fix: add debug log message in ssclash

aria/conbox/protmap.py

@@ -2184,7 +2184,9 @@ class MapFilter(object):
 
         start_list = [ss_start_end[elm][0] for elm in ss_start_end]
         end_list = [ss_start_end[elm][1] for elm in ss_start_end]
-
+        LOG.debug("Checking secondary structures clashes for contact list {0} "
+                  "with secondary structure list {1}".format(str(contact_list),
+                                                             str(ss_list)))
         for icontact, contact in enumerate(contact_list):
             # For each res-res contact
             outcontact = str(hum_contact(contact))

docs/usage.rst

@@ -107,7 +107,7 @@ Translate contact maps as distance restraints and setup ARIA infrastructure.
 +--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``-d DISTFILE``, ``--distfile DISTFILE``               | Pdb or distance matrix iif distance_type set to distfile in conf file, use distances in the given file as target distance to build distance restraints                                                                                                                                                                                                                                                                                                                                                                  |
 +--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| ``-s SSPRED``, ``--ssfile SSPRED``                     | Secondary structure prediction file                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |
+| ``-s SSPRED``, ``--ssfile SSPRED``                     | Secondary structure prediction file. Supported formats are psipred, psipred2, psipred3, ss2 and indextableplus                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
 +--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | ``-p ARIAPROJECT``, ``--ariaproject ARIAPROJECT``      | ARIA project file. This project will be updated with data generated during the ``ariaec setup`` call                                                                                                                                                                                                                                                                                                                                                                                                                    |
 +--------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+