webng.core package

Submodules

webng.core.exc module

exception webng.core.exc.weBNGError

Bases: Exception

Generic errors.

webng.core.version module

webng.core.version.get_version(version=(0, 0, 8, 'alpha', 0))

webng.core.weAnalysis module

class webng.core.weAnalysis.weAnalysis(args)

Bases: object

This is the core analysis class that will be used by the command line tool when called with the subcommand webng analysis.

The class needs the analysis dictionary from the configuration file for initialization and when you use the run method it will go through the dictionary, calling the appropriate analysis tools with the subdictionaries of each, in the appropriate order.

run() → None

webng.core.weConvert module

class webng.core.weConvert.weConvert(args)

Bases: object

This is the class that will be used by the command line tool when it’s called with the subcommand webng setup.

The class needs the dictionary from configuration YAML file for initalization and will use the options there to setup the WESTPA simulation folder.

The run method will use the parsed options and make the WESTPA simulation folder using the templates it contains. TODO: Use jinja for templating instead.

copy_run_network()

this copies the run_network binary with correct permissions to where WESTPA will expect to find it.

make_sim_folders()

make folders WESTPA needs

run()

runs the class functions in appropriate order to make the WESTPA simultion folder

run_BNGL_on_file()

this function runs the BNG2.pl on the given bngl file to get a) .net file for the starting point and b) .gdat file to get the first voronoi center for the simulation

write_dynamic_files()

these files change depending on the given options, in particular sampling and binning options

write_static_files()

these files are always (mostly) the same regardless of given options

webng.core.weTemplater module

class webng.core.weTemplater.weTemplater(args)

Bases: object

This is the class that will be used by the command line tool when it’s called with the subcommand webng template.

The class needs and object containing input/output attributes (usually a argparser object) for initialization.

The run method will write a template webng config file using the given options as well as paths acquired from imported libraries.

run()

Module contents