Thanks Greg,
After testing the code, It works perfectly, thanks!
Unfortunatly, I discovered that it's still not compatible with the aromaticity
method used in the article i mention in another post from Rudolf Naef.
I need to keep aromaticity of all 6 rings (having C or N which is possible
using your function), but also keep info of aromaticity of fused 6 rings (aka.
naphthalene, ...) + convert/keep guanidium moieties aromatic too.
So, I would be more interesting to fine a fast process to revoke aromaticity on
rings that are not 6 members rings only, which should preserve all 6 rings +
fused aromatic rings and also set guanidium salt as aromatic.
Would it be possible to do that ?
Best regards,
Guillaume
________________________________
De : Greg Landrum <greg.land...@gmail.com>
Envoyé : mardi 20 septembre 2016 16:41
À : Guillaume GODIN
Cc : RDKit Discuss
Objet : Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize +
clearAromaticFlags
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
<guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> 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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