add get_ladders() function

src/dssp.py

@@ -19,3 +19,5 @@ else:
     get_helix(pdb_file.residues, turns)
     get_bends(pdb_file.residues)
     get_chirality(pdb_file.residues)
+    bridges = get_bridges(pdb_file.residues)
+    get_ladders(bridges)

src/structure.py

@@ -36,7 +36,7 @@ def get_turns(residues):
     return(turns)
 
 def get_bridges(residues):
-    bridges = []
+    bridges = {}
     bridge = {}
     strongest_bridge = {}
     for i in range(1,len(residues)-4):
@@ -102,9 +102,9 @@ def get_bridges(residues):
                     bridge = {}
         # finally add the strongest bridge at i and j pos
         if(strongest_bridge):
-            bridges.append(Bridge(strongest_bridge['btype'],
+            bridges[strongest_bridge['ipos']] = (Bridge(strongest_bridge['btype'],
                                   strongest_bridge['ipos']))
-            bridges.append(Bridge(strongest_bridge['btype'],
+            bridges[strongest_bridge['jpos']] = (Bridge(strongest_bridge['btype'],
                                   strongest_bridge['jpos']))
     if(len(bridges)>0):
         return(bridges)
@@ -129,15 +129,26 @@ def get_helix(residues, turns):
             i+=1
     return(helix)
 
-def get_ladder(bridges):
+def get_ladders(bridges):
     ladders = {}
-    for i in range(len(bridges)):
+    i = 1
+    while i < len(bridges):
         k = 1
-        while bridges[i] == bridges[i+k]:
+        while (((i in bridges.keys()) and (i+k in bridges.keys())) and
+        (bridges[i].bridge_type == bridges[i+k].bridge_type)):
             k+=1
         if k>1:
             ladders[bridges[i].res_num] = k-1
+            print("ladder", bridges[i].res_num, bridges[i+k-1].res_num)
+            ladders[bridges[i].res_num] = {'start':bridges[i].res_num,
+                                           'end':bridges[i+k-1].res_num}
+            i+=k-1
+        else:
+            i+=1
+     return ladders
+ 
 
+                
 def get_bends(residues):
     bends = {}
     for i in range(2,len(residues)-2):
@@ -229,11 +240,11 @@ def get_chirality(residues):
         
         if(angle>0 and angle<=180):
             sign="+"
-            print("angle", residues[i].resid, "+", angle)
+            print("chirality", residues[i].resid, "+", angle)
             
         if(angle<=0 and angle > -180):
             sign="-"
-            print("angle", residues[i].resid, "-", angle)
+            print("chirality", residues[i].resid, "-", angle)
             
         chirality[residues[i].resid] = sign