BBOMol v0.1.1

New features

• Adding the possibility to select the number of threads used for each DFT calculation.
• Adding the possibility to select the DFT method and the memory allocated for each DFT calculation.
• Adding the option to select the property to be plotted by ** best so far ** plots.
• Now extracting the objective function computation times from EvoMol result files.
• Adding the possibility to add a point in ** best so far ** plots to represent the last value that has been obtained in all runs in the x axis.
• The probability of improvement (POI) merit function can now be used.
• Adding an option to set a threshold on the training set size of the surrogate. If more samples are in the dataset, a subset of the threshold size is drawn with uniform probability.
• Now supporting a random molecular descriptor.

Behaviour changes

• Updating legends of grid molecules drawing so that integer values are written without decimal values.
• Now printing the number of times the target was reached when displaying an ERT array.

Others

• Updating installation procedure and instructions.
• Updating version name.

Bug fixes

• Updating the code so that it is compatible with recent scikit-learn versions.
• Updating the code so that it is compatible with recent pandas versions.
• Fixing bug so that it is possible to plot properties that are represented in several columns in EvoMol output results.
• Updating postprocessing code so that it is possible to load EvoMol output files that do not contain objective computation time information.
• Fixing bug so that BBOMol can be used with latest EvoMol versions (recording computation time of evaluations).
• Fixing bug so that the calculation of the EI for the complete population works even if there are duplicate solutions.
• Fixing bug that occurs when comparing SMILES from init population by recomputing canonical SMILES before comparison
• Fixing bug so that the draw_best_solutions function can save images to disk even when used from a jupyter notebook.

BBOMol v0.1.0

New features

• Adding the possibility to specify the path to a file that contains the initial SMILES list (design of experiments).
• Adding the possibility to set the "io_parameters" attribute of the EvoMol internal optimization.
• Adding the possibility to plot the distribution of a property depending on ranges of calls to the objective function.
• Adding the possibility to draw the best solutions according to a property for each run of each experiment.

Behaviour changes

• The choice of whether retrieving data from initial step for experiments plotting is now also applied on pure EvoMol experiments.
• All subscores are now retrieved for EvoMol experiments.

Descriptors computation updates

• The descriptor module is now moved to a dedicated and disctinct repositiory : ChemDesc. The documentation of BBOMol is updated in consequence. Before moving, the following changes were made to the module :
• Possibility to give a dictionary that maps shingles SMILES to a unique ID that is used as index in the output descriptor.
• Adding a progress bar display during the computation of descriptors.
• Updating the parallel descriptors computation procedure so that no copies are performed to save memory.
• New options for molecular mechanics computation. Now possible to choose the program that performs the optimization and the force field. Options are (OpenBabel, MMFF94), (RDKit, MMFF94) and (RDKit, UFF).