Hi Pat,
Looks like a bug in the SLN parser. I will track it down and get it fixed for
the next release.
Thanks for both the report and the pointer to a source of SLN I can use for
testing; these have been somewhat hard to find.
-greg
On Jan 3, 2013, at 7:55 PM, Patrick Walters <[email protected]> wrote:
> Hi All,
>
> I've been trying to use RDKit to parse the SLN queries in a recent paper from
> Jonathan Baell at Monash
> http://pubs.acs.org/doi/abs/10.1021/ci300461a
>
> RDKit is able to successfully parse most of the queries, but is unable to
> handle 18 of 539. It looks like the problem is with the "&NOT" construct.
> Has anyone run into this? Is anyone aware of a workaround?
>
> Thanks,
>
> Pat
>
> HetC(=O)O-[!R]C[8]:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):Hev:Hev(Any[IS=Hal,C#N,C(F)(F)F,S(=O)=O,C(=O)&NOT=C(=O)OH]):Hev:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):@8
> HetC(=O)O-[!R]C[8]:Hev(Any[IS=Hal,C#N,C(F)(F)F,S(=O)=O,C(=O)&NOT=C(=O)OH]):Hev:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):Hev:Hev(Any[NOT=O,S[TAC=2],C[TAC=4],N[TAC=3]]):@8
> CCH=[!R]C(Any[IS=H,C])Any[IS=C#N,C(=O)&NOT=C(=O)Any[IS=N,O]]
> Any[IS=C,O]CH=[!R]C(Any[IS=C(=O),S(=O),C#N,Hal,C(Hal)(Hal)Hal&NOT=C(=O)OH])Any[IS=C(=O),S(=O),C#N&NOT=C(=O)OH]
> C[1](C(=O)OC[5]:C:C:C:C:C:@5CH=@1)Any[IS=C(=O),C(=S),S(=O),C#N,Hal,C(Hal)(Hal)Hal&NOT=C(=O)OH]
> C[1](=CHOC[5]:C:C:C:C:C:@5C@1=O)Any[IS=C(=O),C(=S),S(=O),C#N,Hal,C(Hal)(Hal)Hal&NOT=C(=O)OH]
> C[1]:N:Any(Any[IS=Hal,S(=O)(=O)C]):Any:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any:@1
> C[1]:N:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any:Any(Any[IS=Hal,S(=O)(=O)C]):Any:@1
> C[1]:N:Any(Any[IS=Hal,S(=O)(=O)C]):Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any:Any:@1
> C[1]:N:Any(Any[IS=Hal,S(=O)(=O)C]):Any:Any:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):@1
> C[1](Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):N:Any(Any[IS=Hal,S(=O)(=O)C]):Any(Any[NOT=N]):Any(Any[NOT=N]):Any:@1
> C[1]:N:Any:Any(Any[IS=Hal,C(C)=NO,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):Any(Any[IS=Hal,S(=O)(=O)C]):Any:@1
> C[1](Any[NOT=N,O]):C(Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):C(Any[IS=Hal,S(=O)(=O)C,C[r](=O)NC]):C(Any[NOT=N,O]):C(Any[NOT=N,O]):C(Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):@1
> C[1](Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):C(Any[IS=Hal,S(=O)(=O)C,C[r](=O)NC]):C(Any[IS=Hal,C#N,C(=O),C(F)(F)F,S(=O)=O&NOT=C(=O)OH]):C(Any[NOT=N,O]):C(Any[NOT=N,O]):C(Any[NOT=N,O]):@1
> N(Any[IS=H,C[TAC=4]&NOT=C[TAC=4]-[R]C[TAC=4]N])(Any[IS=H,C[TAC=4]&NOT=C[TAC=4]-[R]C[TAC=4]N])(Any[IS=H,C[TAC=4]&NOT=C[TAC=4]-[R]C[TAC=4]N])<max=1>
> Any[IS=H,C&NOT=C=O]N[!r](Any[IS=H,C&NOT=C=O])C(=O)C<max=2>
> Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]Hev[!r&NOT=NC(=O)NC(=O)]
> Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O),N*S(=O),N*(C=O)]Hev[!r&NOT=C=O,S(=O)(=O)]Any[IS=CH3,OH,NH2,N(CH3)CH3]
>
>
>
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