overlapping bonds with TBDPS super atom

Hi,

I am confused about an overlapping-bonds result.

If I run the below Java code against onec.mol (attached .. methyl attached to TBDPS), then I find no overlapping bonds.

If I run the below Java code against twoc.mol (attached .. ethyl attached to TBDPS), then I unexpectedly find overlapping bonds.  Visually in Marvinsketch, the ethyl structure looks less sterically hindered than the methyl structure.

Can you please help clarify this for me?  In both cases, TBDPS is contracted.

Thanks very much.  We are using JChem Java API 5.11.2.

Best, Andrew

MolImporter mi = new MolImporter(infile);

Molecule mol = mi.read();

StructureCheckerResult scr = null;

OverlappingBondsChecker obc = new OverlappingBondsChecker();

scr = obc.check(mol);

if (scr!=null) {

            System.out.println("found overlapping bonds");

}

The question was moved to the appropriate forum section.

The relevant experts will respond soon.

János

I can reproduce the error with twoc.mol, but it gives me error only if the TBDPS abbreviated group is expanded. 

The error is reported because the overlapping bond detection threshold is too high (it detects error even if the bonds are not close). We will fix it in Marvin/JChem 14.7.21.

Thank you very much for quick response and confirmation.

Best,

Andrew