Guillaume,
Here's how to read in a molecule and skip aromaticity perception:
In [12]: m =
Chem.MolFromSmiles('c1ccccc1-c1cccnc1-c1cc[nH]c1',sanitize=False)
In [13]:
Chem.SanitizeMol(m,sanitizeOps=Chem.SANITIZE_ALL^Chem.SANITIZE_SETAROMATICITY)
Out[13]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
In [14]: Chem.MolToSmiles(m)
Out[14]: 'C1=CC=C(C2=CC=CN=C2C2=CNC=C2)C=C1'
Then you need to find all of the benzene-like rings and set the appropriate
flags:
In [16]: def set_aroms(m,pattern='[#6]1=[#6][#6]=[#6][#6]=[#6]1'):
...: p = Chem.MolFromSmarts(pattern)
...: matches = m.GetSubstructMatches(p)
...: for match in matches:
...: for mi in match:
...: m.GetAtomWithIdx(mi).SetIsAromatic(True)
...: for bond in p.GetBonds():
...: mb =
m.GetBondBetweenAtoms(match[bond.GetBeginAtomIdx()],match[bond.GetEndAtomIdx()])
...: assert mb
...: mb.SetBondType(Chem.BondType.AROMATIC)
...: mb.SetIsAromatic(True)
...:
...:
In [17]: set_aroms(m)
In [18]: Chem.MolToSmiles(m)
Out[18]: 'C1=CN=C(C2=CNC=C2)C(c2ccccc2)=C1'
Note that the RDKit does have a simplified aromaticity model available out
of the box that only recognizes aromaticity in 5- and 6- rings, but this
isn't quite as simple as what you're looking for.
Best,
-greg
On Tue, Sep 20, 2016 at 6:52 AM, Guillaume GODIN <
[email protected]> wrote:
> Dear All,
>
>
> I would like to kekulize the molecule, but only conserve the aromaticity
> knowledge of C6 (benzene like) type rings
>
>
> So what to need to do after this command?
>
>
> Chem.rdmolops.Kekulize(mol, clearAromaticFlags=True)
>
>
> Should I need to store benzene like location before the Kekulize process
> and restore it after and How to restore it (SetIsAromatic of atoms as true
> and change bondtype )?
>
>
> best regards,
>
>
> Guillaume GODIN
>
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