[Swift-commit] r4840 - SwiftApps/modFTDock

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2011-07-25 14:49:17 -0500 (Mon, 25 Jul 2011)
New Revision: 4840

Added:
   SwiftApps/modFTDock/modftdock-3stages.swift
Log:
Added modftdock 3 stages script

Added: SwiftApps/modFTDock/modftdock-3stages.swift
===================================================================
--- SwiftApps/modFTDock/modftdock-3stages.swift	                        (rev 0)
+++ SwiftApps/modFTDock/modftdock-3stages.swift	2011-07-25 19:49:17 UTC (rev 4840)
@@ -0,0 +1,95 @@
+type file_pdb;
+type file_dat;
+type file_exe;
+type file_score;
+
+app (file_dat dat_file)
+do_one_dock
+( string        param_root,
+  string        param_modulo,
+  file_pdb param_file_static,
+  file_pdb param_file_mobile )
+{
+	modftdock 32
+		"-modulo" @param_modulo
+		"-root"   @param_root
+		"-static" @param_file_static
+		"-mobile" @param_file_mobile
+		"-calculate_grid" @arg("grid","2.5")
+		"-angle_step" "10"
+		"-keep" "10"
+		"-noelec";
+}
+
+app (file_dat o) read_dat (file_dat j[]){
+	cat @filenames(j) stdout=@o;
+}
+
+app (file_dat o) do_the_merge (string in_dir, string wild_card, file_dat sync[]){
+	do_merge in_dir wild_card stdout=@o;
+}
+
+app (file_score s) scoreit (file_exe param_distances_exe,
+                            file_exe param_eval_exe,
+                            file_dat param_merged_dat,
+                            file_exe param_tRNA_score_exe){
+
+///tmp/scoredat.exe /tmp/distances300r.exe /tmp/eval300.exe /tmp/${1}.dat  /tmp/tRNA_score.exe > /tmp/${1}.res
+      score @param_distances_exe @param_eval_exe @param_merged_dat @param_tRNA_score_exe stdout=@s;
+}
+
+string modulus = @arg("m","100");
+string str_roots[] = readData( @arg( "list" ) );
+
+
+foreach str_root, pid in str_roots
+{
+	trace( str_root );
+
+	string str_file_static = @strcat( "input/", str_root, ".pdb" );
+	string str_file_mobile = "input/4TRA.pdb";
+
+	file_pdb file_static < single_file_mapper; file = str_file_static >;
+	file_pdb file_mobile < single_file_mapper; file = str_file_mobile >;
+
+	file_dat dat_files[] < simple_mapper;
+		padding = 3,
+		location = "output",
+		prefix  = @strcat( str_root, "_" ),
+		suffix  = ".dat" >;
+	
+	file_dat merged_file[] < simple_mapper;
+		location = "merged_data",
+		prefix  = str_root,
+		suffix  = ".dat" >;
+
+	file_score score_file[] < simple_mapper;
+		location = "score_data",
+		prefix  = str_root,
+		suffix  = ".res" >;
+
+	int n = @toint(@arg("n","1"));
+	// break docking jobs + do 'em in parallel
+	foreach mod_index in [0:n-1] {
+		string str_modulo = @strcat(mod_index, ":", modulus);
+		dat_files[ mod_index ] = do_one_dock( str_root,
+				str_modulo,
+				file_static,
+				file_mobile );
+	}
+
+//	file_dat out_files[];
+
+        merged_file[pid]=do_the_merge("output/", @strcat(str_root, "_???.dat"), dat_files); //dat_files used for synchronization
+        
+        string str_file_distances_exe = "app/Scoring/distances300r.exe";
+        string str_file_eval_exe = "app/Scoring/eval300.exe";
+        string str_file_tRNA_score_exe = "app/Scoring/tRNA_score.exe";
+
+	file_exe file_distances_exe < single_file_mapper; file = str_file_distances_exe >;
+	file_exe file_eval_exe < single_file_mapper; file = str_file_eval_exe >;
+	file_exe file_tRNA_score_exe < single_file_mapper; file = str_file_tRNA_score_exe >;
+
+        score_file[pid]=scoreit(file_distances_exe, file_eval_exe, merged_file[pid], file_tRNA_score_exe); 
+}
+