Stereo chemistry components

I have a requirement where i need to identify a molecules atom and bond properties. As in, if the molecule has a hash or wedge chirality and e z bonds. Is there a node in Knime which can fulfill my requirement?

What format are your molecules in? If they are in SMILES format, then there is the Speedy SMILES Explicit Chirality Filter (or Splitter) node, which will detect any explicitly defined chiral centres. There isn’t currently a corresponding version for double bond geometry, although it would be pretty straightforward to add one.

Steve

I’ve just added an Explicit Double Bond Geometry Filter/Splitter pair of nodes to the nightly build - see Update to v1.16.0 (Nightly only) - Extract/Inject Column Properties, Vector Distances, Plate handling, Speedy SMILES

Steve

My molecules are in SMILES format. I would like to know the differences between explicit chiral and the actual chiral. Can you please let me know on that?

In addition to it, do we have a node which can identify E or Z Bonds in the molecule?

‘Explicit chiral’ means that there is a stereocentre defined in the SMILES e.g. C[C@H](Br)F, as opposed to a centre which may be chiral but is has no chirality defined, e.g. CC(Br)F

In v1.16.0 of our community contribution (currently only on the nightly/trunk release), there is the Explicit Double Bond Geometry Filter node (and corresponding ‘splitter’ node). This will identify molecules in which double bond geometry is defined explicitly (e.g. C/C=C/C), but it will not attempt to tell you whether a particular double bond is E or Z

Steve

How to add a double bond geometry properties in my application? In your first reply in this thread, you claimed that it would be straightforward to add one,

Sorry, what I meant was that we could add a node which detects whether a SMILES string contains specified double bond geometry. If you want to edit the geometry you will need to look at probably RDKit

Steve

Hi Steve,

Node “Speedy SMILES Chiral Centre Count” doesn’t provide a correct count when the provided molecule (SMILES) has flat bonds (no wedge or dash bonds). Is it possible to get the chiral center count for these kind of molecules too?

Thanks,
Shiva

HI @shiva,

Unfortunately this is not possible with the ‘Speedy SMILES’ nodes, however it can be done using RDKit. See Feature request: number of chiral centers and Access RDKit functionality via Java Snippet node

Steve