Browse Source

Adds Chirality evaluation

Thomas Forest 5 years ago
parent
commit
948ff2d3ab
2 changed files with 80 additions and 36 deletions
  1. 1 0
      src/dssp.py
  2. 79 36
      src/structure.py

+ 1 - 0
src/dssp.py View File

@@ -18,3 +18,4 @@ else:
18 18
     turns = get_turns(pdb_file.residues)
19 19
     get_helix(pdb_file.residues, turns)
20 20
     get_bends(pdb_file.residues)
21
+    get_chirality(pdb_file.residues)

+ 79 - 36
src/structure.py View File

@@ -1,4 +1,5 @@
1 1
 import math
2
+import numpy as np
2 3
 
3 4
 class Structure:
4 5
     def __init__(self, res):
@@ -30,8 +31,8 @@ def get_turns(residues):
30 31
         for j in range(3,6):
31 32
             if(i+j<len(residues)):
32 33
                 if(res.h_bond(residues[i+j])<-0.5):
33
-                    print("TURN", i+1, i+j+1)
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-                    turns[i] = Turn(j,i)
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+                    print(j,"TURN", residues[i].resid, residues[i+j].resid)
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+                    turns[residues[i].resid] = Turn(j,residues[i].resid)
35 36
     return(turns)
36 37
 
37 38
 def get_bridges(residues):
@@ -47,8 +48,8 @@ def get_bridges(residues):
47 48
                and residues[j].h_bond(residues[i+1])<-0.5):
48 49
                 bridge = {'res1':residues[i-1].h_bond(residues[j]),
49 50
                           'res2':residues[j].h_bond(residues[i+1]),
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-                          'ipos':i,
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-                          'jpos':j,
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+                          'ipos':residues[i].resid,
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+                          'jpos':residues[j].resid,
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                           'btype':"para"}
53 54
                 # if(residues[i-1].h_bond(residues[j])+
54 55
                 #    residues[j].h_bond(residues[i+1]))<E_min:
@@ -60,8 +61,8 @@ def get_bridges(residues):
60 61
                and residues[i].h_bond(residues[j+1])<-0.5):
61 62
                 bridge = {'res1':residues[j-1].h_bond(residues[i]),
62 63
                           'res2':residues[i].h_bond(residues[j+1]),
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-                          'ipos':i,
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-                          'jpos':j,
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+                          'ipos':residues[i].resid,
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+                          'jpos':residues[j].resid,
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                           'btype':"para"}
66 67
                 # if(residues[j-1].h_bond(residues[i])+
67 68
                 #    residues[i].h_bond(residues[j+1]))<E_min:
@@ -73,8 +74,8 @@ def get_bridges(residues):
73 74
                and residues[j].h_bond(residues[i])<-0.5):
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                 bridge = {'res1':residues[i].h_bond(residues[j]),
75 76
                           'res2':residues[j].h_bond(residues[i]),
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-                          'ipos':i,
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-                          'jpos':j,
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+                          'ipos':residues[i].resid,
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+                          'jpos':residues[j].resid,
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                           'btype':"anti"}
79 80
                 # if(residues[i].h_bond(residues[j])+
80 81
                 #    residues[j].h_bond(residues[i]))<E_min:
@@ -86,8 +87,8 @@ def get_bridges(residues):
86 87
                and residues[j-1].h_bond(residues[i+1])<-0.5):
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                 bridge = {'res1':residues[i-1].h_bond(residues[j+1]),
88 89
                           'res2':residues[j-1].h_bond(residues[i+1]),
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-                          'ipos':i,
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-                          'jpos':j,
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+                          'ipos':residues[i].resid,
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+                          'jpos':residues[j].resid,
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                           'btype':"anti"}
92 93
                  # if(residues[i-1].h_bond(residues[j+1])+
93 94
                  #   residues[j-1].h_bond(residues[i+1]))<E_min:
@@ -128,40 +129,34 @@ def get_helix(residues, turns):
128 129
             i+=1
129 130
     return(helix)
130 131
 
132
+def get_ladder(bridges):
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+    ladders = {}
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+    for i in range(len(bridges)):
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+        k = 1
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+        while bridges[i] == bridges[i+k]:
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+            k+=1
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+        if k>1:
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+            ladders[bridges[i].res_num] = k-1
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+
131 141
 def get_bends(residues):
132 142
     bends = {}
133 143
     for i in range(2,len(residues)-2):
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-        # print("angle",i,calculer_angles(residues[i-2].atoms["CA"].coords,
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-        #                                 residues[i].atoms["CA"].coords,
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-        #                                 residues[i+2].atoms["CA"].coords))
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-        
138 144
         angle = vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
139 145
                                              position_vector(residues[i-2].atoms["CA"].coords)),
140 146
                               vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
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                                              position_vector(residues[i].atoms["CA"].coords)))
142 148
         if(angle>70):
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             print("angle", residues[i].resid, angle)
150
+            bends[residues[i].resid] = angle
144 151
     return(bends)
145 152
 
146
-def vecteur_deux_points (a, b):
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+def vector_from_pos(a, b):
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     xAB = b[0]-a[0]
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     yAB = b[1]-a[1]
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     zAB = b[2]-a[2]
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     coord_AB = [xAB,yAB,zAB]
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     return coord_AB
152 159
 
153
-def produit_scalaire (a, b, c):
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-    coord_BA = vecteur_deux_points(b, a)
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-    coord_BC = vecteur_deux_points(b, c)
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-    dot_product = coord_BA[0]*coord_BC[0] + coord_BA[1]*coord_BC[1] + coord_BA[2]*coord_BC[2]
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-    return dot_product
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-
159
-
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-def norme_vecteur (a,b):
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-    vecteur = vecteur_deux_points(a,b)
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-    norme = math.sqrt(vecteur[0]**2 + vecteur[1]**2 + vecteur[2]**2)
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-    return norme
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-
165 160
 def vector_norm(v):
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     norm = math.sqrt(v[0]**2 + v[1]**2 + v[2]**2)
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     return norm
@@ -171,7 +166,7 @@ def dot_product(v1,v2):
171 166
     return(dot_product)
172 167
 
173 168
 def position_vector(c):
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-    vector = vecteur_deux_points([0,0,0],c)
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+    vector = vector_from_pos([0,0,0],c)
175 170
     return vector
176 171
 
177 172
 def vectors_substr(v1, v2):
@@ -188,11 +183,59 @@ def vector_angles(v1,v2):
188 183
     deg_angle = rad_angle*(180/math.pi)
189 184
     return deg_angle
190 185
 
191
-def calculer_angles (a,b,c):
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-    dot_product_ABC = produit_scalaire(a,b,c)
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-    norme_BA = norme_vecteur (b,a)
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-    norme_BC = norme_vecteur (b,c)
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-    terme = dot_product_ABC/(abs(norme_BA)*abs(norme_BC))
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-    angle_radian = math.acos(terme)
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-    angle_degre = angle_radian*(180/math.pi)
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-    return angle_degre
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+def calc_dihedral(u1, u2, u3, u4):
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+    """ Calculate dihedral angle method. From bioPython.PDB
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+    (adapted to np.array)
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+    Calculate the dihedral angle between 4 vectors
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+    representing 4 connected points. The angle is in
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+    [-pi, pi].
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+
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+    Adapted function of dihedral_angle_from_coordinates.py 
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+    by Eric Alcaide.
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+    Source : https://gist.github.com/EricAlcaide
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+    URL : https://gist.github.com/EricAlcaide/30d6bfdb8358d3a57d010c9a501fda56
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+    """
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+    #convert coords to numpy arrays
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+    u1 = np.array(u1)
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+    u2 = np.array(u2)
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+    u3 = np.array(u3)
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+    u4 = np.array(u4)
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+    
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+    a1 = u2 - u1
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+    a2 = u3 - u2
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+    a3 = u4 - u3
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+
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+    v1 = np.cross(a1, a2)
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+    v1 = v1 / (v1 * v1).sum(-1)**0.5
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+    v2 = np.cross(a2, a3)
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+    v2 = v2 / (v2 * v2).sum(-1)**0.5
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+    porm = np.sign((v1 * a3).sum(-1))
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+    rad = np.arccos((v1*v2).sum(-1) / ((v1**2).sum(-1) * (v2**2).sum(-1))**0.5)
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+    if not porm == 0:
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+        rad = rad * porm
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+
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+    deg_angle = rad*(180/math.pi)
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+    return deg_angle
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+
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+
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+def get_chirality(residues):
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+
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+    for i in range(1,len(residues)-2):
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+        chirality = {}
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+        angle = calc_dihedral(residues[i-1].atoms["CA"].coords,
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+                              residues[i].atoms["CA"].coords,
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+                              residues[i+1].atoms["CA"].coords,
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+                              residues[i+2].atoms["CA"].coords)
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+        
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+        if(angle>0 and angle<=180):
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+            sign="+"
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+            print("angle", residues[i].resid, "+", angle)
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+            
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+        if(angle<=0 and angle > -180):
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+            sign="-"
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+            print("angle", residues[i].resid, "-", angle)
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+            
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+        chirality[residues[i].resid] = sign
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+        
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+    return chirality
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+