When doing substructure searches we have noticed an inconsistency which can be exemplified as follows:

If one makes a substructure search with a cyclohexane ring (C6H12) one would expect that the hit-set would include all the structures including this structural feature (six carbons in a ring).

That includes compounds with a benzene ring (C6H6) – but that is not the case. If we search our database for a cyclohexane ring with free substitution we get much fewer hits that if we perform the same search with a benzene-ring and free substitution  - it should be the other way around as the hit-set from the benzene ring search (C6H6) should also be included in the cyclohexane-search (C6H12).

JChem .net version 16.2.1.

Hi Dann,

If you would like to use simply six carbon in a ring, which are connected with any types of bonds you have to draw cyclohexane and specify bonds with any bond type. (Cyclohexane means 6 single bonds, while benzene means 6 aromatic bonds, these are chemically different, so their hit sets cannot be included in each other.)

You can further refine bond types in substructure searches with vague bond search options:

https://docs.chemaxon.com/display/docs/Tautomer+search+-+Vague+bond+search+-+sp-Hybridization#Tautomersearch-Vaguebondsearch-sp-Hybridization-vaguebond

Hope this helps, but let me know, if you have further questions.

Regards,

Anna

Hi Anna,

Thanks for taking the time here.

Let me have a look at the documentation link you sent, and I will get back to you.

BR

Dann

Hi Anna,

I have received this from my contact person, could you have a look and get back to me?

Sent you an email with the doc, adding an attachment here did not work for me

BR

Dann

Hi Dann,

could you please send the e-mail with the doc file (mentioned in your previous post) to  jc4o-support@chemaxon.com?

Thank you in advance for your help!

Best regards,

Zsolt

Hi Zsolt,

The email with the document has been forwarded to the address in your post.

BR

Dann

Hi Dann,

the substructure search problem reported by you and the sample document have been forwarded to the JCB team (you were cc-ed on the e-mail).

Please do not hesitate to contact us if you need any further help regarding the JChem for Office/Excel.

Best regards,

Zsolt