Re: [Apbs-users] PYTHON driven APBS: Parameter setting
Biomolecular electrostatics software
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From: Todd D. <to...@cc...> - 2004-10-18 16:20:09
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Hi Markus - I just want to make sure you're aware of the Python wrappers included in the APBS release - they can be found in the tools/python directory. Whether or not this directory automatically compiles is based on your architecture - if you don't see apbslibc.so in this directory, you'll need to run the Makefile explicitly. The directory has a main.py that essentially mirrors the main.c that drives APBS. I've recently added a couple of useful functions which may help you avoid needing to use an input file - instead of using (main.py L145) input_file = sys.argv[1] stdout.write("Parsing input file %s...\n" % input_file) if NOsh_parseFile(nosh, input_file) != 1: etc, etc you should now be able to use sock = Vio_setup("r", "BUFF","ASC", "localhost", "0", inputtext) if not NOsh_parse(nosh, sock): etc, etc where inputtext is a string containing the entire input file. This way you should be able to create the string as desired at the Python level and then pass the string to APBS accordingly. This change is currently only available from the nightly CVS snapshot, which you can download from http://agave.wustl.edu/apbs/download/ If you have any more questions please let me know! Todd On Sat, 2004-10-16 at 12:16, Markus J. Buehler wrote: > Hallo, > > We would like to interface APBS to our PYTHON multiscale simulation > framework for coupling with quantum/force field codes. Therefore, I would > need to set up the parameters not by reading a parameter file, but instead > by setting them directly at the PYTHON layer. > > What steps would I have to take in order to achieve this goal? I was > thinking of instead of calling "Nosh_parseFile (..)", I would set all > required parameters "by hand" (that is, define all required objects to feed > into the simulation such as calc, mgparm, pbeparm...). > > Has anyone ever done this or is there an example where this has been coded? > Is there any advice how to proceed? > > Thanks, > Markus > > ---------------------------------------------------------------------- > Dr. Markus Buehler > Materials and Process Simulation Center > Beckman Institute M/C 139-74 > California Institute of Technology > 1201 East California Blvd., Pasadena, 91125, CA, USA > Email mbu...@wa... > Homepage http://www.wag.caltech.edu/home/mbuehler/ > ---------------------------------------------------------------------- > > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users |