Genetic codes and other repeated ACD lists

Dr J.C. Ison jison at
Fri Apr 8 11:46:43 UTC 2005

Peter Rice wrote:

> Thanks. Domainatrix I assume. Which ones? I will take a look and see how they
> fit in.

The newly committed matgen3d and siggenlig, which both take an "environment 
definition" (amino acid 3D environment) from a list.

At the moment, the environemnts names are "Env1", "Env2" etc but would get more 
meaningful names once the definitions themselves are more settled (pending 
further research on which ones are most useful).

The progs. then use the selection (Env1 or Env2 etc) to call appropriate functions
within the application code.

> > I think it would be nice to support both "standard" lists (ie. ones *with* "values"
> > attribute) and the new style.  Perhaps something like:
> >
> >       values: "@knowntype"
> A missing value will do this. Normally the value is required, so an ACD
> developer (or parser) will know it needs a value. (I hope :-)

They could simply acdprettyify the files as described in your prev. email 
before parsing, so they wouldn't need to do any new coding.

> > to indicate to use the knowntype to get the values, *or*
> >
> >       values: "0: Standard ... etc" as before.
> Yes, that will override the knowntype. Maybe acdvalid can warn if a list or
> select has a knowntype (with its own standadr value) and a defined value attribute

The override / warning are intuitive / sensible.

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