Correction of Bends residues

src/atom.py

@@ -8,12 +8,13 @@ class Atom:
 
 
     def __init__(self, atom_id, atom_name, res_name, chain_id,
-                 res_seq_nb, coordinates):
+                 res_seq_nb, insertion_code, coordinates):
         self.atom_id = atom_id
         self.atom_name = atom_name
         self.res_name = res_name
         self.chain_id = chain_id
         self.res_seq_nb = res_seq_nb
+        self.insertion_code = insertion_code
         self.coord_x = coordinates[0]
         self.coord_y = coordinates[1]
         self.coord_z = coordinates[2]
@@ -27,6 +28,7 @@ class Residue:
             self.resid = atom.res_seq_nb
             self.res_name = atom.res_name
             self.chain_id = atom.chain_id
+            self.insertion_code = atom.insertion_code
             
             
     def h_bond(self, res2):

src/pdb.py

@@ -39,8 +39,9 @@ class PDBFile:
                 atom = Atom(atom_id = int(line[6:11].strip()),
                             atom_name = line[12:16].strip(),
                             res_name = line[17:20].strip(),
-                            chain_id = line[21:22].strip(),
+                            chain_id = line[21:22],
                             res_seq_nb = int(line[22:26].strip()),
+                            insertion_code = line[26:27],
                             coordinates = [float(line[30:38].strip()),
                                      float(line[38:46].strip()),
                                      float(line[46:54].strip()),
@@ -91,6 +92,7 @@ class PDBFile:
                                 res_name = resi.res_name,
                                 chain_id = resi.chain_id,
                                 res_seq_nb = resi.resid,
+                                insertion_code = resi.insertion_code,
                                 coordinates = [hydrogen[2],
                                                hydrogen[3],
                                                hydrogen[4]])

src/structure.py

@@ -121,8 +121,8 @@ def get_helix(residues, turns):
                 k+=1
                 temp_res.append(residues[i])
             if(k>2):
-                print(k,"- HELIX at", i)
-                helix.append(Helix(temp_res,i))
+                print(k,"- HELIX at", residues[i].resid)
+                helix.append(Helix(temp_res,residues[i].resid))
             i = i+k
         else:
             i+=1
@@ -140,7 +140,7 @@ def get_bends(residues):
                               vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
                                              position_vector(residues[i].atoms["CA"].coords)))
         if(angle>70):
-            print("angle", i+1, angle)
+            print("angle", residues[i].resid, angle)
     return(bends)
 
 def vecteur_deux_points (a, b):
@@ -175,9 +175,9 @@ def position_vector(c):
     return vector
 
 def vectors_substr(v1, v2):
-    return ([v2[0]-v1[0],
-             v2[1]-v1[1],
-             v2[2]-v1[2]])
+    return ([v1[0]-v2[0],
+             v1[1]-v2[1],
+             v1[2]-v2[2]])
 
 def vector_angles(v1,v2):
     dot_prod = dot_product(v1,v2)