Hi Greg,
Thanks for reply. Its very helpful. I will try using TemplateExpand.py
I am using RDKit_2012_12_1 on Ubuntu 11.10 (x86).
Thanks
om
On Fri, Feb 22, 2013 at 10:50 AM, Greg Landrum <[email protected]>wrote:
> Dear Om,
>
> Sorry for the slow reply; this ended up getting lost in my inbox.
>
> On Mon, Feb 18, 2013 at 7:58 PM, Om <[email protected]> wrote:
> >
> > I am trying to re-shuffle the side-chain(s) identified after replacing
> core
> > (MCS between two mols) from molecules. The two molecules I am considering
> > are BMS-193884 and irbesartan. Both molecules share biphenyl framework
> and
> > act on different target (antagonist of ETA and AT1 respectively). The
> > approach I have taken is to replace side-chain(s) of BMS-193884 with the
> > side-chain(s) of irbesartan and vice-versa using ReplaceSubstructs to
> > generate new molecules keeping MCS as a core part.
> >
> > I have pasted minimal code below this mail. I do not know whether this
> would
> > be correct approach or not?
>
> As long as you don't have any "extra" dummy atoms in your molecule,
> this should work fine. You should be sure you understand why it's
> working though, because it's somewhat fragile: ReplaceSubstructs()
> forms bonds between the first atom in the replacement that correspond
> to those in the first atom of the thing being replaced.
>
> A small example:
> In [2]: m = Chem.MolFromSmiles('c1ccccc1NCC')
>
> In [3]: p = Chem.MolFromSmarts('NCC')
>
> In [4]: r = Chem.MolFromSmiles('CCO')
>
> In [5]: Chem.MolToSmiles(Chem.ReplaceSubstructs(m,p,r)[0],True)
> Out[5]: 'OCCc1ccccc1'
>
> In [6]: r = Chem.MolFromSmiles('OCC')
>
> In [7]: Chem.MolToSmiles(Chem.ReplaceSubstructs(m,p,r)[0],True)
> Out[7]: 'CCOc1ccccc1'
>
> You example is working because the canonical SMILES algorithm is
> making the dummy atoms the first atoms in the SMILES, so when you
> remove those from the SMILES the attachment point ends up being first.
> Somewhat fragile, but it ought to work.
>
> There is a more robust version of the template expansion in the RDKit
> distribution in the package
> $RDBASE/rdkit/Chem/ChemUtils/TemplateExpand.py that you might want to
> take a look at. That's a command-line tool, but there are useful
> functions inside for what you want to do. This is a common and useful
> pattern, so I probably should add a function to make this easy and
> then some documentation about how to use it.
>
> > Moreover, I am getting dummy atoms in some of the output molecules.
> >
>
> <snip>
>
> >
> > Output:
> >
> > CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2-c2nn[nH]n2)cc1
> > Cc1noc(NS(=O)(=O)c2ccccc2-c2ccc(-c3nn[nH]n3)cc2)c1C
> > CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2-c2nn[nH]n2)cc1
> > CCCCC1=NC2(CCCC2)C(=O)N1[*]c1ccc(-c2ccccc2S(=O)(=O)Nc2onc(C)c2C)cc1
> > CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2-c2ncco2)cc1
> > CCCCC1=NC2(CCCC2)C(=O)N1[*]c1ccccc1-c1ccc(-c2ncco2)cc1
> > CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2S(=O)(=O)Nc2onc(C)c2C)cc1
> > c1coc(-c2ccc(-c3ccccc3-c3nn[nH]n3)cc2)n1
> >
>
> I am not able to reproduce this. When I run your example I get the
> following:
>
> c1coc(-c2ccc(-c3ccccc3-c3nn[nH]n3)cc2)n1
> CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2-c2ncco2)cc1
> CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2S(=O)(=O)Nc2onc(C)c2C)cc1
> Cc1noc(NS(=O)(=O)c2ccc(-c3ccccc3-c3nn[nH]n3)cc2)c1C
> CCCCC1=NC2(CCCC2)C(=O)N1c1ccccc1-c1ccc(-c2ncco2)cc1
> CCCCC1=NC2(CCCC2)C(=O)N1c1ccc(-c2ccccc2S(=O)(=O)Nc2onc(C)c2C)cc1
> Cc1noc(NS(=O)(=O)c2ccccc2-c2ccc(-c3nn[nH]n3)cc2)c1C
> c1coc(-c2ccc(-c3ccccc3-c3nn[nH]n3)cc2)n1
>
> which seems right to me.
>
> Which version of the RDKit are you using?
>
> -greg
>
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