> I have about 50 MOPAC Z-matrix files for which I need 2d
> representations for publication.
Here's one easy way -- without needing to install anything else. I'm assuming
you can use a Linux box with bash, or something similar. I use "curl" but
"wget" can also work here with slightly different command-line options.
for x in *.out; do
echo $x;
inchi=`babel $x -oinchi 2>/dev/null | awk '{print $1;}'`
curl -s -o ${x%%.out}.png
"http://cactus.nci.nih.gov/chemical/structure/${inchi}/image?format=png";
done
Basically, you use OB to convert to an InChI and pass it through the NIH
chemical resolver. There are a number of format options you can specify with
the end of the URL:
http://cactus.nci.nih.gov/blog/?p=136
You mentioned wanting to add some text, so you might look at the header/footer
options in that blog post. Noel mentioned a few Python modules -- this
basically does the same thing.
Hope that helps,
-Geoff
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