Cart to frac - Revision history

Cchem: 1 revision

2016-09-19T02:19:31Z

1 revision

New page

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

* Thanks to [http://en.wikipedia.org/wiki/Fractional_coordinates Wikipedia].

= Example =
<source lang="python">
# 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")
</source>

= The Code =
<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Math_Scripts]]

Pyadmin: 4 revisions

2014-03-28T01:06:31Z

4 revisions

Speleo3: nicer output

2011-11-30T13:35:51Z

nicer output

New page

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

* Thanks to [http://en.wikipedia.org/wiki/Fractional_coordinates Wikipedia].

= Example =
<source lang="python">
# 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")
</source>

= The Code =
<source lang="python">
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)
</source>

[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Math_Scripts]]

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