Find components with different carbon chain length

Hello, 

I would like to find compounds using SMARTs that:

1) contain OH- group and have 4 or less C atoms;

2) contain OH- group and have 5 or less C atoms.

For the 2 search perfectly well worked this SMART [#6]~[#6][OH] |Sg:n:1:5:ht| from previous topic. 

However, the similar SMART [#6]~[#6][OH] |Sg:n:1:1-4:ht| gives as a result also a compounds with a longer side chain. 

The question is, can I (using extended SMARTS) somehow exclude the results of the second search from the first one? And how can standard NOT operator (!) be used with the extended SMARTS.

Hello Olena,

First we would like to clarify what kind of search type are you applying? Are you running full structure / full fragment search or substructure search?

In case of substructure search, the molecules with longer carbon chain will also be hits.

In case of full structure or full fragment search, we recommend to apply SMILES instead of SMARTS.

Nevertheless, the in CXSMARTS, the NOT operator can only be placed in the SMARTS part and not in the extension part.

As for your question regarding the exclusion, do you really want to get those molecules as hits which have 4 or less carbon atom and an OH group AND do not have 5 or less carbon atoms and an OH group ?

Best regards,

Krisztina

 

 

 

Dear Krisztina,

Thank you very much indeed for a prompt reply! 

I am performing a substructure search and, as you perfectly formulated, I need hit molecules

kvajda wrote:

which have 4 or less carbon atom and an OH group AND do not have 5 or less carbon atoms and an OH group

So is it possible in any way to perform such a substructure search?

Sorry, but all the structures fulfilling the 1st condition, do also fulfill the 2nd condition, consequently,  the results will not contain any molecule.

In the reversed mode, if you want the 2nd condition to be fulfilled and the 1st not to be fulfilled, you would run a search for molecules with exactly 5 carbon and an OH group with [#6]~[#6]-[OH] |Sg:n:1:4:ht| and apply full structure or full fragment search.This can be reached in substructure search with: [#6;D1]~[#6;D2]-[OH] |s:0:*,1:*,Sg:n:1:4:ht|

Best regards,

Krisztina