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projet_court
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attempt of NH-->O bonds discovery + correction of get_helix

Thomas Forest 5 years ago
parent
bc420e4656
commit
583d7e33d8
2 changed files with 69 additions and 28 deletions
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  1. 27 4
      src/dssp.py
  2. 42 24
      src/structure.py

+ 27 - 4
src/dssp.py View File 

@@ -3,6 +3,10 @@ import atom
3 3 
 import sys
4 4 
 from structure import *
5 5
6 
+def print_dssp():
7 
+
8 
+    empt_line=" " * 145
9 
+
6 10 
 if(len(sys.argv)<2):
7 11 
     print("Not enough arguments! Run with --help to learn more about proper"
8 12 
           "call structure and parameters.")
 
@@ -15,10 +19,29 @@ else:
15 19 
     #print(get_turns(pdb_file.residues))
16 20 
     #print(pdb_file.residues[27].h_bond(pdb_file.residues[28]))
17 21 
     #print(get_bridges(pdb_file.residues))
22 
+
23 
+
18 24 
     turns = get_turns(pdb_file.residues)
19 25 
     get_helix(pdb_file.residues, turns)
20 
-    get_bends(pdb_file.residues)
21 
-    get_chirality(pdb_file.residues)
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+    # get_bends(pdb_file.residues)
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+    # get_chirality(pdb_file.residues)
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+    # bridges = get_bridges(pdb_file.residues)
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+    # ladders = get_ladders(bridges)
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+    # get_sheets(ladders)
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+
32 
+    # print("NBRIDGES",len(bridges))
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+
22 34 
     bridges = get_bridges(pdb_file.residues)
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-    ladders = get_ladders(bridges)
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-    get_sheets(ladders)
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+
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+    get_bonds(pdb_file.residues)
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+
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+    print(pdb_file.residues[1].h_bond(pdb_file.residues[2]))
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+
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+    residues = pdb_file.residues
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+    e_min = 0
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+    for res in residues:
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+        ene = residues[1].h_bond(res)
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+        if ene <= e_min:
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+            e_min = ene
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+            best_res = res
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+    print(residues[1].resid, best_res.resid,e_min)

+ 42 - 24
src/structure.py View File 

@@ -34,7 +34,7 @@ def get_turns(residues):
34 34 
             if(i+j<len(residues)):
35 35 
                 if(res.h_bond(residues[i+j])<-0.5):
36 36 
                     print(j,"TURN", residues[i].resid, residues[i+j].resid)
37 
-                    turns[residues[i].resid] = Turn(j,residues[i].resid)
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+                    turns[i] = Turn(j,residues[i].resid)
38 38 
     return(turns)
39 39
40 40 
 def get_bridges(residues):
 
@@ -53,11 +53,6 @@ def get_bridges(residues):
53 53 
                           'ipos':residues[i].resid,
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                           'jpos':residues[j].resid,
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                           'btype':"para"}
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-                # if(residues[i-1].h_bond(residues[j])+
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-                #    residues[j].h_bond(residues[i+1]))<E_min:
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-                #    E_min = residues[i-1].h_bond(residues[j])
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-                #    +residues[j].h_bond(residues[i+1])
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-                #    bridge_type = "para"
61 56
62 57 
             if(residues[j-1].h_bond(residues[i])<-0.5
63 58 
                and residues[i].h_bond(residues[j+1])<-0.5):
 
@@ -66,11 +61,6 @@ def get_bridges(residues):
66 61 
                           'ipos':residues[i].resid,
67 62 
                           'jpos':residues[j].resid,
68 63 
                           'btype':"para"}
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-                # if(residues[j-1].h_bond(residues[i])+
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-                #    residues[i].h_bond(residues[j+1]))<E_min:
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-                #    E_min = residues[j-1].h_bond(residues[i])
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-                #    +residues[i].h_bond(residues[j+1])
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-                #    bridge_type = "para"
74 64
75 65 
             if(residues[i].h_bond(residues[j])<-0.5
76 66 
                and residues[j].h_bond(residues[i])<-0.5):
 
@@ -79,11 +69,6 @@ def get_bridges(residues):
79 69 
                           'ipos':residues[i].resid,
80 70 
                           'jpos':residues[j].resid,
81 71 
                           'btype':"anti"}
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-                # if(residues[i].h_bond(residues[j])+
83 
-                #    residues[j].h_bond(residues[i]))<E_min:
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-                #    E_min = residues[i].h_bond(residues[j])
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-                #    +residues[j].h_bond(residues[i])
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-                #    bridge_type = "anti"
87 72
88 73 
             if(residues[i-1].h_bond(residues[j+1])<-0.5
89 74 
                and residues[j-1].h_bond(residues[i+1])<-0.5):
 
@@ -92,11 +77,7 @@ def get_bridges(residues):
92 77 
                           'ipos':residues[i].resid,
93 78 
                           'jpos':residues[j].resid,
94 79 
                           'btype':"anti"}
95 
-                 # if(residues[i-1].h_bond(residues[j+1])+
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-                 #   residues[j-1].h_bond(residues[i+1]))<E_min:
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-                 #   E_min = residues[i-1].h_bond(residues[j+1])
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-                 #   +residues[j-1].h_bond(residues[i+1])
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-                 #   bridge_type = "anti"
80 
+
100 81 
             if(bridge):
101 82 
                 if(bridge['res1']+bridge['res2']<E_min):
102 83 
                     E_min = bridge['res1']+bridge['res2']
 
@@ -107,14 +88,51 @@ def get_bridges(residues):
107 88 
             bridges[strongest_bridge['ipos']] = (Bridge(strongest_bridge['btype'],
108 89 
                                                         strongest_bridge['ipos'],
109 90 
                                                         strongest_bridge['jpos']))
110 
-            bridges[strongest_bridge['jpos']] = (Bridge(strongest_bridge['btype'],
111 
-                                                        strongest_bridge['jpos'],
112 
-                                                        strongest_bridge['ipos']))
91 
+            # bridges[strongest_bridge['jpos']] = (Bridge(strongest_bridge['btype'],
92 
+            #                                             strongest_bridge['jpos'],
93 
+            #                                             strongest_bridge['ipos']))
113 94 
     if(len(bridges)>0):
114 95 
         return(bridges)
115 96 
     else:
116 97 
         return(False)
117 98
99 
+# def get_bonds(residues):
100 
+#     for i,res1 in enumerate(residues):
101 
+#         E_min = 0
102 
+#         strongest_bridge = []
103 
+#         for j in range(-5,6):
104 
+#             if(i+j < len(residues)):
105 
+#                 res2 = residues[i+j]
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+#                 if(res1.h_bond(res2)<-0.5) and (res1.h_bond(res2)<E_min):
107 
+#                     E_min = res1.h_bond(res2)
108 
+#                     strongest_bridge = [res1, res2]
109 
+#         if(len(strongest_bridge)>0):
110 
+#             diff = strongest_bridge[0].resid - strongest_bridge[1].resid
111 
+#             if( abs (diff) > 1 and abs(diff)<=5):
112 
+#                 print(diff)
113 
+
114 
+def get_bonds(residues):
115 
+    bonds = {}
116 
+    k = 0
117 
+    for i,res in enumerate(residues):
118 
+        E_min = 0
119 
+        for j in range(-5,-2):
120 
+            if(i+j<len(residues)):
121 
+                if(residues[i+j].h_bond(res)<-0.5):
122 
+                    k+=1
123 
+                    #if(res.h_bond(residues[i+j])<E_min):
124 
+                    E_min = res.h_bond(residues[i+j])
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+                    res_a = res
126 
+                    res_b = residues[i+j]
127 
+                    if j not in bonds:
128 
+                        bonds[j] = []
129 
+                    bonds[j].append([res_a.resid, res_b.resid])
130 
+                    #turns[residues[i].resid] = Turn(j,residues[i].resid)
131 
+    for key in bonds.keys():
132 
+        print(key, len(bonds[key]))
133 
+
134 
+    print("LH",k)
135 
+
118 136 
 def get_helix(residues, turns):
119 137 
     i = 1
120 138 
     helix = []