Fixing ladder discovery

src/dssp.py

@@ -25,9 +25,9 @@ else:
     get_helix(pdb_file.residues, turns)
     # get_bends(pdb_file.residues)
     # get_chirality(pdb_file.residues)
-    # bridges = get_bridges(pdb_file.residues)
-    # ladders = get_ladders(bridges)
-    # get_sheets(ladders)
+    bridges = get_bridges(pdb_file.residues)
+    ladders = get_ladders(bridges, pdb_file.residues)
+    get_sheets(ladders)
 
     # print("NBRIDGES",len(bridges))
 

src/structure.py

@@ -83,14 +83,15 @@ def get_bridges(residues):
                     E_min = bridge['res1']+bridge['res2']
                     strongest_bridge = bridge
                     bridge = {}
+                    coord_bridge = [i,j]
         # finally add the strongest bridge at i and j pos
         if(strongest_bridge):
-            bridges[strongest_bridge['ipos']] = (Bridge(strongest_bridge['btype'],
+            bridges[coord_bridge[0]] = (Bridge(strongest_bridge['btype'],
                                                         strongest_bridge['ipos'],
                                                         strongest_bridge['jpos']))
-            # bridges[strongest_bridge['jpos']] = (Bridge(strongest_bridge['btype'],
-            #                                             strongest_bridge['jpos'],
-            #                                             strongest_bridge['ipos']))
+            bridges[coord_bridge[1]] = (Bridge(strongest_bridge['btype'],
+                                                        strongest_bridge['jpos'],
+                                                        strongest_bridge['ipos']))
     if(len(bridges)>0):
         return(bridges)
     else:
@@ -143,7 +144,7 @@ def get_helix(residues, turns):
             while(i+k in turns):
                 k+=1
                 temp_res.append(residues[i])
-            if(k>2):
+            if(k>=1):
                 print(k,"- HELIX at", residues[i].resid)
                 helix.append(Helix(temp_res,residues[i].resid))
             i = i+k
@@ -151,10 +152,10 @@ def get_helix(residues, turns):
             i+=1
     return(helix)
 
-def get_ladders(bridges):
+def get_ladders(bridges, residues):
     ladders = {}
     i = 1
-    while i < len(bridges):
+    while i < len(residues):
         k = 1
         if i in bridges.keys():
             temp_bridges = [bridges[i]]
@@ -163,9 +164,9 @@ def get_ladders(bridges):
                 temp_bridges.append(bridges[i+k])
                 k+=1
         if k>1:
-            ladders[bridges[i].res_num] = k-1
+            ladders[i] = k-1
             print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
-            ladders[bridges[i].res_num] = {'start':bridges[i].res_num,
+            ladders[i] = {'start':bridges[i].res_num,
                                            'end':bridges[i+k-1].res_num,
                                            'bridges':temp_bridges}
             i+=k-1
@@ -180,14 +181,15 @@ def get_sheets(ladders):
     Iterate over all residues of one ladder and check if bridge with other residues
     of the other ladders.
     """
-
+    sheets = {}
     for ladder in ladders:
-        for bridge in ladders[ladder]['bridges']:
-            for ladd2 in ladders:
+        for ladd2 in ladders:
+            for bridge in ladders[ladder]['bridges']:
                 if bridge.res_partner in res_list(ladders[ladd2]):
                     print("ladder",ladders[ladder]['start'], ladders[ladder]['end'],"bridge",bridge.res_num, bridge.res_partner,
                     "ladder 2",ladders[ladd2]['start'], ladders[ladd2]['end'])
-                
+            #print("stop ladder 2")
+        print("stop ladder 1")            
 
 def res_list(ladder):
     # TODO : method in ladder class