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#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.