From d745b942bda3ead2dbafd1301f42dc64a470e6da Mon Sep 17 00:00:00 2001
From: Thomas Forest <thomas.forest@etu.univ-paris-diderot.fr>
Date: Wed, 18 Sep 2019 11:51:52 +0200
Subject: [PATCH] Implemented bridge search algorithm

---
 src/atom.py | 60 +++++++++++++++++++++++++++++++++--------------------
 src/dssp.py |  8 ++++++-
 2 files changed, 45 insertions(+), 23 deletions(-)

diff --git a/src/atom.py b/src/atom.py
index 92a78da..a4c754c 100644
--- a/src/atom.py
+++ b/src/atom.py
@@ -262,8 +262,9 @@ def connected_ladders(ladd_1, ladd_2):
     links = []
     for bridge in ladd_1['bridges']:
         if bridge.res_partner in res_list(ladd_2):
-            return([ladd_1['i'], ladd_1['j'], bridge.i, bridge.j,
-                    ladd_2['i'], ladd_2['j']])
+            # return([ladd_1['i'], ladd_1['j'], bridge.i, bridge.j,
+            #         ladd_2['i'], ladd_2['j']])
+            return ladd_2
 
     return False
 
@@ -276,29 +277,44 @@ def get_sheets(ladders):
     """
     ladds = [ elem for elem in ladders.values() ]
     sheets = {}
-    i = 0
-    while i < len(ladds):
-        j = i+1
-        ladd = ladds[i]
-        ladd1 = ladds[i]
-        ladd2 = ladds[j]
 
-        while j < len(ladds):
-            print(connected_ladders(ladd1, ladd2))
+    corresp = {}
+    for ladd1 in ladds:
+        for ladd2 in ladds:
             if connected_ladders(ladd1, ladd2)!=False:
-                ladd1 = ladd2
-                #print(connected_ladders(ladd1, ladd2)[4])
-                ladd2 = ladders[connected_ladders(ladd1, ladd2)[4]]
-            j+=1
-        print(ladd['i'], ladd2['i'])
-        i+=1
-    # for ladder in ladders:
-    #     for ladd2 in ladders:
-    #        if connected_ladders(ladders[ladder], ladders[ladd2]):
-    #            pass
-               #print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge.i, bridge.j,
-               #      "ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j'])
+                corresp_list = [ elem for elem in corresp.keys() ]
+                if ladd1['i'] not in corresp_list and ladd2['i'] not in corresp_list:
+                    ind = len(sheets.keys())
+                    sheets[ind] = []
+                    sheets[ind].append(ladd1)
+                    sheets[ind].append(ladd2)
+                    corresp[ladd1['i']] = ind
+                    corresp[ladd2['i']] = ind
+                elif ladd2 not in corresp_list and ladd1 in corresp_list:
+                    sheets[corresp[ladd1['i']]].append(ladd2)
+                    corresp[ladd2['i']] = corresp[ladd1['i']]
+                elif ladd1 not in corresp_list and ladd2 in corresp_list:
+                    sheets[corresp[ladd2['i']]].append(ladd1)
+                    corresp[ladd1['i']] = corresp[ladd2['i']]
+                    
+    return sheets
 
+def get_sheets2(ladders):
+    """
+    Bridges between ladders.
+    Check if 1 bridge between one ladder and one or more other 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 ladd2 in ladders:
+           if connected_ladders(ladders[ladder], ladders[ladd2]):
+               pass
+               print("ladder",ladders[ladder]['i'], ladders[ladder]['j'],"bridge",bridge.i, bridge.j,
+                    "ladder 2",ladders[ladd2]['i'], ladders[ladd2]['j'])
+
+               
 def res_list(ladder):
     # TODO : method in ladder class
     l=[]
diff --git a/src/dssp.py b/src/dssp.py
index 955df8d..8d72452 100644
--- a/src/dssp.py
+++ b/src/dssp.py
@@ -28,7 +28,7 @@ else:
     # get_chirality(pdb_file.residues)
     bridges = get_bridges(pdb_file.residues)
     ladders = get_ladders(bridges, pdb_file.residues)
-    get_sheets(ladders)  
+    sheets = get_sheets(ladders)  
 
     # print("NBRIDGES",len(bridges))
 
@@ -59,3 +59,9 @@ else:
 for i,ladder in enumerate(ladders.values()):
     print(chr(65+i))
     
+for ind, sheet in sheets.items():
+    print(ind, sheet)
+    for ladder in sheet:
+        print(ladder['start'], ladder['end'])
+
+