NeRF function

gistfile1.txt

    # 3 atoms from the previous residue
    # The first residue already has the first 3 atoms laid out
    a = prev_res.a.clone()
    b = prev_res.b.clone()
    c = prev_res.c.clone()
    d = @a
    na = [@b,@c]
    
    # Bond lengths, bond angles and torsions (already in radians, as extracted from the DB)
    blengths = [1.53, 1.453, 1.325]
    bangles = [PXL.Math.degToRad(115), PXL.Math.degToRad(109), PXL.Math.degToRad(121)]
    torsions = [prev_res.omega, prev_res.psi, @phi]
   
    for i in [0..2]
      ab = PXL.Math.Vec3.sub(b,a)
      abn = PXL.Math.Vec3.normalize(ab)
      bc = PXL.Math.Vec3.sub(c,b)
      bcn = PXL.Math.Vec3.multScalar(bc,1.0/blengths[i])
      R = blengths[i]
   
      # Initial 4th atom position
      d.x = R * Math.cos(bangles[i])
      d.y = R * Math.cos(torsions[i]) * Math.sin(bangles[i])
      d.z = R * Math.sin(torsions[i]) * Math.sin(bangles[i])
     
      # Move to reference fram
      n = PXL.Math.Vec3.cross(ab,bcn).normalize()
      nbc = PXL.Math.Vec3.cross(n,bcn)

      m = new PXL.Math.Matrix3([bcn.x, bcn.y, bcn.z, nbc.x, nbc.y, nbc.z, n.x, n.y, n.z])
      d.x = -d.x
      m.multVec(d)
      d.add(c)

     # shift along to the next atom
     if i != 2
        a = b
        b = c
        c = d
        d = na[i]