inchi issues

Hi,

I have checked the conversion from SDF to InChI using molconvert and I have observed some issues:

1) The molconvert tool ignores the bond stereo flags denoting that the conformation of a double bond is not specified. For example, for DB00265, the molconvert output is InChI=1S/C13H17NO/c1-4-8-13(15)14(5-2)12-10-7-6-9-11(12)3/h4,6-10H,5H2,1-3H3/b8-4+, but it should be InChI=1S/C13H17NO/c1-4-8-13(15)14(5-2)12-10-7-6-9-11(12)3/h4,6-10H,5H2,1-3H3.

2) The ChEBI datatase uses a different way to denote that the conformation of a double bond is not specified. However, there is the same issue. For example, for ChEBI:17205, the molconvert output is InChI=1S/C7H8O5/c8-5(7(11)12)3-1-2-4-6(9)10/h1,3H,2,4H2,(H,9,10)(H,11,12)/p-2/b3-1+, but it should be InChI=1S/C7H8O5/c8-5(7(11)12)3-1-2-4-6(9)10/h1,3H,2,4H2,(H,9,10)(H,11,12)/p-2.

3) The molconvert tool probably does not support axial chirality. For example, for ChEBI:38413, the molconvert output is InChI=1/C18H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-3,12,14H,4-11,15-17H2,1H3,(H,19,20)/b3-2+, but it should be InChI=1S/C18H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-3,12,14H,4-11,15-17H2,1H3,(H,19,20)/b3-2+/t13-/m1/s1.

Best regards,
Jakub Galgonek

Hi,

Thanks for the report, I am just investigating what happens with the molecule.

Janos

Hi,

In the first two cases, if you use mdl molfile for input, our inchi export calculates the stereo based on the atom coordinates. If you use smiles you will got the proper inchi.

 

In the third case you are right, the MolConverter/inchi export does not support the axial chirality.

We will fix it soon.

Thanks for the report,

Janos

jkendi wrote:

In the first two cases, if you use mdl molfile for input, our inchi export calculates the stereo based on the atom coordinates.

Hi,

Just to be sure, do you agree that this is also a bug and will be fixed too?

Thank you,
Jakub

Hi,

Yes, this is a bug too, we will fix both.

Janos

Hi,

The bugfixes will be available in version 6.4.

Janos

Hi,

Thank you.

Jakub