On Wed, Mar 23, 2016 at 10:15 AM, Otis Rothenberger <osrot...@icloud.com>
wrote:
> Bob,
>
> C(\C)/1=C/C=C.C\1=C
>
> Resolver cannot read this, and I’m now thinking that it’s, understandably,
> geometry confused. I don’t know how to read these things, so I’m not sure.
> Interestingly, if I send the molfile to the new inchi.js, it creates an
> inchi, but NIST reports the resulting structure as being geometry
> ambiguous. That’s the nice thing about NIST. It fails gracefully with a
> valid inchi, simply showing connectivity structures with links to NIST
> possibilities.
>
>
This has to do with the ordering of the terms in the SMILES that Jmol is
generating and sending to NCI.
$ load $C(\C)/1=C/C=C.C\1=C
script ERROR: java.io.FileNotFoundException:
http://cactus.nci.nih.gov/chemical/structure/C(\C)/1=C/C=C.C\1=C/file?format=sdf&get3d=True
----
load <<<<"$C(\C)/1=C/C=C.C\1=C"
$ load $C/1(\C)=C/C=C.C\1=C
C7H10
So it appears that the connector /1 has to come before the branch (C). This
is not specified in the SMILES documentation, as far as I can tell, but I
can consider it a bug in Jmol anyway, since NCI does not read it.
Bob
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