""
Select the resonance isomer that is isomorphic to the parameter isomer, with the lowest unpaired
electrons descriptor.
First, we generate all isomorphic resonance isomers.
Next, we return the candidate with the lowest unpaired electrons metric.
The metric is a sorted list with indices of the atoms that bear an unpaired electron
"""
cython.declare(
candidates=list,
sel=Molecule,
cand=Molecule,
metric_sel=list,
metric_cand=list,
)
candidates = resonance.generate_isomorphic_resonance_structures(mol)
sel = candidates[0]
metric_sel = _get_unpaired_electrons(sel)
for cand in candidates[1:]:
metric_cand = _get_unpaired_electrons(cand)
if metric_cand < metric_sel:
sel = cand
metric_sel = metric_cand
return sel
def _generate_minimum_resonance_isomer(mol):
"""
Select the resonance isomer that is isomorphic to the parameter isomer, with the lowest unpaired
electrons descriptor.
First, we generate all isomorphic resonance isomers.
Next, we return the candidate with the lowest unpaired electrons metric.
The metric is a sorted list with indices of the atoms that bear an unpaired electron
This function is currently deprecated since InChI effectively eliminates resonance,
see InChI, the IUPAC International Chemical Identifier, J. Cheminform 2015, 7, 23, doi: 10.1186/s13321-015-0068-4
"""
cython.declare(
candidates=list,
sel=Molecule,
cand=Molecule,
metric_sel=list,
metric_cand=list,
)
warnings.warn(
"The _generate_minimum_resonance_isomer method is no longer used"
" and may be removed in RMG version 2.3.", DeprecationWarning)
candidates = resonance.generate_isomorphic_resonance_structures(
mol, saturate_h=True)
sel = candidates[0]
metric_sel = _get_unpaired_electrons(sel)
for cand in candidates[1:]:
metric_cand = _get_unpaired_electrons(cand)
if metric_cand < metric_sel:
sel = cand
metric_sel = metric_cand
return sel
def generate_minimum_resonance_isomer(mol):
"""
Select the resonance isomer that is isomorphic to the parameter isomer, with the lowest unpaired
electrons descriptor, unless this unnecessarily forms a charged molecule.
First, we generate all isomorphic resonance isomers.
Next, we return the candidate with the lowest unpaired electrons metric.
The metric is a sorted list with indices of the atoms that bear an unpaired electron
"""
cython.declare(
atom=Atom,
candidates=list,
sel=Molecule,
cand=Molecule,
metric_sel=list,
charge_sel=int,
charge_cand=int,
metric_cand=list,
)
candidates = resonance.generate_isomorphic_resonance_structures(mol)
sel = mol
metric_sel = get_unpaired_electrons(sel)
charge_sel = sum([abs(atom.charge) for atom in sel.vertices])
for cand in candidates:
metric_cand = get_unpaired_electrons(cand)
if metric_cand < metric_sel:
charge_cand = sum([abs(atom.charge) for atom in cand.vertices])
if charge_cand <= charge_sel:
sel = cand
metric_sel = metric_cand
charge_sel = charge_cand
return sel
def generate_minimum_resonance_isomer(mol):
"""
Select the resonance isomer that is isomorphic to the parameter isomer, with the lowest unpaired
electrons descriptor, unless this unnecessarily forms a charged molecule.
First, we generate all isomorphic resonance isomers.
Next, we return the candidate with the lowest unpaired electrons metric.
The metric is a sorted list with indices of the atoms that bear an unpaired electron
"""
cython.declare(
atom=Atom,
candidates=list,
sel=Molecule,
cand=Molecule,
metric_sel=list,
charge_sel=int,
charge_cand=int,
metric_cand=list,
)
candidates = resonance.generate_isomorphic_resonance_structures(mol)
sel = mol
metric_sel = get_unpaired_electrons(sel)
charge_sel = sum([abs(atom.charge) for atom in sel.vertices])
for cand in candidates:
metric_cand = get_unpaired_electrons(cand)
if metric_cand < metric_sel:
charge_cand = sum([abs(atom.charge) for atom in cand.vertices])
if charge_cand <= charge_sel:
sel = cand
metric_sel = metric_cand
charge_sel = charge_cand
return sel
def _generate_minimum_resonance_isomer(mol):
"""
Select the resonance isomer that is isomorphic to the parameter isomer, with the lowest unpaired
electrons descriptor.
First, we generate all isomorphic resonance isomers.
Next, we return the candidate with the lowest unpaired electrons metric.
The metric is a sorted list with indices of the atoms that bear an unpaired electron
This function is currently deprecated since InChI effectively eliminates resonance,
see InChI, the IUPAC International Chemical Identifier, J. Cheminform 2015, 7, 23, doi: 10.1186/s13321-015-0068-4
"""
cython.declare(
candidates=list,
sel=Molecule,
cand=Molecule,
metric_sel=list,
metric_cand=list,
)
warnings.warn("The _generate_minimum_resonance_isomer method is no longer used"
" and may be removed in RMG version 2.3.", DeprecationWarning)
candidates = resonance.generate_isomorphic_resonance_structures(mol, saturate_h=True)
sel = candidates[0]
metric_sel = _get_unpaired_electrons(sel)
for cand in candidates[1:]:
metric_cand = _get_unpaired_electrons(cand)
if metric_cand < metric_sel:
sel = cand
metric_sel = metric_cand
return sel