I am looking for a free and open-source software written or wrapped for Python that would simply allow me to generate bunch of figures (in eps, jpg, or pdf format) from a set of xyz files, e.g. water clusters of different sizes.
I am aware of PyMol, but it seems a bit complicated to use (it has its own script language) for such a simple task and I guess it does not recognize xyz files, so I'd first need to convert to pdb format, etc.
In case you really need it has to be written in python probably you want to try Atomic Simulation Environment (ASE). It has a GUI that "allows users to visualize, manipulate, and render molecular systems and atoms objects".
Let me add (even when you are asking explicitly for codes written in Python), just in case that what you need is to create images from .xyz files (regardless of the language), Jmol probably will suits you, as it reads .xyz files straightforwardly. For saving your image once it is loaded, you will need to open a console in Jmol and type:
write image 1200 720 jpg 90 "filename.jpg"
where:
1200 and 720 are the width and height of your image (choose the ones you want to)
90 is the quality of the compression
import pymolpymol.read('xyz')etc.? – Armut Sep 18 '15 at 22:03