[Swift-commit] r2444 - text/hpdc09submission

[noreply at svn.ci.uchicago.edu]

Author: wilde
Date: 2009-01-14 12:29:43 -0600 (Wed, 14 Jan 2009)
New Revision: 2444

Modified:
   text/hpdc09submission/paper.latex
Log:
Added stub of example for DOCK (from Zhengiong).


Modified: text/hpdc09submission/paper.latex
===================================================================
--- text/hpdc09submission/paper.latex	2009-01-14 18:23:47 UTC (rev 2443)
+++ text/hpdc09submission/paper.latex	2009-01-14 18:29:43 UTC (rev 2444)
@@ -1064,7 +1064,41 @@
 as well as a file containing the minimum value achieved from that model.
 The processing of these models on Ranger was achieved in <45 minutes.
 
+\subsection{Molecular Dynamics with DOCK}
 
+\begin{verbatim}
+(file t,DockOut tarout) dockcompute (DockIn infile, string targetlist) { 
+  app { 
+    rundock @infile targetlist stdout=@filename(t) @tarout; 
+    } 
+} 
+ 
+type params { 
+      string  ligandsfile; 
+      string  targetlist; 
+} 
+ 
+#params pset[] <csv_mapper;file="paramslist.txt">; 
+doall(params pset[]) 
+{ 
+  foreach params,i in pset { 
+  DockIn infile < single_file_mapper; file=@strcat("/home/houzx/dock- 
+run/databases/KEGG_and_Drugs/",pset[i].ligandsfile)>; 
+  file sout <single_file_mapper; file=@strcat("/home/houzx/dock- 
+run/databases/results/stdout/",pset[i].targetlist,"-",i,"-stdout.txt")>; 
+  DockOut tout <single_file_mapper; file=@strcat(pset[i].ligandsfile,"-result.tar.gz")>; 
+#  DockOut tout <"result.tar.gz">; 
+#  sout =  dockcompute(infile,pset[i].targetlist); 
+  (sout,tout) =  dockcompute(infile,pset[i].targetlist); 
+ 
+ } 
+} 
+ 
+params p[]; 
+p = readdata("paramslist.txt"); 
+doall(p); 
+\end{verbatim}
+
 \section{Usage Experience}
 
 \subsection{Use on large numbers of sites in the Open Science Grid}