I am looking for a node that allows the detection of patterns in 3D such as the detection of intramolecular hydrogen bonds like in the figure below.
Acually, this is possible in 2D by searching for a specific SMARTS patterns but not sure this is doable in 3D.
Is this possible with rdkit or CDK or any other kit?
I’m not aware of any node that makes functionality like this available.
There are two reasonably easy solutions using a scripting node (either Java or Python depending on which language you’re more comfortable with and which toolkit you want to use):
- If you have a SMARTS pattern for identifying potential hydrogen bonds which you are happy with, you could apply that to the molecule and then check the actual distances in the current conformer to see if they are compatible with an H bond.
- You could just look at all H - heteroatom distances and see if there are any which are significantly longer than a single bond but shorter than a van der waals contact.
I hope this helps,
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