Changed
- Name of `moldrug.fitness.get_mol_cost` to `moldrug.fitness.__get_mol_cost` function.
- The class `moldrug.utils.GA` does not have any more the method `roulette_wheel_selection`; now is part a function that could be called from `moldrug.utils`
- `max` for `max_conf` in `moldrug.constraintconf.constraintconf()` function.
- Entrance point constraintconf was changed to constraintconf_moldrug and now it is link to `moldrug.cli.__constraintconf_cmd` instead `moldrug.constrainconf.constraintconf_cmd`.
- Name of the function `moldrug.fitness.vinadock` now is `moldrug.fitness.__vinadock`.
- Name of the function `moldrug.cli.moldrug_cmd` now is `moldrug.cli.__moldrug_cmd`.
Fixed
- Cleaning the code
- If `vina_executable` is provided (to any cost function) and it represents a path. It will be try to convert to absolute path. Previously relative path to the executable were not understood properly.
- Improve docs.
Added
- `ad4map` in all the cost functions of the `moldrug.fitness` module. This parameters specify the path where the ad4 map files are. To use this feature you must have the AutoDcok Vina v1.2.3 of above. Now you can use the force fields of AD4 inside of Vina. Future release will extend the integration with this versions.
- `moldrug.utils.to_dataframe`. THis function was previously isolated as a method of the class `moldrug.utils.GA`; now it could also be called as a function.
- `kept_gens` attribute to the `Individual`s inside of `moldrug.utils.GA`. This is a set that contains the generations for which the Individual was conserved.
- `acceptance` attribute to `moldrug.utils.GA`. This is a dictionary that has as keyword the generation ID, and as values a dictionary with keywords: `accepted` (number of generated molecules accepted on the current generation) and `generated` (number of total molecules generated)
- Print `Accepted rate= accepted / generated` during running.
- Add hydrogens before create pdbt file with meeko when constrain docking i used.
- `seed_mol` of `moldrug.utils.GA` now could be a list (or iterable in a general way) of RDKit molecules. This feature could be used to combine several MolDrug runs and create a final runs with this combined population.
- `seed_mol` from the command line could be: a valid SMILES, a list of valid SMILES or a list of path to the `_pop.pbz2` binary files. In the last case all the populations will be combined and sorted based on the cost attribute. If the result population is less that `popsize` new structures will be generated to complete the initial population. The individuals of this initial population will be reinitialized and the cost function will be calculated.