display helix

src/atom.py

@@ -167,8 +167,8 @@ class Residue:
             return False
         
         if(self.get_turns(residues) and residues[i-1].get_turns(residues)):
-            print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].resid)
-            return(self.get_turns(residues).turn_type, residues[i].resid)
+            #print(self.get_turns(residues).turn_type,"- HELIX at", residues[i].indice)
+            return(self.get_turns(residues).turn_type, residues[i].indice)
         return(False)
 
     def get_ladder(self, residues):
@@ -470,14 +470,38 @@ def build_turns_patterns(residues):
             for k in range(turn.turn_type):
                 if turn.turn_type == 3:
                     turns_3[i+1+k] = turn.turn_type
-                    #print(i+1+k, turn.turn_type)
                 if turn.turn_type == 4:
                     turns_4[i+1+k] = turn.turn_type
-                    #print(i+1+k, turn.turn_type)
                 if turn.turn_type == 5:
                     turns_5[i+1+k] = turn.turn_type
     return[turns_3, turns_4, turns_5]
 
+def build_helix_patterns(residues):
+    helix_3 = {}
+    helix_4 = {}
+    helix_5 = {}
+    for i,res in enumerate(residues):
+        helix = residues[i].get_helix(residues)
+        if(helix):
+            helix_type = residues[i].get_helix(residues)[0]
+            helix_pos = residues[i].get_helix(residues)[1]
+            #print("TYPE", helix_type)
+            for k in range(helix_type):
+                if helix_type == 3:
+                    helix_3[i+1+k] = "G"
+                if helix_type == 4:
+                    helix_4[i+1+k] = "H"
+                if helix_type == 5:
+                    helix_5[i+1+k] = "I"
+        #print(helix_3)
+    return[helix_3, helix_4, helix_5]
+
+def print_helix_pattern(residues, res, helix):
+    i = residues.index(res)+1
+    if i in helix.keys():
+        return (helix[i])
+    else:
+        return(' ')
 
 def print_turn_pattern(residues, res, turns):
     i = residues.index(res)+1

src/dssp.py

@@ -59,11 +59,10 @@ residues = pdb_file.residues
 bridges = get_bridges(residues)
 ladders = get_ladders(bridges, residues)
 sheets = get_sheets(ladders)  
-
+helix = build_helix_patterns(residues)
 # iterating over residues
 for i,res in enumerate(residues):
     #res.get_turns(residues, turns)
-    #res.get_helix(residues)
     kappa = res.get_bends(residues)[0]
     bend_symbol = res.get_bends(residues)[1]
     t_co = res.get_tco(residues)
@@ -78,5 +77,10 @@ for i,res in enumerate(residues):
     turn_3 = print_turn_pattern(residues, res, turns[0])
     turn_4 = print_turn_pattern(residues, res, turns[1])
     turn_5 = print_turn_pattern(residues, res, turns[2])
-    print(i+1, res.resid, res.chain_id, res.res_letter, turn_3, turn_4, turn_5, bend_symbol, chirality, round(t_co, 3), round(kappa,1),
-          round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1))
+
+    helix_3 = print_helix_pattern(residues, res, helix[0])
+    helix_4 = print_helix_pattern(residues, res, helix[1])
+    helix_5 = print_helix_pattern(residues, res, helix[2])
+    
+    print(i+1, res.resid, res.chain_id, res.res_letter, helix_3, helix_4, helix_5, turn_3, turn_4, turn_5, bend_symbol, chirality, round(t_co, 3), round(kappa,1),
+           round(alpha, 1), round(phi, 1), round(psi,1), round(x_ca,1), round(y_ca,1), round(z_ca,1))

src/structure.py

@@ -24,8 +24,8 @@ class Bridge(Structure):
 
 class Helix(Structure):
 
-    def __init__(self, residues, res_num):
+    def __init__(self, residues, res_num, helix_type):
         self.residues = residues
         self.res_num = res_num
         Structure.res = res_num
- 
+        self.helix_type = helix_type