rcdk::matches() function bugs

There is an issue for substructure match function. I got true value even if the substructure is not in the query molecule.

Please include a minimal reproducible example (AKA a reprex). If you've never heard of a reprex before, start by reading https://www.tidyverse.org/help/#reprex.

There is an issue for substructure match function. I got true value even if the substructure is not in the query molecule.

mol = parse.smiles('CN(C)c1cccc2c(S(=O)(=O)Oc3ccc4c5c3OC3C(=O)CC(O)C6(O)C(C4)N(CC4CC4)CCC536)cccc12')
query =  'CN(C)CCc1ccccc1'
rcdk::matches(query,mol)

Screenshots

"rcdk::matches(query2,mol1)
CN(C)c1cccc2c(S(=O)(=O)Oc3ccc4c5c3OC3C(=O)CC(O)C6(O)C(C4)N(CC4CC4)CCC536)cccc12.match
TRUE"

System (please complete the following information):

OS: windows 11
R-4.1.1

@rajarshi

Hi, thanks for your report. So I am less familiar with the SMARTS but here's what I've found:

rcdk::matches uses SMARTSQueryTool under the hood.
SMARTSQueryTool is deprecated
SMARTSPattern is prefferred.
I am not familiar enough with SMARTS to know if your example is truly expected to be negative. You should probaby confirm on the CDK users mailing list with your specific pattern.
rcdk should either fix or deprecate this function (@rajarshi would need to weigh in there)

If you try it out at https://www.simolecule.com/cdkdepict/depict.html, the supplied SMARTS pattern does match the the molecule. However, I agree that we should fix the function to use SMARTSPattern

…

On Sun, Feb 12, 2023 at 12:19 AM zachcp ***@***.***> wrote: Hi, thanks for your report. So I am less familiar with the SMARTS but here's what I've found: - rcdk::matches uses SMARTSQueryTool <https://github.com/CDK-R/cdkr/blob/master/rcdk/R/matching.R#L16> under the hood. - SMARTSQueryTool is deprecated <https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.html> - SMARTSPattern <https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/smarts/SmartsPattern.html> is prefferred. - I am not familiar enough with SMARTS to know if your example is truly expected to be negative. You should probaby confirm on the CDK users mailing list <https://cdk.github.io/cdk/latest/docs/api/org/openscience/cdk/smarts/SmartsPattern.html> with your specific pattern. - rcdk should either fix or deprecate this function ***@***.*** <https://github.com/rajarshi> would need to weigh in there) — Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAIMOJR6AXJTU4XQJU5VATWXAUCTANCNFSM6AAAAAARQYH6EY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Rajarshi Guha | http://blog.rguha.net | @rguha <https://twitter.com/rguha>

Dear Rajarshi,

Thank you for your reply!

I found that the rdkit substructer matching fucntion did the same mistake. Please kindly find the picture below:

As a matter of fact, the substructure that I am looking for is an benzene structure with an ammonia side chain, which is totally different from the naphthalene structure. I believed the reason is that the algorithm took the naphthalene structure as an alkyl structure.

Best regards,
Junjie

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rcdk::matches() function bugs #136

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rcdk::matches() function bugs #136

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zachcp commented on Feb 12, 2023

rajarshi commented on Feb 12, 2023

YANGJJ93MS commented on Feb 14, 2023

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