def fix_mobile_h(mol, inchi, u1, u2):
"""
Identifies a system of atoms bearing unpaired electrons and mobile hydrogens
at the same time.
The system will consist of a central atom that does not bear any mobile hydrogens,
but that is bound to an atom that does bear a mobile hydrogen, called the "original atom".
The algorithm identifies the "new partner" atom that is part of the mobile hydrogen
system.
Next, the mobile hydrogen is transferred from the original atom, to the new partner,
and a bond is removed and added respectively.
Finally, the central atom and the original atom will each receive an unpaired electron,
and the bond between them will decrease in order.
"""
mobile_hydrogens = inchiutil.parse_H_layer(inchi)
if mobile_hydrogens:
# WIP: only consider the first system of mobile hydrogens:
mobile_hydrogens = mobile_hydrogens[0]
#find central atom:
central, original, new_partner = util.swap(mobile_hydrogens, [u1, u2])
central, original, new_partner = \
mol.atoms[central - 1], mol.atoms[original - 1], mol.atoms[new_partner - 1]
# search hydrogen atom and bond
hydrogen = None
for at, bond in original.bonds.iteritems():
if at.number == 1:
hydrogen = at
mol.removeBond(bond)
break
new_h_bond = Bond(new_partner, hydrogen, order='S')
mol.addBond(new_h_bond)
mol.getBond(central, new_partner).decrementOrder()
central.radicalElectrons += 1
original.radicalElectrons += 1
return True
return False
def fix_mobile_h(mol, inchi, u1, u2):
"""
Identifies a system of atoms bearing unpaired electrons and mobile hydrogens
at the same time.
The system will consist of a central atom that does not bear any mobile hydrogens,
but that is bound to an atom that does bear a mobile hydrogen, called the "original atom".
The algorithm identifies the "new partner" atom that is part of the mobile hydrogen
system.
Next, the mobile hydrogen is transferred from the original atom, to the new partner,
and a bond is removed and added respectively.
Finally, the central atom and the original atom will each receive an unpaired electron,
and the bond between them will decrease in order.
"""
mobile_hydrogens = inchiutil.parse_H_layer(inchi)
if mobile_hydrogens:
# WIP: only consider the first system of mobile hydrogens:
mobile_hydrogens = mobile_hydrogens[0]
#find central atom:
central, original, new_partner = util.swap(mobile_hydrogens, [u1, u2])
central, original, new_partner = \
mol.atoms[central - 1], mol.atoms[original - 1], mol.atoms[new_partner - 1]
# search hydrogen atom and bond
hydrogen = None
for at, bond in original.bonds.iteritems():
if at.number == 1:
hydrogen = at
mol.removeBond(bond)
break
new_h_bond = Bond(new_partner, hydrogen, order='S')
mol.addBond(new_h_bond)
mol.getBond(central, new_partner).decrementOrder()
central.radicalElectrons += 1
original.radicalElectrons += 1
return True
return False