Adds Chirality evaluation
Thomas Forest
parent
dfeb566ee0
commit
948ff2d3ab
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@ -18,3 +18,4 @@ else:
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turns = get_turns(pdb_file.residues)
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get_helix(pdb_file.residues, turns)
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get_bends(pdb_file.residues)
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get_chirality(pdb_file.residues)
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115
src/structure.py
115
src/structure.py
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@ -1,4 +1,5 @@
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import math
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import numpy as np
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class Structure:
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def __init__(self, res):
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@ -30,8 +31,8 @@ def get_turns(residues):
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for j in range(3,6):
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if(i+j<len(residues)):
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if(res.h_bond(residues[i+j])<-0.5):
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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)
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return(turns)
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def get_bridges(residues):
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@ -47,8 +48,8 @@ def get_bridges(residues):
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and residues[j].h_bond(residues[i+1])<-0.5):
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bridge = {'res1':residues[i-1].h_bond(residues[j]),
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'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"}
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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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@ -60,8 +61,8 @@ def get_bridges(residues):
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and residues[i].h_bond(residues[j+1])<-0.5):
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bridge = {'res1':residues[j-1].h_bond(residues[i]),
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'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"}
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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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@ -73,8 +74,8 @@ def get_bridges(residues):
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and residues[j].h_bond(residues[i])<-0.5):
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bridge = {'res1':residues[i].h_bond(residues[j]),
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'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"}
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# if(residues[i].h_bond(residues[j])+
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# residues[j].h_bond(residues[i]))<E_min:
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@ -86,8 +87,8 @@ def get_bridges(residues):
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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]),
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'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"}
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# 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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@ -128,40 +129,34 @@ def get_helix(residues, turns):
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i+=1
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return(helix)
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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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def get_bends(residues):
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bends = {}
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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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angle = vector_angles(vectors_substr(position_vector(residues[i].atoms["CA"].coords),
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position_vector(residues[i-2].atoms["CA"].coords)),
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vectors_substr(position_vector(residues[i+2].atoms["CA"].coords),
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position_vector(residues[i].atoms["CA"].coords)))
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if(angle>70):
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print("angle", residues[i].resid, angle)
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bends[residues[i].resid] = angle
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return(bends)
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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
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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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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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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
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@ -171,7 +166,7 @@ def dot_product(v1,v2):
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return(dot_product)
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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)
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return vector
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def vectors_substr(v1, v2):
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@ -188,11 +183,59 @@ def vector_angles(v1,v2):
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deg_angle = rad_angle*(180/math.pi)
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return deg_angle
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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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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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a1 = u2 - u1
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a2 = u3 - u2
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a3 = u4 - u3
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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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deg_angle = rad*(180/math.pi)
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return deg_angle
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def get_chirality(residues):
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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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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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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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chirality[residues[i].resid] = sign
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return chirality
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