[Swift-commit] r2782 - in SwiftApps/LigandAtlas: . dock

[noreply at svn.ci.uchicago.edu]

Author: zzhang
Date: 2009-03-30 11:47:51 -0500 (Mon, 30 Mar 2009)
New Revision: 2782

Added:
   SwiftApps/LigandAtlas/dock/
   SwiftApps/LigandAtlas/dock/dock6.swift
   SwiftApps/LigandAtlas/dock/dock7.swift
Log:
swift script on BGP



Added: SwiftApps/LigandAtlas/dock/dock6.swift
===================================================================
--- SwiftApps/LigandAtlas/dock/dock6.swift	                        (rev 0)
+++ SwiftApps/LigandAtlas/dock/dock6.swift	2009-03-30 16:47:51 UTC (rev 2782)
@@ -0,0 +1,97 @@
+type Mol {}
+type Bin {}
+type Common {}
+type DOCKOut {}
+type Molout{}
+type DockRunSummary {}
+type file {}
+
+(external bout)bcast (Bin binary, Common flex_def, Common flex_tbl, Common grid_bmp, Common
+grid_in, Common grid_nrg, Common grid_out, Common rec_box, Common receptor,
+Common sample_grid, Common selected_spheres, Common template_in, Common vdw,
+Common awkscript)
+{
+        app {
+            bcast @filename(binary)  @filename(flex_def)
+            @filename(flex_tbl) @filename(grid_bmp) @filename(grid_in)
+            @filename(grid_nrg) @filename(grid_out) @filename(rec_box)
+            @filename(receptor) @filename(sample_grid)
+	    @filename(selected_spheres)
+            @filename(template_in) @filename(vdw) @filename(awkscript);
+        }
+}
+
+/*app (DOCKOut ofile, Molout moloutfile) rundock_zhao (Mol molfile, Bin binary, Common flex_def, Common
+flex_tbl, Common grid_bmp, Common grid_in, Common grid_nrg, Common grid_out,
+Common rec_box, Common receptor, Common sample_grid, Common selected_spheres,
+Common template_in, Common vdw, Common awkscript)*/
+
+app (DOCKOut ofile) rundock_zhao (Mol molfile, Bin binary, Common flex_def, Common
+flex_tbl, Common grid_bmp, Common grid_in, Common grid_nrg, Common grid_out,
+Common rec_box, Common receptor, Common sample_grid, Common selected_spheres,
+Common template_in, Common vdw, Common awkscript, external bout)
+{
+   rundock_zhao @filename(molfile) @filename(binary) @filename(flex_def)
+   @filename(flex_tbl) @filename(grid_bmp) @filename(grid_in)
+   @filename(grid_nrg) @filename(grid_out) @filename(rec_box)
+   @filename(receptor) @filename(sample_grid) @filename(selected_spheres)
+   @filename(template_in) @filename(vdw) @filename(awkscript) stdout=@filename(ofile);
+}
+
+app (DockRunSummary finalfile) sumdockresults(DOCKOut r[] )
+{
+   summary @filenames(r) stdout=@filename(finalfile);
+}
+
+
+Mol texts[] <filesys_mapper;location="input/", suffix=".mol2">;
+//Mol texts[] <filesys_mapper;suffix=".mol2">;
+
+
+(DOCKOut result[])doall(Mol texts[])
+{
+  Bin binary <"common/dock6.O3.cn">;
+  Common flex_def <"common/flex.defn">;
+  Common flex_tbl <"common/flex_drive.tbl">;
+  Common grid_bmp <"common/grid.bmp">;
+  Common grid_in <"common/grid.in">;
+  Common grid_nrg <"common/grid.nrg">;
+  Common grid_out <"common/grid.out">;
+  Common rec_box <"common/rec_box.pdb">;
+  Common receptor <"common/receptor_charged.mol2">;
+  Common sample_grid <"common/sample_grid.in">;
+  Common selected_spheres <"common/selected_spheres.sph">;
+  Common template_in <"common/template.in">;
+  Common vdw <"common/vdw_AMBER_parm99.defn">;
+  Common awkscript <"common/awkscript">;
+
+  external bout;
+
+  bout=bcast(binary, flex_def, flex_tbl, grid_bmp, grid_in, grid_nrg, grid_out, rec_box, receptor, sample_grid, selected_spheres, template_in, vdw, awkscript);
+
+  foreach p,i in texts {
+    /*DOCKOut r <regexp_mapper;  
+             source=@p,  
+             match="input/(.*)\\.mol2",  
+             transform="result/\\1.out"  
+    >;*/
+    
+    /*Molout mof <regexp_mapper;  
+             source=@p,  
+             match="input/(.*)\\.mol2",  
+             transform="result/\\1.mol2.scored"  
+    >;*/
+
+  result[i] = rundock_zhao(p, binary, flex_def, flex_tbl, grid_bmp, grid_in,
+  grid_nrg, grid_out, rec_box, receptor, sample_grid, selected_spheres, template_in, vdw, awkscript, bout);
+  }
+
+  
+}
+ 
+// Main
+
+DockRunSummary summary <"summary.txt">;
+DOCKOut result[];
+result=doall(texts);
+summary = sumdockresults(result);

Added: SwiftApps/LigandAtlas/dock/dock7.swift
===================================================================
--- SwiftApps/LigandAtlas/dock/dock7.swift	                        (rev 0)
+++ SwiftApps/LigandAtlas/dock/dock7.swift	2009-03-30 16:47:51 UTC (rev 2782)
@@ -0,0 +1,91 @@
+type Mol {}
+type Bin {}
+type Common {}
+type DOCKOut {}
+type Molout{}
+type DockRunSummary {}
+type file {}
+
+(external bout)bcast (Bin binary, Common flex_def, Common flex_tbl, Common grid_bmp, Common
+grid_in, Common grid_nrg, Common grid_out, Common rec_box, Common receptor,
+Common sample_grid, Common selected_spheres, Common template_in, Common vdw,
+Common awkscript)
+{
+        app {
+            bcast @filename(binary)  @filename(flex_def)
+            @filename(flex_tbl) @filename(grid_bmp) @filename(grid_in)
+            @filename(grid_nrg) @filename(grid_out) @filename(rec_box)
+            @filename(receptor) @filename(sample_grid)
+	    @filename(selected_spheres)
+            @filename(template_in) @filename(vdw) @filename(awkscript);
+        }
+}
+
+app (DOCKOut ofile, Molout moloutfile) rundock_zhao (Mol molfile, Bin binary,
+Common flex_def, Common flex_tbl, Common grid_bmp, Common grid_in, Common
+grid_nrg, Common grid_out, Common rec_box, Common receptor, Common sample_grid, Common selected_spheres,
+Common template_in, Common vdw, Common awkscript, external bout)
+{
+   rundock_zhao @filename(molfile) @filename(binary) @filename(flex_def)
+   @filename(flex_tbl) @filename(grid_bmp) @filename(grid_in)
+   @filename(grid_nrg) @filename(grid_out) @filename(rec_box)
+   @filename(receptor) @filename(sample_grid) @filename(selected_spheres)
+   @filename(template_in) @filename(vdw) @filename(awkscript) stdout=@filename(ofile);
+}
+
+app (DockRunSummary finalfile) sumdockresults(DOCKOut r[] )
+{
+   summary @filenames(r) stdout=@filename(finalfile);
+}
+
+
+Mol texts[] <filesys_mapper;location="input/", suffix=".mol2">;
+//Mol texts[] <filesys_mapper;suffix=".mol2">;
+
+
+(DOCKOut result[])doall(Mol texts[])
+{
+  Bin binary <"common/dock6.O3.cn">;
+  Common flex_def <"common/flex.defn">;
+  Common flex_tbl <"common/flex_drive.tbl">;
+  Common grid_bmp <"common/grid.bmp">;
+  Common grid_in <"common/grid.in">;
+  Common grid_nrg <"common/grid.nrg">;
+  Common grid_out <"common/grid.out">;
+  Common rec_box <"common/rec_box.pdb">;
+  Common receptor <"common/receptor_charged.mol2">;
+  Common sample_grid <"common/sample_grid.in">;
+  Common selected_spheres <"common/selected_spheres.sph">;
+  Common template_in <"common/template.in">;
+  Common vdw <"common/vdw_AMBER_parm99.defn">;
+  Common awkscript <"common/awkscript">;
+
+  external bout;
+
+  bout=bcast(binary, flex_def, flex_tbl, grid_bmp, grid_in, grid_nrg, grid_out, rec_box, receptor, sample_grid, selected_spheres, template_in, vdw, awkscript);
+
+  foreach p,i in texts {
+    /*DOCKOut r <regexp_mapper;  
+             source=@p,  
+             match="input/(.*)\\.mol2",  
+             transform="result/\\1.out"  
+    >;*/
+    
+    Molout mof <regexp_mapper;  
+             source=@p,  
+             match="input/(.*)\\.mol2",  
+             transform="result/\\1.mol2.scored"  
+    >;
+
+  (result[i], mof) = rundock_zhao(p, binary, flex_def, flex_tbl, grid_bmp, grid_in, grid_nrg, grid_out, rec_box, receptor, sample_grid, selected_spheres, template_in, vdw, awkscript, bout);
+  }
+
+  
+}
+ 
+// Main
+
+DockRunSummary summary <"summary.txt">;
+DOCKOut result[];
+result=doall(texts);
+summary = sumdockresults(result);