How to get the formula of the constant part of a polymer?

Dear ChemAxon team,

I am using the Java API v6.1.3 and I would like to get the formula for a constant part of a polymer, starting from a molfile. How can I do it?

Example:

Given the following compound (see attached molfile ChEBI_15693.mol), which is an aldose, with a RepeatingUnitSgroup (SRU):

If I do:

import chemaxon.struc.Molecule;

[...]

MolImporter importer = new MolImporter(new ByteArrayInputStream(structure.getBytes()));
Molecule mol = importer.read();
[...] mol.getFormula()

I get:

(CH2O)nC2H4O2

How do I get  C2H4O2 only?

I tried the two following possibilities:

1. I can't perform mol.removeAllSGroups() before calling getFormula() (Molecule.removeAllSGroups() is protected)

2, I tried the ElementalAnalyserPlugin, getFormula(), but I get:

java.lang.NullPointerException
    at chemaxon.struc.Molecule.addSgroupClone(Molecule.java:1046)

[...]

 

Do you have a suggestion to get C2H4O2 out of this molfile in a clean way?

Thanks for you support,

Thierry

Hi Thierry,

Unfortunately there is no convenient way of doing such thing. I can suggest you to use the functionality of the SelectionMolecule for this. Here is a simple code that calculates the formula for the parts that are not in any Sgroup:

SelectionMolecule sm = new SelectionMolecule();
for (MolAtom ma : m.getAtomArray()) {
   if (m.findSgroupOf(ma) == null) {
       sm.add(ma);
    }
}
System.out.println("Formula for selection: " + sm.getFormula());

 

Please let us know if this solution is suitable for you.

Regards,

Peter

Dear Peter,

The solution that you propose is working fine in my context.

Thanks for your help indeed!

Best regards,

 

Thierry