[BioPython] SD/MDL file parser

[Andrew Dalke]

Hi Noel,

> The whole frowns system is a bit overkill for simple manipulations of 
> SD
> fields. I am planning to cannabalise the mdl parser and writer of 
> frowns
> to make it more straightforward for myself. Thanks for the heads up
> regarding multiple fields, though.

The question is, what's overkill and what's not?  If you only
want the SD data then you can leave the connection table as an
unprocessed blob of text.  In that case a parse is about 25 lines
of code.

> I'll probably see you there so, as I'll be attending.

I'll see you then in a couple of weeks.

> Is it possible/worthwhile to write a parser using Martel? Or would you
> say that there are too many non-standard sd files out there for a 
> single
> parser to have general applicability?

When I wrote Martel I tested against an SD file ... and an
RXN file, and a molfile.  Somewhere is a Martel expression for
those formats.  It's not on this laptop so I need to check my
older one.  That's home in Santa Fe and I can't log into that
machine now since I'm traveling.  If you can dig up an old
Martel distribution (pre-Biopython integration) you might
be able to get ahold of it.

I don't think the diversity of an SD file format is that
large.  After all, many programs have SD file readers and
I don't hear anywhere near as many problems as with supporting,
say, the PDB format.

Still, if you only need the SD data reader then it isn't too
hard to do yourself, and there are few ways to make subtle
mistakes.

					Andrew
					dalke at dalkescientific.com