0.6.0

Added:

• Add dm.utils.fs.copy_dir() to recursively copy directories across filesystems + tests.
• Add dm.utils.fs.mkdir + tests.
• Add a new dm.descriptors module with compute_many_descriptors and batch_compute_many_descriptors + tests.
• Add dm.viz.match_substructure to highlight one or more substructures in a list of molecules + tests. Note that the current function does not show different colors per match and submatch because of a limitation in MolsToGridImage. We plan to address this in a future version of datamol.
• Add a new mcs module backed by rdkit.Chem.rdFMCS with find_mcs function + tests.
• Add a new function dm.viz.utils.align_2d_coordinates to align 2d coordinates of molecules using either a given pattern or MCS.
• Add dm.canonical_tautomer to canonicalize tautomers.
• Add dm.remove_stereochemistry().
• Add a bond_line_width arg to to_image.
• Add dm.atom_list_to_bond()
• Add enable flag to dm.without_rdkit_log()
• Add a tutorial about the filesystem module.
• Add a tutorial about the viz module (still incomplete).
• Add dm.substructure_matching_bonds to perform a standard substructure match but also return the matching bonds instead of only the matching atoms.
• Add new dm.isomers module + move relevant functions from dm.mol to dm.isomers
• Add dm.add_hs and dm.remove to add and remove hydrogens from molecules.

Changed:

• Set fsspec minimum version to >=2021.9.
• Pimp up dm.utils.to_image to make it more robust (don't fail on certain molecules due to incorrect aromaticity) and also propagate more drawing options to RDKit such as legend_fontsize and others.
• Add a new align argument in dm.to_image() to align the 2d coordinates of the molecules.
• In dm.to_image, use_svg is now set to True by default.
• Change the default mol_size from 200 to 300 in to_image.
• Link datamol.utils.fs to datamol.fs.
• Change default chunk_size in copy_file from 2048 to 1024 * 1024 (1MB).
• Support parallel chunked distances computation in dm.similarity.cdist

Authors:

• Hadrien Mary