Moldrug

Added

- `moldrug.constraintconf.gen_aligned_conf`
- In case that `moldrug.constraintconf.generate_conformers` fails with `rdkit.Chem.AllChem.ConstrainedEmbed` it will try with `moldrug.constraintconf.gen_aligned_conf`.
- `moldrug.fitness.is_inside_box`
- `constraint_check_inside_box` arguments to the cost functions of `moldrug.fitness`. If the coordinates of the constraint conformation are outside the box; use always local_only, by default False

Changed

- The output error name when constraint fails has a idx prefix. E.g. 33_conf_27_error.pbz2 now is: idx_33_conf_27_error.pbz2. Now it is easy to delete all of this files at the end of the simulation if they are not needed.

Fix

- Clean code.
- Improve docs.

Added

- Warning in case `moldrug.utils.Local` or `moldrug.utils.GA` are called with a different **MolDrug** as they were initialized.

Changed

- Convert to absolute path `receptor_pdbqt_path` and `vina_executable` (in case that it points to a file) inside of `moldruf.fitness.__vinadock`.

Fixed

- Bug for hydrogens coordinates when constrain docking was used.
- Improve docs.

Fixed

- Cleaning code.
- Sort the initial population based on the cost attribute when it is saved on disk.
- Improve docs.

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.

Added

- `score_only` bool parameter to `moldrug.fitness.get_mol_cost`.
- Print starting date when MolDrug is called from the command line.

Removed

- Type Hints `int` for attribute `idx` on`moldrug.utils.Individual`.

Changed

- If vina fails inside `moldrug.fitness.vinadock`; give as pdbqt the string "VinaFailed".
- If the molecule has a molecular weight highest than `wt_cutoff` when `moldrug.fitness.CostOnlyVina` (or `moldrug.fitness.CostMultiReceptorsOnlyVina`) is called; the pdbqt attribute of the returned Individual will be the string "TooHeavy" (or the list of strings List["TooHeavy"])

Fixed

- Bug on `moldrug.fitness.vinadock` during searching of MCS between `Individual.mol` and `constraint_ref`. Before was needed to manually specified the atom ids of the `seed_mol` that match `constraint_ref`, now it is not needed any more.
- Bug during handling exception in `moldrug.constraintconf.generate_conformers`.
- Bug during handling exception `moldrug.constraintconf.generate_conformers` in `moldrug.fitness.vinadock`.
- Bug(s) when constraint docking is used on different vina versions. The output of vina is not the same and therefore `moldrug.fitness.vinadock` failed.

Changed

- In case `constraint = True` in `moldrug.fitness.vinadock`, `ref_smi` will be the the MCF between `individual.mol` amd `constraint_ref` instead the SMILES string of `constraint_ref` when `moldrug.constrainconf.generate_conformers` is internally called.

Added

- `moldrug.fitness.get_mol_cost` function.
- Attribute `genID` to the generated individuals during a `moldrug.utils.GA` run.