Cart to frac

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Overview

This script will convert the real space orthonormal cartesian coordinates of a selection to the fractional coordinates given the loaded cell symmetry.

Example

# load the script
 
run cart_to_frac.py
 
# fetch a protein and test
 
fetch 1rx1, async=0
 
# get the coordinates for the organic small
# molecule as fractional coordinates
 
print cart_to_frac("org")

The Code

from pymol import cmd
 
def cart_to_frac(objSel,quiet=0,_self=cmd):
    """
    Returns an array of fractional atomic coordinates
    for a given object or selection.
 
    PARAMS
      objSel -- any object or selection
 
      quiet -- suppress output (default, no)
 
      _self -- core CMD object; or none
 
    RETURNS
      Python list of fractional coordinates
 
    NOTES/EXAMPLES
      cart_to_frac org
 
      x = cart_to_frac("solvent", quiet=1)
    """
    import numpy
    from numpy import cos, sin, sqrt
 
    a2r = numpy.pi / 180.0
 
    # get the model and coordinates
 
    m = _self.get_model(objSel)
    cart_coord = numpy.matrix(m.get_coord_list())
 
    # get the symmetry information
    try:
        a,b,c,alpha,beta,gamma,gp = _self.get_symmetry(objSel)
    except:
        print "Error-Failed to get symmetry. Please ensure you have a"
        print "valid object with proper crystal symmetry loaded."
        return None
 
    # convert to radians
 
    alpha = a2r * alpha
    beta  = a2r * beta
    gamma = a2r * gamma
 
    # (scaled) volume of the cell
 
    v = sqrt(1 -cos(alpha)*cos(alpha) - cos(beta)*cos(beta) - cos(gamma)*cos(gamma) + 2*cos(alpha)*cos(beta)*cos(gamma))
 
    tmat = numpy.matrix( [
      [ 1.0 / a, -cos(gamma)/(a*sin(gamma)), (cos(alpha)*cos(gamma)-cos(beta)) / (a*v*sin(gamma))  ],
      [ 0.0,     1.0 / b*sin(gamma),         (cos(beta) *cos(gamma)-cos(alpha))/ (b*v*sin(gamma))  ],
      [ 0.0,     0.0,                        sin(gamma) / (c*v)                                    ] ]
      )
 
    r = cart_coord * tmat.T
 
    if not quiet:
        for (x,y,z) in r.tolist():
            print '%8.5f %8.5f %8.5f' % (x,y,z)
 
    # return the Nx3 results
    return r
 
cmd.extend("cart_to_frac", cart_to_frac)
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