def ReadAtomSuffix(self, tree, atom):
constraint = None
#'+','-','.',':','+.','-.','*'
if tree[0] == '+.':
constraint = AtomRadical(False, ConstraintNumber('=1'))
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(1))
elif tree[0] == '-.':
constraint = AtomRadical(False, ConstraintNumber('=1'))
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(-1))
elif tree[0] == '+':
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(1))
elif tree[0] == '-':
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(-1))
elif tree[0] == '.':
constraint = AtomRadical(False, ConstraintNumber('=1'))
elif tree[0] == ':':
constraint = AtomRadical(False, ConstraintNumber('=2'))
elif tree[0] == ':.':
constraint = AtomRadical(False, ConstraintNumber('=3'))
elif tree[0] == '*':
from rdkit.Chem import GetPeriodicTable
#if type(atom).__name__ == 'QueryAtom':
# raise NotImplementedError('Onium $,&,X atoms not supported yet')
atomicnum = atom.GetAtomicNum()
atom = rdqueries.AtomNumEqualsQueryAtom(atomicnum)
valence = GetPeriodicTable().GetDefaultValence(atomicnum)
atom.ExpandQuery(rdqueries.TotalValenceEqualsQueryAtom(valence +
1))
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(1))
elif tree[0] == '?':
pass
else:
s = "Unsupported atom suffic: '" + tree[0] + "'"
raise NotImplementedError(s)
return constraint
def __call__(self,comb_mol,mapped_index):
atom = comb_mol.GetAtomWithIdx(mapped_index[self.idx])
if self.valence != 0:
from rdkit.Chem import GetPeriodicTable
atomicnum = atom.GetAtomicNum()
atom = rdqueries.AtomNumEqualsQueryAtom(atomicnum)
valence = GetPeriodicTable().GetDefaultValence(atomicnum)
atom.ExpandQuery(rdqueries.TotalValenceEqualsQueryAtom(valence+self.valence))
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(self.charge))
comb_mol.ReplaceAtom(self.idx,atom)
atom.SetNumRadicalElectrons(self.radical)
atom.SetFormalCharge(self.charge)
def ReadAtomType(self, tree):
i = 0
constraints = list()
if tree[i][0] == 'AtomPrefix':
constraints.append(self.ReadAtomPrefix(tree[i][1:]))
i += 1
assert tree[i][0] == 'Symbols'
atom = self.ReadSymbols(tree[i][1:])
i += 1
if len(tree) > i:
constraint = self.ReadAtomSuffix(tree[i][1:], atom)
if constraint:
constraints.append(constraint)
else:
# no suffix means it's neutral. RDkit atom with 0 formal charge and
# radical electron finds all variables of formal charge and radical
# electrons, so they need to be treated.
atom.ExpandQuery(rdqueries.FormalChargeEqualsQueryAtom(0))
constraints.append(AtomRadical(False, ConstraintNumber('=0')))
# return atom
return atom, constraints