From de6f723d2f091e70d5fcc92167d3ba2f0addf728 Mon Sep 17 00:00:00 2001
From: Thomas Forest <thomas.forest@etu.univ-paris-diderot.fr>
Date: Wed, 18 Sep 2019 16:13:15 +0200
Subject: [PATCH] Before dropping bp2

---
 src/atom.py      | 50 +++++++++++++++++++++++++++++++++++++-----------
 src/dssp.py      | 13 +++++++++++--
 src/structure.py |  8 +++++++-
 3 files changed, 57 insertions(+), 14 deletions(-)

diff --git a/src/atom.py b/src/atom.py
index fd9385d..d3c7388 100644
--- a/src/atom.py
+++ b/src/atom.py
@@ -243,11 +243,12 @@ def get_bridges(residues):
     bridges = {}
     bridge = {}
     strongest_bridge = {}
+    selected_bridges = []
     for i in range(1,len(residues)-4):
         E_min = 0
         for j in range(i+2,len(residues)-1):
             # select triplet with the minimal energy 
-
+            
             if(residues[i-1].h_bond(residues[j])<-0.5
                and residues[j].h_bond(residues[i+1])<-0.5):
                 bridge = {'res1':residues[i-1].h_bond(residues[j]),
@@ -292,20 +293,47 @@ def get_bridges(residues):
                 if(bridge['res1']+bridge['res2']<E_min):
                     E_min = bridge['res1']+bridge['res2']
                     strongest_bridge = bridge
+                    if strongest_bridge not in selected_bridges:
+                        selected_bridges.append(strongest_bridge)
                     coord_bridge = [i,j]
                     bridge = {}
+
         # finally add the strongest bridge at i and j pos
         if(strongest_bridge):
-            bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
-                                                     strongest_bridge['ipos'],
-                                                     strongest_bridge['jpos'],
-                                                     [strongest_bridge['i'],
-                                                      strongest_bridge['j']]))
-            bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
-                                               strongest_bridge['jpos'],
-                                               strongest_bridge['ipos'],
-                                               [strongest_bridge['i'],
-                                               strongest_bridge['j']]))
+            if(len(selected_bridges)>1):
+                bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
+                                                         strongest_bridge['ipos'],
+                                                         strongest_bridge['jpos'],
+                                                         [strongest_bridge['i'],
+                                                          strongest_bridge['j']],
+                                                         selected_bridges[-2]['btype'],
+                                                         selected_bridges[-2]['ipos'],
+                                                         selected_bridges[-2]['jpos'],
+                                                         [selected_bridges[-2]['i'],
+                                                          selected_bridges[-2]['j']]))
+                                              
+                bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
+                                                         strongest_bridge['ipos'],
+                                                         strongest_bridge['jpos'],
+                                                         [strongest_bridge['i'],
+                                                          strongest_bridge['j']],
+                                                         selected_bridges[-2]['btype'],
+                                                         selected_bridges[-2]['ipos'],
+                                                         selected_bridges[-2]['jpos'],
+                                                         [selected_bridges[-2]['i'],
+                                                          selected_bridges[-2]['j']]))
+            else:
+                bridges[strongest_bridge['i']] = (Bridge(strongest_bridge['btype'],
+                                                         strongest_bridge['ipos'],
+                                                         strongest_bridge['jpos'],
+                                                         [strongest_bridge['i'],
+                                                          strongest_bridge['j']]))
+                                              
+                bridges[strongest_bridge['j']] = (Bridge(strongest_bridge['btype'],
+                                                         strongest_bridge['ipos'],
+                                                         strongest_bridge['jpos'],
+                                                         [strongest_bridge['i'],
+                                                          strongest_bridge['j']]))
     if(len(bridges)>0):
         return(bridges)
     else:
diff --git a/src/dssp.py b/src/dssp.py
index 8d4c5b5..148f747 100644
--- a/src/dssp.py
+++ b/src/dssp.py
@@ -61,6 +61,8 @@ 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)
     kappa = res.get_bends(residues)[0]
@@ -81,6 +83,13 @@ for i,res in enumerate(residues):
     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),
+    if i in bridges.keys():
+        bp1 = bridges[i].j
+    else:
+        bp1 = 0
+    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, bp1,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))
+
+
+for bridge in bridges:
+    print(bridges[bridge].i, bridges[bridge].j)
diff --git a/src/structure.py b/src/structure.py
index 1c206ad..ab6d585 100644
--- a/src/structure.py
+++ b/src/structure.py
@@ -14,13 +14,19 @@ class Turn(Structure):
                         
 class Bridge(Structure):
 
-    def __init__(self, bridge_type, res_num, res_partner, indices):
+    def __init__(self, bridge_type, res_num, res_partner, indices,
+                 second_bridge_type=None, second_resnum=None,
+                 second_res_partner=None, second_indices=None):
         self.bridge_type = bridge_type
         self.res_num = res_num
         self.res_partner = res_partner
         Structure.res = res_num
         self.i = indices[0]
         self.j = indices[1]
+        self.second_bridge_type = second_bridge_type
+        self.second_resnum = second_resnum
+        self.second_res_partner = second_res_partner
+        self.second_indices = second_indices
 
 class Helix(Structure):