Thanks, that's worked brilliantly. Seems quicker than my original
approach too.
On 21/01/2016 15:17, Brian Kelley wrote:
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 <mailto: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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