Thanks for the response, Greg.
Sorry for the lost attachment. Essentially I had an indole, N-linked to a
phenyl, amide linked to pyridine. My basic approach worked, but there are
still obvious failures.
You are absolutely correct on all counts. I've also found problems with a
variety of special cases in which the non-cyclic atom is required for
aromaticity. Lots of special cases to consider.
I'll integrate your suggestions and do done error checking.
On May 31, 2013 9:55 PM, "Greg Landrum" <[email protected]> wrote:
> Hi Kirk,
>
> Quick FYI: the attachment on the original message didn't make it through.
> Still, I think the idea is clear enough.
>
> A general question I'd have is whether or not you really want to
> completely ignore the nature of the bond to the non-ring atom. For example,
> with this scheme you're going to end up getting the same ring systems for
> quinone and 1,4 cyclohexadiene derivatives:
> O=C1C=CC(=O)C=C1 -> C1C=CCC=C1
> CC1C=CC(C)C=C1 -> C1C=CCC=C1
>
> Similarly, sulfones in rings will lead to thioethers:
> O=S1(=O)CCCC1 -> S1CCCC1
>
> Is that desirable? If not, you could try adding dummies connected with an
> appropriate bond type so that you get:
> O=C1C=CC(=O)C=C1 -> *=C1C=CC(=*)C=C1
>
>
> On Fri, May 31, 2013 at 11:41 PM, Robert DeLisle <[email protected]>wrote:
>
>> Maybe the logic is that sophisticated after all - Code Block 4 below.
>>
>>
> The trick with adding the Hs to Ns is, unfortunately, necessary. You
> should be adding them to aromatic heteroatoms.
>
> Code Block 4:
>> from rdkit import Chem
>> from rdkit.Chem import AllChem
>>
>> sdin = Chem.SDMolSupplier('test.sdf')
>> sdout = Chem.SDWriter('rings.sdf')
>>
>> for m in sdin:
>>
>> em = Chem.EditableMol(Chem.Mol())
>> indexmap = {}
>>
>> for a in m.GetAtoms():
>>
>> if ( a.IsInRing() ):
>> indexmap[a.GetIdx()] = em.AddAtom(Chem.Atom(a.GetAtomicNum()))
>>
>> for b in m.GetBonds():
>>
>> if ( b.IsInRing() ):
>> em.AddBond(
>> indexmap[b.GetBeginAtomIdx()],indexmap[b.GetEndAtomIdx()],b.GetBondType() )
>>
>> for a in m.GetAtoms():
>> if ( a.IsInRing() and a.GetAtomicNum() == 7 ):
>>
>
> I would replace the above line with:
> if a.GetIsAromatic() and a.GetAtomicNum() != 6:
>
>
>> for b in a.GetBonds():
>> if ( not b.IsInRing() ):
>> em.AddBond(em.AddAtom(Chem.Atom(1)), indexmap[a.GetIdx()],
>> Chem.BondType.SINGLE)
>>
>> for nm in Chem.GetMolFrags(em.GetMol(), asMols=True):
>>
>
> You probably should be calling either Chem.SanitizeMol() or
> Chem.RemoveHs() here. I'd recommend the second variant because I don't
> think you want the Hs in the output.
>
>
>> AllChem.Compute2DCoords(nm)
>> sdout.write(nm)
>>
>
> -greg
>
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