understanding vague bond level

Hi

I'm curious as to why this

jcsearch -q 'C1=CC=CC=C1' --vagueBond:n -s 'c1ccccc1'

matches but this

jcsearch -q 'C=C' --vagueBond:3 -s 'c1ccccc1'

doesn't

(15.11.23)

I'm trying to understand why a particular kekule query is not matching in our own smarts filtering code based on the java API (all be it an older version of the toolkit at the moment).

Is there standardisation of the query in jcsearch or some other default that means kekule benzene matches an aromatic phenyl?

Thanks

Stephen

Hi Stephen,

Your guess is correct, by default, jcsearch runs with default standardisation (general aromatization and removing explicit H atoms from the query). You can define custom standardizer actions for a jcsearch command like:

no standardize actions:

jcsearch -q 'C1=CC=CC=C1' --vagueBond:n -s 'c1ccccc1' --standardize ''

basic aromatization and clean 2D:

jcsearch -q 'C1=CC=CC=C1' --vagueBond:n -s 'c1ccccc1' --standardize 'aromatize:b..clean2d'

 

Best regards,

Krisztina