Hi Greg,
I see what I was doing wrong, I had put the ring closures inside the
brackets when I was mapping the atoms. (Which explains why I didn't see
any output there). That was simple error on my side, thanks so much Greg!!
Matt
On Mon, Sep 21, 2015 at 11:32 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Hi Matt,
>
> The problem is that you haven't included any atom mapping information that
> allows the RDKit to know what to do with the reactants you provide.
>
> Here's a short demo of what you're doing:
>
> In [11]: rxn = AllChem.ReactionFromSmarts('C=C1CC=CC=C1>>Cc1ccccc1')
>
> In [12]: ps = rxn.RunReactants((Chem.MolFromSmiles('C=C1CC=CC=C1'),))
> [02:28:59] reactant 0 has no mapped atoms.
> [02:28:59] product 0 has no mapped atoms.
>
> In [13]: Chem.MolToSmiles(ps[0][0])
> Out[13]: 'Cc1ccccc1'
>
> In [14]: ps = rxn.RunReactants((Chem.MolFromSmiles('CC=C1C(F)C=CC=C1'),))
>
> In [15]: Chem.MolToSmiles(ps[0][0])
> Out[15]: 'Cc1ccccc1'
>
>
> (notice the warning after line [12])
>
> And here's how to fix it:
>
> In [16]: rxn =
> AllChem.ReactionFromSmarts('[C:1]=[C:2]1[C:3][C:4]=[C:5][C:6]=[C:7]1>>[C:1][c:2]1[c:3][c:4][c:5][c:6][c:7]1')
>
> In [17]: ps = rxn.RunReactants((Chem.MolFromSmiles('C=C1CC=CC=C1'),))
>
> In [18]: Chem.MolToSmiles(ps[0][0])
> Out[18]: 'Cc1ccccc1'
>
> In [19]: ps = rxn.RunReactants((Chem.MolFromSmiles('CC=C1C(F)C=CC=C1'),))
>
> In [20]: Chem.MolToSmiles(ps[0][0])
> Out[20]: 'CCc1ccccc1F'
>
>
> I hope that helps,
> -greg
>
>
>
> On Mon, Sep 21, 2015 at 4:41 PM, Matthew Lardy <mla...@gmail.com> wrote:
>
>> I've repeated the previously seen behavior in Python in case anyone would
>> like to take a look there. I am trying to clean a dirty library from a
>> vendor and I just want to re-aromatize these molecules. Sorry that the
>> code looks so ugly, but the output is exactly the same.
>>
>> Thanks!
>> Matt
>>
>> Output (not to file):
>> Cc1ccccc1
>> Cc1ccccc1
>> ....
>> Cc1ccccc1
>> Cc1ccccc1
>>
>> The code that generated it:
>> #!/usr/bin/python
>>
>> from rdkit import Chem
>> from rdkit.Chem import AllChem,Draw
>> from rdkit.Chem import ChemicalFeatures
>> from rdkit import RDConfig
>> import os
>> import sys
>> import gzip
>>
>> suppl = Chem.SDMolSupplier('w.sdf')
>> rxn = AllChem.ReactionFromSmarts('C=C1CC=CC=C1>>Cc1ccccc1')
>>
>> gz = gzip.open('output.sdf.gz', 'w+')
>> writer = Chem.SDWriter(gz)
>>
>> for m in suppl:
>> if not m: continue
>> ps = rxn.RunReactants((m,))
>> if (len(ps) > 0):
>> # uniq = set([Chem.MolToSmiles(x[0],isomericSmiles=True) for x in
>> ps])
>> print Chem.MolToSmiles(ps[0][0])
>> #for p in uniq:
>> # print Chem.MolToSmiles(p)
>> #for prod in uniq:
>> # writer.write(prod)
>> else:
>> writer.write(m)
>> writer.close()
>> gz.close()
>>
>>
>> On Mon, Sep 21, 2015 at 12:39 PM, Matthew Lardy <mla...@gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> I am attempting to transform a functional group in a series of
>>> molecules. The reaction is pretty simple (a re-aromatization):
>>>
>>> C=C1CC=CC=C1>>Cc1ccccc1
>>>
>>> The code which generates this runs without error (and it was written in
>>> Java). What I don't understand is that the products of the reaction are
>>> just Cc1ccccc1. The rest of the molecule is completely missing. Trying to
>>> map these atoms didn't reproduce the error, it did not run. Is there a
>>> trick to simply run something like this on every occurrence in a molecule?
>>>
>>> Thanks in advance, and my code fragment is below,
>>> Matt
>>>
>>> Here is my code:
>>>
>>> SDMolSupplier suppl1 = new
>>> SDMolSupplier(cParser.getValue("-in"));
>>> ROMol rdmol;
>>> //String line = "";
>>>
>>> while (!suppl1.atEnd())
>>> {
>>> try {
>>> rdmol = suppl1.next();
>>> molId++;
>>>
>>> ROMol_Vect reacts = new ROMol_Vect();
>>> reacts.add(rdmol);
>>>
>>> String ID = rdmol.getProp("_Name");
>>> System.err.println("MOL_ID: " + ID);
>>> ROMol_Vect_Vect prods = umr.runReactants(reacts);
>>>
>>>
>>> System.out.println("Reagents: " + reacts.size());
>>> System.err.println("Product AMT: " + prods.size());
>>> if (prods.size() < 1) {
>>> // Write out untransformed molecules if they don't
>>> have the pattern
>>> //writer.write(rdmol);
>>> ;
>>> } else {
>>> for (int i = 0; i < prods.size(); i++)
>>> {
>>> System.err.println("In here finally");
>>> prods.get(i).get(0).setProp("_Name",ID);
>>> // Why am I getting the query back to me?
>>> writer.write(prods.get(i).get(0));
>>> }
>>> }
>>> } catch (Exception e) {
>>> System.err.println(e);
>>> } catch (Error e) {
>>> System.err.println(e);
>>> }
>>> }
>>>
>>>
>>>
>>
>>
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>>
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>>
>
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