wedge bonds not visible

[shyamramesh]

I am using RDKITJS to render this mol in browser.Unable to get the wedge bond displayed. In other tools same mol file shows wedge bond correctly.

What option am I missing in get_mol or in drawingoptions? Can someone help?

==================

     RDKit          2D

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 6 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.500000 0.000000 0.000000 0
M  V30 2 C 0.750000 -1.299000 0.000000 0
M  V30 3 C -0.750000 -1.299000 0.000000 0
M  V30 4 C -1.500000 0.000000 0.000000 0
M  V30 5 C -0.750000 1.299000 0.000000 0
M  V30 6 C 0.750000 1.299000 0.000000 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 3 1 3 4
M  V30 4 1 4 5
M  V30 5 1 5 6
M  V30 6 1 6 1 CFG=1
M  V30 END BOND
M  V30 END CTAB
M  END

[shyamramesh]

Any help / inputs?

[ptosco]

That wedge bond should not be there since there is no chiral center, hence by default RDKit removes it.
You may restore the wedging specified in your V3000 molblock by passing useMolBlockWedging to get_svg_with_highlights():

const mol = rdkitModule.get_mol(`
     RDKit          2D

  0  0  0  0  0  0  0  0  0  0999 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 6 6 0 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.500000 0.000000 0.000000 0
M  V30 2 C 0.750000 -1.299000 0.000000 0
M  V30 3 C -0.750000 -1.299000 0.000000 0
M  V30 4 C -1.500000 0.000000 0.000000 0
M  V30 5 C -0.750000 1.299000 0.000000 0
M  V30 6 C 0.750000 1.299000 0.000000 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 3 1 3 4
M  V30 4 1 4 5
M  V30 5 1 5 6
M  V30 6 1 6 1 CFG=1
M  V30 END BOND
M  V30 END CTAB
M  END
`);
const svg = mol.get_svg_with_highlights(JSON.stringify({ useMolBlockWedging: true }));

[shyamramesh]

Thanks a lot. Will try this.

[shyamramesh]

Is there any documentation that lists all options to get_svg_with_highlights()?

[Acylation]

Hi please check rdkit/rdkit#5178.