I have a large dataset and would like to identify both the presence of intramolecular hydrogen bonds and the times that such occurs per target molecule (i.e. yes or no and if yes the number of times it appears per molecule). Would it be feasible to do so with match?
Thank you in advance!!!
The "hydrogen bonds" can only be visualized graphically after generating the 3D structure in the conformer tool.
I attached an example figure. The green lines are the "hydrogen bonds".
I would like to thank you for your infos. Since I do have a large amount of datasets and would like to analyze and identify intramolecular hydrogen bonds as in the case shown in the attached example (example1.mrv) I was thinking if it could be possible to screen my database with molecular descriptors i.e. describing a substructure motif as shown in the attached example (example2.mrv). Thus, would it be feasible to identify this motif via substructure searching (match)?
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Yes, it is possible. See the JChem Query Guide for available features you can use in your query patterns:
There are many interfaces also for searching or returning the number of substructure hits for earch molecules: API, command-line, GUI (e.g. Instant JChem, etc.)
Let us know your preference and I can give some guidance.
Thank you for your reply. I would like to use command-line (i guess I should use screenmd?) could you please assist to this?
screenmd is a possible way, but in that case a custom descriptor has to be created, which may be quite complicated and involve some Java coding.
I would rather recommend jcsearch, which directly filters the matching molecules. See documentation here:
Let us know if you have further questions.