3.0.0 - 2022.11.23

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 Individuals 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.