feat: support ss format

docs/tutorial.rst

@@ -285,10 +285,11 @@ analysis pipeline.
 Contact map analysis
 --------------------
 
-To quickly see several plots and stats related to the reference structure
-or/with the EC contact maps. We can use the ``maplot`` subcommand. The first
-argument in this command will always be set as the reference map/pdb for the
-contact map, ROC or precision-recall plots.
+Aside ConKit_  :abbr:`Command Line Interface CLI)` tools, the
+:ref:`maplot <./usage>` command line has been implemented to show statistics
+between contact maps and the reference which can be a structure in PDB_ format.
+The first argument in this command will always be set as the reference map/pdb
+for the contact map, ROC or precision-recall plots.
 
 
 .. code-block:: console

src/aria/conbox/protein.py

@@ -51,6 +51,7 @@ class SsList(object):
                           r'\s+(?P<h_conf>\d?\.?\d*)'
                           r'\s+(?P<e_conf>\d?\.?\d*)'
                           r'\s+(?P<c_conf>\d?\.?\d*)'),
+        'ss': re.compile(r'^(?P<ss_pred>[HECBTG]+)'),
     }
     # psipred_reg = re.compile(r'^(?P<up_index>\d+)'
     #                          r'\s+(?P<up_residue>[AC-IK-NP-TVWYZ])'
@@ -184,8 +185,18 @@ class SsList(object):
                  filename, sstype)
 
         self.ssdict = reg_load(ssregex, filename)
+
+        # Change the format of the ssdict if we have ss type format
+        if sstype == "ss":
+            tmpdict = {}
+            for sstridx in sorted(self.ssdict.keys()):
+                for ssidx, ss in enumerate(self.ssdict[sstridx]["ss_pred"]):
+                    tmpdict[ssidx + 1] = {"ss_pred": ss}
+            self.ssdict = tmpdict
+
         ss_index_dict = {'H': 1, 'C': 1, 'E': 1}
         for line_id in sorted(self.ssdict.keys()):
+
             # Modif champ ss_pred
             # Si line_id
             if line_id != min(self.ssdict.keys()) and \