#xyz2openscad
##Description A GNU Guile script for generating 3D open-scad molecule models from .xyz files. The script will print the open-scad source file to std-out.
##Usage
guile xyz2openscad.scm <input-file> > <output-file>
or
./xyz2openscad.scm <input-file> > <output-file>
(you need to make the script executable via chmod first of course)
This scripts supports piping the xyz file into it, which makes it easy to use with open-babel.
The following example assumes you have a file called "molecule.smi" which contains a smiles string for a molecule.
obabel molecule.smi -o xyz --gen3d | guile xyz2openscad.scm > molecule.scad
or
obabel molecule.smi -o xyz --gen3d | ./xyz2openscad.scm > molecule.scad
converts the smiles string to an xyz-file via open-babel, pipes the result into the GNU Guile script, which generates an open-scad script and saves it as "molecule.scad".
For the .xyz file specifications visit
http://en.wikipedia.org/wiki/XYZ_file_format
(the script essentially ignores the first two lines of input).
##Requirements This script has been tested with GNU Guile 2.0.11.
##More information
The van der Waals radii of the atoms were taken from the web, so no guarantee there. These can be expanded and/or changed easily, just take a look at the script and the rest should be self-explaining.
Should the .xyz-file contain an atomtype for which the script contains no data, a van der Waals radius of 1 Angstroem will be assumed. The atom will also be colored red in the resulting open-scad script and there will be a comment explaining things at the right location in the open-scad script.