Does anyone have some tips on how to get started using the 3D-e-Chem Pharmacophore from Molecule node to generate pharmacophore models?
After installing the extension (I’m using KNIME 4.1.1) I did a quick test with aspirin and ibuprofen, and, while the node executes and gives a pharmacophore output column, none of the relevant features are being detected. For example, I don’t get any aromatic rings, hydrogen bond acceptors, or hydrogen bond donors.
This does not change if 3D coordinates are explicitly specified.
This does not change if hydrogens are implicit.
When hydrogens are explicit I get the following error:
Execute failed: Unknown "null" type, should be one of AROM,HYBH,NEGC,HACC,HYBL,HDON,POSC,EXCL,LIPO
Sulfur-containing molecules (I tried with cysteine) end up being marked as having an aromatic ring when none exists.
I haven’t been able to locate any documentation about the requirements for this node.
Any insight would be greatly appreciated.