RDKit 2D Depiction of molfiles can have wrong orientation (Bug)

In some cases the 2D Depiction rendered in the table for RDKit Molecule cells does not match the orientation of the molfile. It tends to be "upside down".

Left: RDKit (wrong)

Right. Marvin as drawn in MarvinSketch and exported as Molfile

If the cell is rendered with Marvin Rendered manually, orientation is correct. If you convert the Cell back to a molecule cell and use Marvin renderer (or indigo) it is again correct. If you write and SD-File, it is correct as well.

Conclusion is that the internal representation is correct however the rendering ignores orientation or there is a bug where it rotates the molecule 180 degrees on y-axis (flips it upside-down).

If the input has coordinates, the rendered should display the molecule exactly as drawn. Else there can be a lot of confusion esepcially when working with aligned structures.

Thank you for hopefully fixing this.


The problem here, which is a bug, is that the RDKit drawing code is using a standard (computer) drawing convention that Y increases towards the bottom of the page. This unfortunately doesn't match the human idea that Y should increase towards the top. 

The easy work-around is just to turn your monitor upside down when you look at an RDKit rendering. ;-)

Jokes aside: It's a known problem and is on the list of things to be fixed for the next release (in the next couple of months). It is, unfortunately, not as trivial to fix as it sounds.