3.2.2 - 2022.12.12

Fixed

• Bug: The initial individual was not printed properly.

Removed

• Redundant code in moldrug.utils.GA

3.2.0 - 2022.11.28

Fix

• Bug: 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. (on the last version the naming was not changing)

Removed

• moldrug.fitness.is_inside_box
• Bug: constraint_check_inside_box option for the cost functions of moldrug.fitness

3.1.0 - 2022.11.28

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.

3.0.3 - 2022.11.26

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.

3.0.1 - 2022.11.24

Fixed

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

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.

2.1.12 - 2022.09.29

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 onmoldrug.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"])

2.1.7 - 2022.09.02

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.

2.1.0 - 2022.08.30

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. The work around for constraint docking is explained here: Constraint Docking.
• 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.

2.0.0 - 2022.08.25

Added

• The functions duplicate_conformers, get_mcs, generate_conformers, constraintconf and constraintconf_cmd and the class ProteinLigandClashFilter. The code was borrowed from Pat Walters. 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..

  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.