Indigo hangs on indigo.loadMolecule(string mol) for this very large molecule

[Colin Batchelor]

Hello,

Bit mysterious this: loadMolecule hangs on attempting to load the attached molfile.

Any idea what's going on? Would it be possible to set a timeout?

Best wishes,
Colin.

[Colin Batchelor]

I should add that clearly this molecule is nonsense and I shouldn't be feeding it to Indigo anyway, but it might reveal something that might cause Indigo to hang on a legitimate molecule.

[Mikhail Rybalkin]

Hello Colin!

The problem appeared in the algorithms that tries to find stereocenters when loading a structure with 3D coordinates. Structure is very symmetric and our algorithm got stuck with trying to find what kind of stereocenters are not really stereocenters (when substitutes are symmetric).I have an idea how to fix this issue, and will try to include in the upcoming release.

For now you can disable this feature by setting "skip-3d-chirality" option to true: http://ggasoftware.com/opensource/indigo/api/options#inputoutput

Best regards,

Mikhail

[Colin Batchelor]

Great; thank you.

If it helps, I have another one (attached).

Best wishes,
Colin.

[Mikhail Rybalkin]

Hi Colin!

You can try the latest Indigo 1.1.3 where this issue has been fixed: http://ggasoftware.com/download/indigo

Let me know if you still have other molecules with the similar issues.

Mikhail