Re: [OpenBabel-scripting] Generating Input Decks in Scripts (possibly off-topic)

[Andrew D. F. <fa...@po...>]

Thanks for the feedback, Geoff.

To be a little more specific about what I am doing, I'm doing some
thermodynamics with substituted pyridines, Because I'm generating all the
initial structures by hand, and there are about 55 species involved (actually
more than double that with various charged species involved), I'd rather not
manually create an structure for each species, but if I am going to do any sort
of automated data reduction on this set, I need to be sure that the atom
numbering and the internal coordinates in the z matrix are consistent  I do have
 optimized structures for pyridine and one of the substituted species at a high
level of theory to use as starting points for construction.

As an example

runsystem -t optimize -p meta -s methyl -c neutral -b sto6g (just as a mock-up)

would construct the zmatrix for 3-methylpyridine and optimize it as a neutral
species at STO-6G (in reality, I'll be putting codes in rather than words, but
it makes the example easier to read  8-).  I have bits and pieces to do this
already, but I am getting hung up on the best way to manage merging the two
fragments into the final zmatrix with consistent numbering and internal angles.
Does anyone have any elegant solutions for this, or will I end up dragging a
long case statement around?

Thanks again,
	Andy

Geoffrey Hutchison wrote:
> Hi Andrew,
> 
> I don't think your question is off-topic at all. I'm actually adding  
> in the openbabel-discuss general list as well, since I don't think  
> this is really restricted to scripting languages.
> 
> Open Babel is really good at automation. I've done similar sorts of  
> tasks. For example, the 2.1 betas and development code offer flags  
> for setting the keywords for many standard quantum chemistry packages  
> from the command-line.
> 
> e.g. (turning a folder full of .xyz files into a set of foo.com files  
> for some "G" package.)
> 
> babel *.xyz -xk "#n B3LYP/6-31G* Opt" -ocom -m
> # here you see a one-line set of keywords from the command-line.  
> Here's another example using a text file of keywords
> # -ocom sets the output format to .com and -m indicates a batch-mode  
> command over all the .xyz files
> 
> babel *.xyz -xf keywords.txt -ocom -m
> # where keywords.txt is a text file with as much as you want for the  
> header
> 
> I generally write up small shell scripts to automate some of these  
> actions, often including interaction with the queue system (e.g.,  
> splitting 200 jobs into 5-10 lists of jobs before other users of the  
> cluster kill me). I'd be glad to share more details if people are  
> interested.
> 
> Cheers,
> -Geoff


-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fa...@po... | That shines on me               | Disclaimer:  I don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself