Re: [Cdk-devel] MDL Tech Support question on bond type = 4

[Rich A. <rap...@oc...>]

On Mon, 8 Aug 2005 12:53:25 -0400 (EDT), Miguel wrote
> > The response from MDL seemed pretty clear: the molfile V2000 specification
> > is
> > typographically correct and MDL registration software will accept only
> > those
> > V2000 molfiles containing bond types 1, 2, and 3.
> 
> Rich,
> 
> Good job for being tenacious and pursuing this.

Thanks. This particular issue might seem relatively unimportant, but I think
the bigger issue is the process by which we, as developers, translate written
specifications into software. I think it also highlights the critical
importance that detailed written specifications play in ensuring conformance.

> Personally, I am still skeptical of the response from MDL.

Me too, but other than the written specification and its interpretation by MDL
representatives and MDL software, what else can we go on? MDL is the owner,
curator, and arbiter of the specification.

> I have never used any MDL software, nor any other commerical 
> chemistry software for that matter. And I don't know what 
> 'registration' means ... and I do not know what an 'SSS' query is. 
> So my opinion is not worth too much. Given that caveat:

I interpret "registration" to mean submission of a concrete molecular
structure to a database application for later retrieval by a query mechanism.
"SSS" stands for "Substructure Search".

> Therefore, I continue to choose to believe that
>  * values 1 through 4 represent legitimate/valid data values in the
> underlying data
>  * values 1 through 8 represent query specification for some type of
> substructure querying system that they have
>  * values 5 through 8 are wildcard specifications that only make 
> sense in the context of a query

This is a difficult issue because clearly good software has been written that
takes this point of view. I do believe there is a big difference between
software that reads bond order = 4 in the context of a concrete molecule, and
software that writes it. The latter is much more important if interoperability
with other software is the goal.

cheers,
rich