fix: solve conflict issue between pdbqual and setup config parameters

aria/conbox/conf/config.ini

@@ -36,7 +36,7 @@ default_cutoff:                             8.0
 ;ca_ca:
 ;cb_cb:
 ;sc_sc:
-bool
+
 [setup]
 ; ------------------------------ TBL parameters ------------------------------ #
 ; longrange_hb                  : True, False [False]
@@ -209,7 +209,7 @@ prosa_enabled:                              yes
 whatif_executable:
 whatif_enabled:                             yes
 clashlist_executable:
-clahlist_enabled:                           no
+clashlist_enabled:                           no
 pickle_output:                              no
 ; --------------------------- Iteration parameters --------------------------- #
 ; /!\ Parameters below can be formatted as a list if we want different values
@@ -266,7 +266,6 @@ L:
 
 [pdbqual]
 trash_directory:                            /tmp
-prosa:                                      False
 skip_prefix:                                fitted
 csh_executable:                             csh
 

aria/conbox/pdbqual.py

@@ -32,15 +32,15 @@ class AriaEcPdbqual(CommandProtocol):
         runChecks(
             workingDirectory=self.settings.pdbqual["output_directory"],
             trashDirectory=self.settings.pdbqual["trash_directory"],
-            procheckExe=self.settings.main.get("procheck_executable", "procheck"),
-            procheckOnOff=1 if self.settings.main.get("procheck_enabled", "no") in ("yes", True, "True") else 0,
-            whatIfExe=self.settings.main.get("whatif_executable", "whatif"),
-            whatifOnOff=1 if self.settings.main.get("whatif_enabled", "no") in ("yes", True, "True") else 0,
-            clashlistExe=self.settings.main.get("clashlist_executable", "clashlist"),
-            clashlistOnOff=1 if self.settings.main.get("clashlist_enabled", "no") in ("yes", True, "True") else 0,
-            prosaExe=self.settings.main.get("prosa_executable", "prosa"),
-            prosaOnOff=1 if self.settings.pdbqual.get("prosa_enabled", "no") in ("yes", True, "True") else 0,
-            cshExe=self.settings.pdbqual.get("csh_executable", "csh"),
+            procheckExe=self.settings.setup["procheck_executable"],
+            procheckOnOff=1 if self.settings.setup["procheck_enabled"] in ("yes", True, "True") else 0,
+            whatIfExe=self.settings.setup["whatif_executable"],
+            whatifOnOff=1 if self.settings.setup["whatif_enabled"] in ("yes", True, "True") else 0,
+            clashlistExe=self.settings.setup["clashlist_executable"],
+            clashlistOnOff=1 if self.settings.setup["clashlist_enabled"] in ("yes", True, "True") else 0,
+            prosaExe=self.settings.setup["prosa_executable"] if self.settings.main["prosa_executable"] else "",
+            prosaOnOff=1 if self.settings.setup["prosa_enabled"] in ("yes", True, "True") else 0,
+            cshExe=self.settings.pdbqual["csh_executable"],
             howManyPdb=len(self.settings.pdbqual["infiles"]),
             verbose=1,
             fileList=self.settings.pdbqual["infiles"],