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Substructure Search Result issue
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Dann

Joined: 13 Nov 2004
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Link to postPosted: Thu Sep 29, 2016 2:33 pmPost subject: Substructure Search Result issue Reply with quote

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.

Anna
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Joined: 27 Feb 2012
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Link to postPosted: Fri Sep 30, 2016 12:43 pmPost subject: Reply with quote

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

 

Dann

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Link to postPosted: Fri Sep 30, 2016 1:03 pmPost subject: Reply with quote

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

Dann

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Link to postPosted: Fri Oct 07, 2016 2:26 pmPost subject: Reply with quote

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

Zsolt
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Joined: 18 Jun 2010
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Link to postPosted: Fri Oct 07, 2016 3:51 pmPost subject: Reply with quote

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

Dann

Joined: 13 Nov 2004
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Link to postPosted: Fri Oct 07, 2016 4:01 pmPost subject: Reply with quote

Hi Zsolt,

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

BR

Dann

Zsolt
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Link to postPosted: Tue Oct 25, 2016 8:30 amPost subject: Reply with quote

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

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