Does substructure matching work when an sdf file is searched with a scaffold with R1 and R2 or A's for any atom or X?
I find that the query substructure is present in the hits but there are attachment at points other than R1, R2 etc. that should not be there.
R-sites in the query molecules are used for combinatorial substructure matching. For example, the attached molecule q_r.png defines combinatorial structure, and when such structure is specified as a query it will match t_r.png. If no r-group is defines for r-site, then it is supposed to be empty. This is why it matches your target molecule.
As I understand, you need the following rules: R1 in the query matches R1 in the target. Am I understood correct?
Also you can use A and X in the query, they match any atom and halogen atom respectively.
With best regards,
Well what I wanted really was to use the top substructure where R1 site is defined with the 5 membered het ring and search structures.
Thus a structure like t_r.png should be a hit but not structures where there are attachments at points other then R1 in q_r.png, even if the fivemembered he ring portion is exactly the same..
I do not understand the question. You can specify the query q_r.png as it matches t_matched.png and do not matches t_not_matched.png.
Could you give an example of incorrect behavior?