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Avoid cryptic symbols in API #7

Closed franknoe closed 9 years ago

franknoe commented 9 years ago

Many API functions have functions named after specific symbols used in a paper. Since there is no unique or even agreed-upon way of using symbols for these equations, I would rather use brief terms / words in most cases.

Examples in dTRAM

    'set_lognu',
    'iterate_lognu',
    'iterate_fi',
    'get_pk',
    'get_p',
    'get_fk',
cwehmeyer commented 9 years ago

So, in this style?

set_lognu -> initialize_log_lagrangian_multipliers iterate_lognu -> update_log_lagrangian_multipliers iterate_fi -> update_ground_state_free_energies get_pk -> estimate_all_transition_matrices get_p -> estimate_single_state_transition_matrix get_fk -> get_thermodynamic_free_energies

franknoe commented 9 years ago

Maybe a bit briefer (the name doesn't need to tell the full story, it just needs to be recognizable) ||

|set_lognu| -> |init_lagrangian_mult| |iterate_lognu| -> |update_lagrangian_mult| |iterate_fi| -> |update_conf_energies| |get_pk| -> |estimate_transition_matrices| |get_p| -> |estimate_transition_matrix| |get_fk| -> |get_therm_energies|

Am 04/10/15 um 08:02 schrieb Christoph Wehmeyer:

So, in this style?

|set_lognu| -> |initialize_log_lagrangian_multipliers| |iterate_lognu| -> |update_log_lagrangian_multipliers| |iterate_fi| -> |update_ground_state_free_energies| |get_pk| -> |estimate_all_transition_matrices| |get_p| -> |estimate_single_state_transition_matrix| |get_fk| -> |get_thermodynamic_free_energies|

— Reply to this email directly or view it on GitHub https://github.com/markovmodel/thermotools/issues/7#issuecomment-145320471.

Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de

Mail: Arnimallee 6, 14195 Berlin, Germany