Chapter 11, leftover active decoys

[altayg]

Did you forget to drop the leftover active decoy molecules or did you left them as is deliberately?

After this ratio check, there is no further dropping for the 12 leftover active decoys:

charged = revised_decoy_df[revised_decoy_df["charge"] != 0]
charged.shape[0]/revised_decoy_df.shape[0] # 0.00263

charged.shape[0] # 12

[PatWalters]

The active molecules and decoy molecules are two different sets. The reason that there are a few charged molecules left in the set is that the NeutraliseCharges function does not have the appropriate SMARTS patterns for neutralization of all of the molecules. When I looked at the 12 structures, it was either functionality like N-oxides or what appears to be incorrect structures from the DUD-E database. Pat

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On Thu, Sep 26, 2019 at 2:20 PM Goekman Altay ***@***.***> wrote: Did you forget to drop the leftover active decoy molecules or did you left them as is deliberately? After this ratio check, there is no further dropping for the 12 leftover active decoys: charged = revised_decoy_df[revised_decoy_df["charge"] != 0] charged.shape[0]/revised_decoy_df.shape[0] # 0.00263 charged.shape[0] # 12 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=AAVCVTKYWOV7BBSS7TAODNDQLT4QNA5CNFSM4I25NY7KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HN6ZDYQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAVCVTJFAZUWUPXNMALZNQLQLT4QNANCNFSM4I25NY7A> .

[altayg]

Would it not be better to remove them and not include in the model?

[PatWalters]

Probably, although I don't think it would make that much of a difference. Pat

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On Fri, Sep 27, 2019 at 1:11 PM Goekman Altay ***@***.***> wrote: Would it not be better to remove them and not include in the model? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15?email_source=notifications&email_token=AAVCVTNSNYDRBF2F4FBM6JLQLY5FPA5CNFSM4I25NY7KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7ZRFQI#issuecomment-536023745>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAVCVTINEZHTOQQJHY44OM3QLY5FPANCNFSM4I25NY7A> .