Generate framework including side chain atoms.

Hello,

I would like to generate framework graphs for a set of molecules, but maintain all side chain and substituent atoms. In essence this would convert all atoms to carbon and all bond to single but keep all the atoms. E.g.

CCCn1c(cc(=O)c2cc(F)ccc12)-c1cccc(Cl)c1 would become CCCC1C(CC(C)C2CC(C)CCC12)C1CCCC(C)C1.

Is this possible?

Thanks and regards,

Tim Ritchie.

Hi, 

We are investigating this issue and will come back with a solution soon. 

Thank you for your patience. 

Daniel

Dear Tim,

Currently the mentioned conversion is available only via API functions. 

The following Java method generates the requested framework:

public Molecule generate(final Molecule mol) {


	final Molecule framework = mol.clone();

	
	// dearomatize molecule
	framework.dearomatize();

	// replace atoms to carbon
	for (final MolAtom atom : framework.getAtomArray()) {
		atom.setAtno(6);
	}

		
	// change bonds to single
	for (final MolBond bond : framework.getBondArray()) {
		bond.setType(1);
	}

	return framework;

}

 

If you would like to use this function from Sketch or cxcalc, please see the documentation of Marvin Services.

 

Best regards,
Laszlo