Re: [InChI-discuss] InChI standard generation options (request for comments)

[Igor P. <igo...@gm...>]

Andrew,
thank you for the feedback.

Though right now I am not in a position to answer all your questions
definitely, let me comment on some issues.
> If you don't want to change the existing program, make a new binary
> called "inchi", which is a lot easier to remember and type than
> "cInChI-1", and specify that this program always generates the right
> InChI and InChI keys, without needing any extra options.
Agree. Thanks to all you inchi-discuss members and your suggestions, it is
[nearly] exactly what will appear in InChI software v. 1.02 final release.

> the options mentioned.  The "/FixedH" option causes some problems
> when using the InChiKey with ChemSpider.  ChemSpider does not use the
>  "/FixedH" option, so
> InChI=1/C8H7Cl2NO3/c9-4-1-5(10)7(2-6(4)11)14-3-8(12)13/h1-2H,3,1
>
> not FixedH - InChIKey=VMNPETQUBQUXAP-UHFFFAOYAG
>  FixedH    - InChIKey=VMNPETQUBQUXAP-XWKXFZRBCY
>
> If you do the search at http://www.chemspider.com/Search.aspx then
> you'll find that the first option (which does not use /FixedH) gets a
> hit for ChemSpider ID: 71702, while the second option (with /FixedH)
> finds nothing.

Let me attract your attention to the fact that solution of the problem may
be not only by omitting FixedH layer upon InChI/InChIKey generation. Another
one is to use InChIKey created with FixedH but just search in ChemSpider for
the 1st block of that key (note that ChemSpider understands this).

For your example, search in the ChemSpider for the _1st_ block of InChIKey
VMNPETQUBQUXAP
returns the same hit, ChemSpider ID 71702, as one you mentioned.

As an added bonus, you may also search in Google for that _1st_ block:
http://www.google.com/search?q=VMNPETQUBQUXAP
and find one more result which corresponds to InChIKey created (in contrast
to ChemSpider) with FixedH layer, VMNPETQUBQUXAP-XWKXFZRBCY:
http://sci-toys.com/scichem/jqp011/79383.html
(Note that search in Google by a full key created without FixedH,
VMNPETQUBQUXAP-UHFFFAOYAG, returns nothing - which is exactly opposite to
ChemSpider's behavior).

Best regards,
Igor



On Fri, May 30, 2008 at 10:48 PM, Andrew Dalke <da...@da...>
wrote:

> This thread started last January but I had nothing to add until now.
>
> One of my clients added InChI support to an in-house system.  The
> first version they wrote did not use any of the switches mentioned
> here.  Their assumption, like Beda Kosata's, is that the program
> without any parameters should give the right answers.  Especially
> there should be no reason to have to specify that I want the code to
> work correctly.
>
> If you don't want to change the existing program, make a new binary
> called "inchi", which is a lot easier to remember and type than
> "cInChI-1", and specify that this program always generates the right
> InChI and InChI keys, without needing any extra options.
>
> For those who use the system as a library, again, the default
> arguments should be correct, and the documentation and release notes
> say what needs to be done to get old behavior.
>
> Anyway, I pointed out Igor's message, quoted above, and we tried out
> the options mentioned.  The "/FixedH" option causes some problems
> when using the InChiKey with ChemSpider.  ChemSpider does not use the
> "/FixedH" option, so
>
> InChI=1/C8H7Cl2NO3/c9-4-1-5(10)7(2-6(4)11)14-3-8(12)13/h1-2H,3,1=
>
> not FixedH - InChIKey=VMNPETQUBQUXAP-UHFFFAOYAG
>  FixedH    - InChIKey=VMNPETQUBQUXAP-XWKXFZRBCY
>
> If you do the search at http://www.chemspider.com/Search.aspx then
> you'll find that the first option (which does not use /FixedH) gets a
> hit for ChemSpider ID: 71702, while the second option (with /FixedH)
> finds nothing.
>
> Because we want to support links to ChemSpider we decided to not use
> the recommended /FixedH option.
>
> This isn't necessarily a problem in InChIKeys per se.  This is more a
> problem of knowing how to use the keys, and how to generate them, and
> how to search using them.  This information about best practices
> isn't published anywhere that I know of, and what little there is,
> like the quoted email, seems to contract what others are doing.
>
> Is such a document available?
>
> I also note that the "/Fnud" is for 1.02 and the current version is
> only 1.02beta.  Is there any timeline for when the bug fix will be
> available?
>
> While I'm here, I notice that the official InChI page is redirected to
>   http://old.iupac.org/inchi/
> Is this still the official web site or does "old" mean there's a new
> page somewhere?
>
>                                Andrew
>                                da...@da...
>
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> InChI-discuss mailing list
> InC...@li...
> https://lists.sourceforge.net/lists/listinfo/inchi-discuss
>