molfile loader: direction of bond #15 makes no sense

[Colin Batchelor]

Hello,

(Using c# API, 1.1beta-4.)

Reading in the mol below, when I try

Indigo m_i = new Indigo();
foreach (IndigoObject molecule in m_i.iterateSDFile(sdf))
{
IndigoObject matcher = m_i.substructureMatcher(molecule);
}

I get the error "molfile loader: direction of bond #15 makes no sense"
- it looks fine to me but is there something subtle I'm missing?

--8<--

ACD/Labs08111116102D

17 18 0 0 1 0 0 0 0 0 1 V2000
2.3069 -1.9905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3069 -3.3136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4459 -1.3001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1678 -3.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4459 -3.9810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5850 -1.9905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5850 -3.3136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1678 -1.3001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3069 -0.6673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -3.3136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4459 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.9905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9329 -5.0682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2934 -5.0107 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7528 -1.3001 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2781 -4.6425 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
3.4459 -5.3041 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 8 1 0 0 0 0
1 9 1 1 0 0 0
2 4 1 0 0 0 0
2 5 1 0 0 0 0
2 16 1 6 0 0 0
3 6 1 0 0 0 0
3 11 1 1 0 0 0
4 10 1 0 0 0 0
4 13 1 6 0 0 0
4 14 1 1 0 0 0
5 7 1 0 0 0 0
5 17 2 0 0 0 0
6 7 2 0 0 0 0
6 15 1 1 0 0 0
8 12 1 0 0 0 0
10 12 1 0 0 0 0
M END
--8<--

Many thanks,
Colin.

[Mikhail Rybalkin]

Hello Colin,

This molecule contains invalid-marked stereocenter. Rightest up bond
connected to the double bond cannot make stereopyramid because such
configuration is planar. So this right bond doesn't really belong to a
stereocenter and Indigo throws error about it by default. This is done
to inform user that this molecule has mistakes. But it is possible to
ignore this error.
To ignore this error you need to set corresponding option:
m_i.setOption("ignore-stereochemistry-errors", "true")

List with the all options is available here: http://ggasoftware.com/opensource/indigo/api/options
If stereochemistry errors are ignored then molecule is loaded but
invalid stereoinformation is discarded (if it is possible).

With best regards,
Mikhail Rybalkin