Re: [Cdk-user] Murcko Framework / aromaticity

[Pascal M. <pas...@gm...>]

Hi,


> Each of the components should only do the minimal promised work, which gives maximum
> flexibility in wiring things together as you like them.
> In your example, you would always need to do aromaticity detection (using some
> CDKHueckelAromaticityDetector.java or so) to do the detection before doing the Murcko stuff.
> The reasoning in this case, (...)

Ok, I think I understand...
But do you agree that the Murcko framework should retain the bond
order? I.e., that a benzene should not be a cyclohexane in the
frameworks?

And should, or not, the framework retain all cycles? Reading the
reference publication, I think so, but the following code generate up
to 3 or 6 framework in my tests.
E.g.
C[N+]1(CCC[C@@H]1COC(=O)[C@@](c2ccccc2)(C3CCCCC3)O)C ZINC00000585
gives 3 frameworks:
C(C1CCCCC1)C2CCCCC2 ZINC00000585_1
C(CC1CCCCC1)OCC2[N+]CCC2 ZINC00000585_2
C(OCC1[N+]CCC1)CC2CCCCC2 ZINC00000585_3
(2 and 3 are by the way identical, due to the phenyl conversion in
cyclohexyl - although I now use
CDKHueckelAromaticityDetector.detectAromaticity(mol)

And is intended that the nitrogen keeps the charge in the framework?
(I don't know what the behaviour should be in this case...)

Here is my code:

GenerateFragments gf=new GenerateFragments();
boolean bolFalse = false;
while(reader.hasNext()){
    Molecule mol = (Molecule)reader.next();
    CDKHueckelAromaticityDetector.detectAromaticity(mol);
    gf.generateMurckoFragments(mol,bolFalse,bolFalse,3);
    String[] smiles=gf.getMurckoFrameworksAsSmileArray();
    if (smiles.length > 0) {
        for (int i = 0; i < smiles.length; i++) {
        System.out.print(smiles[i]);
        System.out.print(" ");
        System.out.print(mol.getProperty(CDKConstants.TITLE));
        System.out.print("_");
        System.out.println(i+1);
    }
}



By the way, is there a better way of printing like
System.out.println(smiles[i]), " ", mol.getProperty(CDKConstants.TITLE);
?

Thanks again,
Regards,
Pascal