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Generate framework including side chain atoms.
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Tim

Joined: 19 Sep 2009
Posts: 65

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Link to postPosted: Mon Mar 14, 2016 9:17 amPost subject: Generate framework including side chain atoms. Reply with quote

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.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Mon Mar 21, 2016 3:12 pmPost subject: Reply with quote

Hi, 

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

Thank you for your patience. 

Daniel

László
ChemAxon personnel
Joined: 14 Jan 2011
Posts: 78

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Link to postPosted: Tue Mar 22, 2016 3:37 pmPost subject: Reply with quote

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 

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