From 4cd628fa50fd073a253aeaec85f485e2c5e0c5dd Mon Sep 17 00:00:00 2001
From: Thomas Forest <thomas.forest@etu.univ-paris-diderot.fr>
Date: Sun, 15 Sep 2019 14:47:21 +0200
Subject: [PATCH] Corrected get_bridges func

---
 src/structure.py | 93 ++++++++++++++++++++++++++++++++++++------------
 1 file changed, 70 insertions(+), 23 deletions(-)

diff --git a/src/structure.py b/src/structure.py
index 7cf5a7c..45f11ef 100644
--- a/src/structure.py
+++ b/src/structure.py
@@ -1,13 +1,14 @@
 
 class Turn:
 
-    def __init__(self, turn_type):
+    def __init__(self, turn_type, res_num):
         self.turn_type = turn_type
                         
 class Bridge:
 
-    def __init__(self, bridge_type):
+    def __init__(self, bridge_type, res_num):
         self.bridge_type = bridge_type
+        self.res_num = res_num
 
 class Helix:
 
@@ -20,11 +21,13 @@ def get_turns(residues):
         for j in range(3,6):
             if(i+j<len(residues)):
                 if(res.h_bond(residues[i+j]<-0.5)):
-                    turns.append(Turn(j))
+                    turns.append(Turn(j,i))
     return(turns)
 
 def get_bridges(residues):
     bridges = []
+    bridge = {}
+    strongest_bridge = {}
     for i in range(1,len(residues)-4):
         E_min = 0
         for j in range(i+2,len(residues)-1):
@@ -32,28 +35,72 @@ def get_bridges(residues):
 
             if(residues[i-1].h_bond(residues[j])<-0.5
                and residues[j].h_bond(residues[i+1])<-0.5):
-                if(residues[i-1].h_bond(residues[j])+
-                   residues[j].h_bond(residues[i+1]))<E_min:
-                   E_min = residues[i-1].h_bond(residues[j])
-                   +residues[j].h_bond(residues[i+1])
+                bridge = {'res1':residues[i-1].h_bond(residues[j]),
+                          'res2':residues[j].h_bond(residues[i+1]),
+                          'ipos':i,
+                          'jpos':j,
+                          'btype':"para"}
+                # if(residues[i-1].h_bond(residues[j])+
+                #    residues[j].h_bond(residues[i+1]))<E_min:
+                #    E_min = residues[i-1].h_bond(residues[j])
+                #    +residues[j].h_bond(residues[i+1])
+                #    bridge_type = "para"
                    
             if(residues[j-1].h_bond(residues[i])<-0.5
                and residues[i].h_bond(residues[j+1])<-0.5):
-                if(residues[j-1].h_bond(residues[i])+
-                   residues[i].h_bond(residues[j+1]))<E_min:
-                   E_min = residues[j-1].h_bond(residues[i])
-                   +residues[i].h_bond(residues[j+1])
-                #bridges.append(Bridge("para"))
-                    
-                
-            if((residues[i].h_bond(residues[j])<-0.5
-                and residues[j].h_bond(residues[i])<-0.5)
-               or(residues[i-1].h_bond(residues[j+1])<-0.5
-                  and residues[j-1].h_bond(residues[i+1])<-0.5)):
+                bridge = {'res1':residues[j-1].h_bond(residues[i]),
+                          'res2':residues[i].h_bond(residues[j+1]),
+                          'ipos':i,
+                          'jpos':j,
+                          'btype':"para"}
+                # if(residues[j-1].h_bond(residues[i])+
+                #    residues[i].h_bond(residues[j+1]))<E_min:
+                #    E_min = residues[j-1].h_bond(residues[i])
+                #    +residues[i].h_bond(residues[j+1])
+                #    bridge_type = "para"
 
-                #bridges.append(Bridge("anti"))
-        #bridges.append(strongest_bridge)
-    return(bridges)
+            if(residues[i].h_bond(residues[j])<-0.5
+               and residues[j].h_bond(residues[i])<-0.5):
+                bridge = {'res1':residues[i].h_bond(residues[j]),
+                          'res2':residues[j].h_bond(residues[i]),
+                          'ipos':i,
+                          'jpos':j,
+                          'btype':"anti"}
+                # if(residues[i].h_bond(residues[j])+
+                #    residues[j].h_bond(residues[i]))<E_min:
+                #    E_min = residues[i].h_bond(residues[j])
+                #    +residues[j].h_bond(residues[i])
+                #    bridge_type = "anti"
+                   
+            if(residues[i-1].h_bond(residues[j+1])<-0.5
+               and residues[j-1].h_bond(residues[i+1])<-0.5):
+                bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
+                          'res2':residues[j-1].h_bond(residues[i+1]),
+                          'ipos':i,
+                          'jpos':j,
+                          'btype':"anti"}
+                 # if(residues[i-1].h_bond(residues[j+1])+
+                 #   residues[j-1].h_bond(residues[i+1]))<E_min:
+                 #   E_min = residues[i-1].h_bond(residues[j+1])
+                 #   +residues[j-1].h_bond(residues[i+1])
+                 #   bridge_type = "anti"
+            if(bridge):
+                if(bridge['res1']+bridge['res2']<E_min):
+                    E_min = bridge['res1']+bridge['res2']
+                    strongest_bridge = bridge
+                    bridge = {}
+        # finally add the strongest bridge at i and j pos
+        if(strongest_bridge):
+            bridges.append(Bridge(strongest_bridge['btype'],
+                                  strongest_bridge['ipos']))
+            bridges.append(Bridge(strongest_bridge['btype'],
+                                  strongest_bridge['jpos']))
+    if(len(bridges)>0):
+        return(bridges)
+    else:
+        return(False)
 
-def get_helix(turns):
-    pass
+def get_helix(residues, turns):
+    for i in range(residues):
+        for j in range(i+1,i+5):
+            if