Generate framework including side chain atoms.

User fca09bdbff

14-03-2016 08:17:16


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.

ChemAxon d51151248d

21-03-2016 14:12:59


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

Thank you for your patience. 


ChemAxon 5fc3e8d7d0

22-03-2016 14:37:37

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

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

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

return framework;



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


Best regards,