Moldrug

Fixed

- Bug during the calculation of probabilities when costs are larger numbers.
- Expose hidden error if some Exception ocurred during parallel run.

Added

- `moldrug.constrainconf` module.
- Raise `ValueError` if `ref_smi` is invalid in `moldrug.utils.constrainconf.generate_conformers`.

Changed

- In case `constraint = True` in `moldrug.fitness.vinadock`, `ref_smi` will be the SMILES string of `constraint_ref` when `moldrug.constrainconf.generate_conformers` is internally called. This is in order to avoid error when `moldrug.utils.constrainconf.generate_conformers` tries to guess `ref_smi` based on MCS and fails, [see this RDKit bug](https://github.com/rdkit/rdkit/issues/5518). The work around for constraint docking is explained here: [Constraint Docking](https://moldrug.readthedocs.io/en/latest/notebooks/constraint_docking.html).
- `moldrug.fitness.generate_conformers` does not fail. In case of Exception it returns the same `mol` without conformers and write the error in a log file into the working directory.
- The attribute name `bestcost` by `best_cost` of `moldrug.utils.GA`.
- The functions `duplicate_conformers`, `get_mcs`, `generate_conformers`, `constraintconf` and `constraintconf_cmd` and the class `ProteinLigandClashFilter` were moved from `moldrug.fitness` module to `moldrug.constrainconf` module.
- Entrance point constraintconf now it is link to `moldrug.constrainconf.constraintconf_cmd` instead `moldrug.fitness.constraintconf_cmd`.

Added

- The functions `duplicate_conformers`, `get_mcs`, `generate_conformers`, `constraintconf` and `constraintconf_cmd` and the class `ProteinLigandClashFilter`. The code was borrowed from [Pat Walters](https://github.com/PatWalters/fragment_expansion/blob/master/rdkit_eval/rd_gen_restricted_confs.py). It is used if constraint docking is needed.
- `constraintconf` can be called from the command line.
- `moldrug.fitness.vinadock()` a simple wrapper around vina. This function will be used for all the implemented cost functions inside of the module `moldrug.fitness`. It could be used for constraint docking.
- `moldrug.data.constraintref`. This module is used for testing in case constraint docking is needed. It has two MolBlock strings: `r_6lu7` and `r_x0161`. That could be easily converted in RDKit molecules..

python
from rdkit import Chem
from moldrug.data import constraintref
mol = Chem.MolFromMolBlock(constraintref.r_x0161)


This molecule is needed for the keyword argument `constraint_ref` of the functions of the `moldrug.fitness` module in case of constraint docking is used.
- Constraint docking capability in all implemented cost functions of the module `moldrug.fitness`.
- `moldrug.data.receptor_pdb`. This module is similar to `moldrug.data.receptor_pdbqt` but in pdb format.
- Documentation and tutorials.

Changed

- `moldrug.utils.make_sdf` only will create the sdf file based on the `pdbqt` attribute. If `pdbqt` is a list, it will work as previous version works with `pdbqts` attribute.
- Name of the module `moldrug.data.receptors` to `moldrug.data.receptor_pdbqt`.
- Name of keyword argument `receptor_path` to `receptor_pdbqt_path` on the cost functions: `moldrug.fitness.Cost` and `moldrug.fitness.CostOnlyVina`.
- Name of keyword arguments `receptor_path`, `vina_score_types`, `boxcenters` and `boxsizes` to `receptor_pdbqt_path`, `vina_score_type`, `boxcenter` and `boxsize` respectively on the cost functions: `moldrug.fitness.CostMultiReceptors` and `moldrug.fitness.CostMultiReceptorsOnlyVina`.
- `smiles` attribute in `moldrug.utils.Individual` now it is always without explicit Hs, despite if the mol attribute has them.

Changed

- `moldrug.utils.Individual` now is a hashable object.
- `moldrug.utils.GA.SawIndividuals` now is a `set` instead of a `list`
- `moldrug.utils.update_reactant_zone` sets the keywords `matchValences` and `ringMatchesRingOnly` to True on rdFMCS.FindMCS. This prevent undesired effects. E.g:

python
from moldrug.utils import update_reactant_zone
from rdkit import Chem
mol1 = Chem.MolFromSmiles('c1ccccc1')
mol2 = Chem.MolFromSmiles('CCCN')
update_reactant_zone(parent=mol1,offspring=mol2 parent_replace_ids = [0,2])


Before the results was: `([0, 2, 3], [])`. Now it is: `([0, 1, 2, 3], [])`. The behavior was because the `ringMatchesRingOnly` is set to `False` by default inside RDKit.

Removed

- `moldrug.utils.timeit`. No longer needed.

Added

- Documentation.

Removed

- `Popen` option in `moldrug.utils.run`.

Changed

- `RuntimeError` by `warnings.warn` when vina run fails and save every error as `idx_error.pbz2`. Where idx is the index of the failed individual.
- Print format when `mutate` fails inside of `moldrug.utils.GA`

Added

- Print MolDrug's version when the command line is used.

Fixed

- Hidden `RuntimeError` in `moldrug.fitness` module.
- Bug printing number of generations in final info.

Removed

- Unused code in `moldrug.home` module.
- 3D conformation in the `mol` attribute of the Individual during initialization.
- The use of `grow_mol` in the initialization of the populating when `get_similar = True`. Now the population is initialized with `mutate_mol` and the same set of crem parameters used during the searching.
- The automatic addition of Hs in the case where `min_size` and/or `max_size` were equal to zero. Now if your intention is work with the hydrogens, you must provided a SMILES with the explicit Hs. In the future the input could be just a RDKit mol. Now you must specify if you would like to add explicit Hs to the molecule withe keyword `AddHs`; default is False and is used for both `moldrug.utils.GA` and `moldrug.utils.Local`.

Added

- Handling vina RuntimeError and keeping track for debug. This feature is used to identify what is the error. In the future will be removed.
- Two new fitness functions: `moldrug.fitness.CostOnlyVina` and `moldrug.fitness.CostMultiReceptorsOnlyVina`. They only use the information of vina scoring function. See the [docs](https://moldrug.readthedocs.io/en/latest/source/modules/fitness.html) for more info about it.
- Tracking of atom indexes during generations in order to use `protected_ids` and `replace_ids` options of `mutate_mol` function of [CReM](https://github.com/DrrDom/crem). Before it was not possible; the use of these features generate undesired solutions because the indexes are not static over generations. Even so, there are still some problems for symmetric molecules. We are working on it.

Changed

- The whole MolDrug works base on the RDKit mol instead of the SMILES string:
1. `moldrug.utils.Individual` is now initialized `mol` instead `smiles`. Now the SMILES string is generated internally, it still used as identifying for the instance.
2. `moldrug.utils.GA` changed `smiles` for `seed_mol` and it is not needed the `mol` variable any more.
3. `moldrug.utils.Local` changed `mol` for `seed_mol` in the initialization variables..
4. `moldrug.utils.confgen` changed smiles for `mol` variable.

Fixed

- Minor cleaning code.
- Bug during the import of user custom cost function.

Added

- `outdir` option for the command line.
- User custom desirability.