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.
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);
}
catch(Exception e){
System.out.println("ERROR");
}
List maplist = (List)l.get(0);
for (Iterator i = maplist.iterator(); i.hasNext(); ) {
RMap rmap = (RMap)i.next();
idlist.add( new Integer( rmap.getId1() ) );
}
HashSet hs = new HashSet(idlist);
for (Iterator i = hs.iterator(); i.hasNext();) {
needle.removeBond(m.getBond( ((Integer)i.next()).intValue() ));
}
for (int i=0; i<needle.getAtomCount(); i++){
if ( needle.getConnectedAtomsCount(needle.getAtom(i)) ==0)
needle.removeAtom(needle.getAtom(i));
}
for (int i=0; i<needle.getBondCount(); i++){
if ( needle.getBond(i).getAtomCount()<2 )
needle.removeBond(i);
}
}
return new Molecule(needle);
}
What is wrong in this code?
Do you know any way to make this?
Thanks a lot!!
PD: Sorry for my english!
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