Without a concrete example, this solution may not be appropriate, but I
believe the function you want is "ReplaceCore".
ReplaceCore(...)
ReplaceCore( (Mol)mol, (Mol)coreQuery [, (bool)replaceDummies=True [,
(bool)labelByIndex=False [, (bool)requireDummyMatch=False]]]) -> Mol :
Removes the core of a molecule and labels the sidechains with dummy
atoms.
I just have python available currently so this may not be appropriate, but
here goes:
>>> m1 = Chem.MolFromSmiles("Cc1ccccc1N")
>>> m2 = Chem.MolFromSmiles("c1ccccc1")
>>> mcs = MCS.FindMCS([m1, m2])
>>> frag = Chem.ReplaceCore(m1, Chem.MolFromSmarts(mcs.smarts))
>>> print "SideChains:", Chem.MolToSmiles(frag)
SideChains: [*]C.[*]N
I hope this helps (at least the steps).
Now if you are just trying to extract side chains from the results of
reactions, we have recently added helper functions to solve that (They
should be exposed in the next release).
ReduceProductToSideChains(...)
ReduceProductToSideChains( (Mol)product [, (bool)addDummyAtoms=True])
-> Mol :
reduce the product of a reaction to the side chains added by the
reaction.
The output is a molecule with attached wildcards indicating where the
product was attached. The isotope of the dummy atom is the reaction map
number of the product's atom (if available).
If this would be useful, let us know, I would be happy to have a tester
prior to release.
Brian Kelley
On Thu, Jan 21, 2016 at 9:41 AM, James Wallace <chp11...@sheffield.ac.uk>
wrote:
> Hi,
> I'm using the KNIME implementation to write my own nodes, and I'm
> running into an issue. For the process I'm trying to do I'm trying to
> subtract the MCS between two molecules away from the larger molecule, to
> leave a list of fragments. I'm aware of the substructure matching, but
> I'm not sure how to subtract the matching atoms from a molecule graph
> within RDKit. As I say, I'm working with the Java version, but any
> pointers towards the fucntions needed would be useful. At the moment
> I've got (in pseudo code)
>
> RWMol mol1a = RWMol.MolFromSmiles(reactant_string, 0, true);
> RWMol mol2a = RWMol.MolFromSmiles(product_string, 0, true);
>
> frag_bonds = mol2a.GetSubstructMatches(mol1a);
>
> But I'm unsure as to what to do with the array of matches to achieve
> what I want. Can I strip out the dummy atoms automatically, or is this
> something that is best achieved by processing the SMILES string?
>
>
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