[Dock-fans] DOCK output files - Conformer clusters?

Scott Brozell sbrozell at scripps.edu
Wed Apr 9 15:37:29 PDT 2008


The cluster membership for the conformers is not saved and
has never been emitted.  We have added this to the todo list.


On Mon, 7 Apr 2008, Scott Brozell wrote:

> On Wed, 2 Apr 2008, Christian Schudoma wrote:
> > the DOCK output files NAME_scored.mol2 contain a record "Cluster size" 
> > for each scored position/cluster.
> Yes this file contains the clusterheads.
> http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFileOutput
> > Is there any way to find out which conformer belongs to which cluster 
> > (except re-clustering it manually of course)? They don't seem to be 
> > sorted by their cluster-"membership" and there are no indices or such in 
> > the conformers output (i.e. NAME_conformers.mol2)
> Apparently not.
> *_conformers.mol2 is ranked by score even if rank*_ligands is no.
> I have forwarded this to the developers responsible for clustering
> for comment.

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