This workflow demonstrates how to align molecules according to a substructure, so they are all shown in the same orientation (in this example accoring to the carbocylic acid). The bit of the molecules according to which they should be aligned is drawn in the sketcher component. The resulting SMARTS is used in the RDKit Generate Coords node to change the 2D coordinates of the atoms (set the rendering to SDF by right-clicking on the column header and check the changed coordinates).
Required extension: RDKit
This workflow aligns molecules according to a substructure (e.g. carboxylic acid) 2D depiction. However the orientation of this substructure itself seems to be arbitrary. Is there a way to suggest the orientation of the substructure (e.g. sketched or sdf import) and generate the 2D depictions of molecules aligned according to that specific substructure orientation?
Hi,
I have the same request, does someone have an solution?
Moreover, it seems that the depiction of aligned molecule are sometimes weird, for example a methyl group could overlap with another group and a red point is depicted.
Thanks,
Emilie