On Nov 13, 2007, at 2:49 PM, Javi Muriel Zafra wrote:
>
> Hi all!
> I need to know how I can obtain the no common structure between two
> molecules.
> I use the method UniversalIsomorphismTester.getOverlaps to get the
> MCSS. Then I need to know, furthermore MCSS between this molecules,
> the no common structure in each molecule.
Note that if you want the substructure of X that is not part of the
MCSS between X & Y, you may have more than one substructure. As an
example consider
CSC1CC1NC and C1CC1CCC
The MCSS is C1CC1. But the uncommon parts for the first one will be
CS and NC and the uncommon part of the second one will be just CCC
If this is what you want, then see http://
cheminfo.informatics.indiana.edu/~rguha/code/java/NoMCSS.java
> I do the following:
>
> // This method return the no common structure between m and mcs,
> where mcs is the mcss between m and another molecule
> // So, if I remove from m the bonds which appear in mcs, I have the
> no common structure, but don't work exactly.
> public static Molecule getneedle(Molecule m, Molecule mcs) {
> Molecule needle = new Molecule(m);
> Vector idlist = new Vector();
>
> List l = null;
> try{
> l = UniversalIsomorphismTester.getSubgraphMaps(m, mcs);
It is easier if you use getSubgraphAtomsMaps, since we can then
remove atoms and associated bonds in one go
Once you have deleted atoms and bonds, you will in general end up
with a molecule that has disconnected components. Using the
ConnectivityChecker it is easy to create a IMoleculeSet from such a
molecule. The contents of the IMoleculeSet are the 'uncommon' parts
of a molecule (i.e., the molecule minus the MCSS)
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
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