PatWalters
commented
5 years ago Thanks, Andrew, I'll change that.
On Fri, Oct 5, 2018 at 7:02 AM Andrew Dalke notifications@github.com wrote:
In Notes.txt you write that you replaced $(CF2) with [CF2] to make it something that RDKit will parse.
The "[CF2]" means "atom with isotope number 2 and is carbon and fluorine", which is impossible to match.
I think the SMARTS of $(CF2) is trying to be $(C(F)F). The "CF2" is supposed to be a SMARTS expression, but in this case it has the unclosed ring closure "2". SMARTSViewer also complains about the $(CF2) saying "SMARTS Warning: Unpaired ring bonds!"
This suggests that the ChEMBL tool ignores the illegal SMARTS. I wonder if it matches CF (when there aren't 2 fluorines), or if it ignores that term (ie, not match CF at all), or ignores any matches.
I see nothing wrong with your other fixes.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/PatWalters/rd_filters/issues/3, or mute the thread https://github.com/notifications/unsubscribe-auth/ACoqzTnS3ewkwni2WCGsoe1Y8_0DYI2Aks5uhzxWgaJpZM4XKAvM .
pieterhbos
In Notes.txt you write that you replaced $(CF2) with [CF2] to make it something that RDKit will parse.
The "[CF2]" means "atom with isotope number 2 and is carbon and fluorine", which is impossible to match.
I think the SMARTS of $(CF2) is trying to be $(C(F)F). The "CF2" is supposed to be a SMARTS expression, but in this case it has the unclosed ring closure "2". SMARTSViewer also complains about the $(CF2) saying "SMARTS Warning: Unpaired ring bonds!"
This suggests that the ChEMBL tool ignores the illegal SMARTS. I wonder if it matches CF (when there aren't 2 fluorines), or if it ignores that term (ie, not match CF at all), or ignores any matches.
I see nothing wrong with your other fixes.