substructure match count -allHits

Hi,





I was looking for a function that would give me a count of the hits for a structure on a substrate. The closest I found was if you used jcsearch with --allHits it would give a count and the location for each hit.





Two questions


1. With --allHits it only listed the structures when used with a DB input but it list the counts if from a file. Is that the way it is designed to work?





2. --allHits gave lots of extra text description is there a way to just get the count or an array with the structure id and the count?





Thanks,








Darcy

Hi Darcy,

darcy wrote:

1. With --allHits it only listed the structures when used with a DB input but it list the counts if from a file. Is that the way it is designed to work?

Yes, unfortunately the database operation is only prepared to decide if a match is present, but not to enumerate all.

darcy wrote:

2. --allHits gave lots of extra text description is there a way to just get the count or an array with the structure id and the count?

For this I recommend to use Chemical Terms expressions. (Particularly functions field() and matchCount().) For example:

Code:

evaluate -e "field('CdId'); matchCount('CCCC')" file.sdf

produces:

Quote:

101;1 102;2 103;0 104;0 105;0 106;0 107;4

('CCCC' is a SMARTS substructure expression.)





You can also add Chemical Terms columns easily in Instant JChem: http://www.chemaxon.com/instantjchem/webPages/htmlFiles/chemical_terms_fields.html


Which can be easily exported together with the Id column.





Best regards,


Szabolcs