check to handle missing I/O/P dirs if drug unset

foldx/runFoldx.py

@@ -73,6 +73,14 @@ pdb_filename = args.pdb_file
 # Just the filename, thanks
 #pdb_name = Path(in_filename_pdb).stem
 
+
+# Handle the case where neither 'drug' 
+# nor (indir,outdir,process_dir) are defined
+if not drug:
+    if not indir or not outdir or not process_dir:
+        print('ERROR: if "drug" is not specified, you must specify Input, Output, and Process directories')
+        sys.exit()
+
 #==============
 # directories
 #==============
@@ -80,8 +88,7 @@ if not datadir:
     datadir = homedir + '/' + 'git/Data'
     
 if not indir:
-    indir = 
+    indir = datadir + '/' + drug + '/input'
-    datadir + '/' + drug + '/input'
     
 if not outdir:
     outdir = datadir + '/' + drug + '/output'
@@ -141,6 +148,7 @@ print('Arguments being passed:'
 , '\n=============================================================')
 
 #### Delay for 10 seconds to check the params ####
+print('Sleeping for 10 seconds to give you time to cancel')
 time.sleep(10)
 #=======================================================================