Re: [Rdkit-discuss] Molecule substructure replacement gives "interesting" results (fragmented)

[greg l. <gre...@gm...>]

Don't have time for a long reply, but the short answer is that ReplaceSubstructs is not guaranteed  to get all the bonds from the core correctly set back up (that's not an easy problem). Your best bet is to use a chemical reaction to do the transformations you need for your normalization.

-greg

On Jun 15, 2012, at 7:08 PM, JP <jea...@in...> wrote:

> Perhaps an easier example...
> 
> Replacing a substructure by itself also gives fragments (!?).  I don't
> understand why.
> 
> #!/usr/bin/env python
> 
> from rdkit import Chem
> from rdkit.Chem import AllChem
> 
> mol = Chem.MolFromSmiles("c1cc2c(cc1)C(O)=C(NC)C(=N)C2=O")
> 
> for a in mol.GetAtoms():
>    print a.GetIdx(), " -> ", a.GetSmarts()
> 
> q = Chem.MolFromSmiles("[OH]C=CC=N")
> r = Chem.MolFromSmiles("[OH]C=CC=N")
> 
> print mol.GetSubstructMatches(q) # we have a match
> modified = AllChem.ReplaceSubstructs(mol, q, r)
> for m in modified:
>    print Chem.MolToSmiles(m) # fragmented ?! WHY ?!
> 
> -
> Jean-Paul Ebejer
> Early Stage Researcher
> 
> 
> On 15 June 2012 11:06, JP <jea...@in...> wrote:
>> Hi there,
>> 
>> I have a list of molecules of which I want all to be in the same
>> tautomeric (does this word even exist?) form.
>> 
>> This "cheat" works fine using ReplaceSubstructs on my 100+ molecule
>> with the exception of one case, where the resulting molecule is being
>> fragmented.  Can someone explain why this is the case?
>> 
>> Now to code:
>> 
>> #!/usr/bin/env python
>> 
>> from rdkit import Chem
>> from rdkit.Chem import AllChem
>> 
>> mol = Chem.MolFromSmiles("COc1c(/N=C2\C(=O)c3c(cccc3)C(O)=C2n2nnc3ccccc23)cccc1")
>> q = Chem.MolFromSmarts("OC1=CC(=N)C(=O)c2ccccc12")
>> r = Chem.MolFromSmiles("NC1=CC(=O)c2ccccc2C1=O", sanitize=False)
>> 
>> modified = AllChem.ReplaceSubstructs(mol, q, r, replaceAll=True)[0]
>> 
>> # the following gives COc1ccccc1.NC1=CC(=O)c2ccccc2C1=O.n1nc2ccccc2n1
>> # fragmented ?! WHY ?!
>> print Chem.MolToSmiles(modified)
>> 
>> 
>> -
>> Jean-Paul Ebejer
>> Early Stage Researcher
> 
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