Subject: Re: GOLD ouput files filtering

From: Jason Cole <[email-masked]>
Date: Thu, 28 Mar 2002 10:47:52 +0000

Hi Yogesh,

Glad to hear that you like the program.

Unfortunatly, there is no easy way from within gold to minimise the
overall output that it produces. What you see is what you get. Most of
our users write wrapper scripts to achieve this, that read the files as
they are produced and delete those that they dont want. This has the
advantage of allowing flexibility in selection - a user is able to
select docked solutions on the basis of properties unrelated to golds
own scoring function, which can be specific to a particular system.

Your question is, however, probably one of the more common development
requests that we get for gold. It poses one difficult issue; what to
throw away? Different users have different requirements  - some would
like to save all information for the best N dockings, some would like to
only save the top ranked solution for all dockings. Others would just
like to save everything but in a compressed format rather than the
current rather verbose format that gold uses - this is necessary for
re-ranking for example.

I'd value any feedback on this issue, form any user of Gold who has this
problem - what would users prefer? Also, what do users extract from the
various log files in GOLD, that could be condensed down into a more
compact format? Would a set of 'stub' example scripts written in python
or perl be useful?

Jason
CCDC