[BioPython] Torsional angle

[Andrew Dalke]

Hi Omid,

> Could someone please help me with measuring a torsional angle given  
> the PDB coordinates of the 4 atoms involved in it.


See the thread including
   http://www.rcsb.org/pdb/lists/pdb-l/200409/001936.html
and more details in
    
http://www.math.fsu.edu/~quine/IntroMathBio_04/torsion_pdb/ 
torsion_pdb.pdf

There is Biopython code for computing a torsional angle.

 >>> from Bio.PDB import Vector
 >>> p1 = Vector.Vector( [0.0, 0.0, 1.0] )
 >>> p2 = Vector.Vector( [0.0, 0.0, 0.0] )
 >>> p3 = Vector.Vector( [0.0, 1.0, 0.0] )
 >>> p4 = Vector.Vector( [1.0, 1.0, 0.0] )
 >>> Vector.calc_dihedral(p1, p2, p3, p4)
1.5707963267948966
 >>>

However, I think that's only in CVS.  The code is

def calc_dihedral(v1, v2, v3, v4):
     """
     Calculate the dihedral angle between 4 vectors
     representing 4 connected points. The angle is in
     ]-pi, pi].

     @param v1, v2, v3, v4: the four points that define the dihedral  
angle
     @type v1, v2, v3, v4: L{Vector}
     """
     ab=v1-v2
     cb=v3-v2
     db=v4-v3
     u=ab**cb
     v=db**cb
     w=u**v
     angle=u.angle(v)
     # Determine sign of angle
     try:
         if cb.angle(w)>0.001:
             angle=-angle
     except ZeroDivisionError:
         # dihedral=pi
         pass
     return angle

This depends on a Bio.PDB-specific Vector class which
implements the "angle" method.

     def angle(self, other):
         "Return angle between two vectors"
         n1=self.norm()
         n2=other.norm()
         c=(self*other)/(n1*n2)
         # Take care of roundoff errors
         c=min(c,1)
         c=max(-1,c)
         return arccos(c)


					Andrew
					dalke at dalkescientific.com