In a recent message (see below):
Apparently a paragraph from my previous e-mail and a comment to it by Dr P. Murray-Rust became mixed together to such an extent that without a special study it is barely possible to figure out where the comment begins and ends.
Frankly, this makes me feel somewhat uncomfortable.
Probably we need some rules to make the text easily attributable to its author.
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>Subject: [InChI-discuss] Hydrogen atoms
>List-Id: Discussions related to the IUPAC International Chemical Identifier (InChI) <inchi-discuss.lists.sourceforge.net>
>Date: 03 Jul 2005 10:27:59 +0100
>On Jul 3 2005, D. Tchekhovskoi wrote:
>Please find the answers and additional comments below.
>Most probably the creator of the hydrogen-free Ferrocene's InChI provided InChI-1 program with atoms C in cyclopentadienes that have 1 double and 2 single bonds, including a single C-Fe bond. InChI by default uses carbon valence = 4 and cannot tell a single bond from a coordination bond. Therefore it could not add any atom H to such a structure. The creator should have either increased the formal valence of carbons or provided explicit atoms H connected to carbons. Two possibilities of including explicit H in Ferrocene are in the attached Molfiles.
>This emphasizes the danger of using any valence-based methods for adding hydrogens and why I think the community should not use it. In my experience of compound data files there are always some molecules where automatic hydrogen addition has produced garbage, as in this case. it is the responsibility of the submitter of the information to make sure that all hydrogens and charges/radicals are explicit. If InChI (or any other system) is used to add hydrogens it is *certain* that there are compounds which will produce garbage. It is also clear that we need metadata to record what modifications, if any, InChI has made to the initial input - personally I would not accept any InChI where the program had been asked to add hydrogens. This is not a criticism of InChI - it's sumply that chemistry is more complex than can be encapsulated in a program.
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