Cleaned up getScores.tcsh.

src/MolecularDockingKit/getScores.tcsh

@@ -1,23 +1,33 @@
 #!/bin/tcsh
 
-#################################################################
-#                                                               #
-# This script extracts the docking scores for all the drugs and #
-# sorts them.                                                   #
-#                                                               #
-#################################################################
+###################################################################
+#                                                                 #
+# This script extracts the docking scores for all the drugs and   #
+# sorts them.                                                     #
+#                                                                 #
+###################################################################
 
+# Remove existing allScores.txt file
 rm -f allScores.txt
 
+# Navigate to the rDock_inputs directory
 cd rDock_inputs/
-  foreach mol(`cat ../moleculeLists/fileList.txt | xargs`)
+
+# Loop through each molecule in the fileList.txt
+foreach mol (`cat ../moleculeLists/fileList.txt | xargs`)
     cd $mol
-      set score = `grep -iwA1 "<SCORE>" "$mol"_docking_out_sorted.sd | tail -1`
-      echo "$mol $score" >> ../../allScores.txt
+
+    # Extract the docking score for the current molecule
+    set score = `grep -iwA1 "<SCORE>" "${mol}_docking_out_sorted.sd" | tail -1`
+
+    # Write the molecule name and its score to allScores.txt
+    echo "$mol $score" >> ../../allScores.txt
+
     cd ..
-  end
+end
+
+# Navigate back to the main directory
 cd ..
 
+# Sort the allScores.txt file based on the docking scores and save it to sorted_allScores.txt
 sort -k2g allScores.txt > sorted_allScores.txt
-
-