3.4.0 - 2023.03.10

Added

• Continuation option to the command line.
• moldrug.cli.CommandLineHelper class to work with the parameters passed through the command line.
• checkpoint option to moldrug.utils.GA.
• MolDrug-Dashboard add-on. This is not included on the package itself, but could be used online or locally. In the case of locally you must check Streamlit, the requirements.txt and the app script.
• retunr_mol option to utils.to_dataframe

Changed

• The warnings are not printed for: moldrug.fitness._vinadock and moldrug.constraintconf.generate_conformers. Now, only at the end of a MolDrug simulation a note will be printed if the error.tar.gz file is created.
• moldrug.utils.run does not print extra info if the command fails. It only raises the corresponded RuntimeError.
• moldrug.fitness.__vinadock by moldrug.fitness._vinadock.
• Remove conformers that clash with the protein in case of score_only, for local_only vina will handle the clash.

Fixed

• Small bug during initialization of population with multiple seed_mol. Now seed_mol with the same amount of elements as popsize are not submitted to mutations, only evaluation.
• Problems with default parameters definition on the command line. Parameters with default values by the type of run defined in the configuration file are not needed to redefined any more; moldrug.cli will guess those.