0.6.9

Added:

• Support for selfies<2.0.0 in tests

Changed:

• Behaviour of all inchi functions to return None with a warning instead of silently returning an empty string
• Order of str evaluation on convertion function. isinstance(str) is now evaluated before is None

Fixed:

• Bug in unique_id making this evaluation falling back on 'd41d8cd98f00b204e9800998ecf8427e' on unsupported inputs. Instead None is returned now

Authors:

• Emmanuel Noutahi

0.6.8

Changed:

• Add remove_hs flag in dm.read_sdf().

Authors:

• Hadrien Mary

0.6.7

Added:

• Add dm.descriptors.n_aromatic_atoms
• Add dm.descriptors.n_aromatic_atoms_proportion
• Add dm.predictors.esol
• Add dm.predictors.esol_from_data

Changed:

• Make descriptors a folder (backward compatible).
• Rename any_descriptor to any_rdkit_descriptor to be more explicit.

Authors:

• Hadrien Mary

0.6.6

Added:

• Add dm.conformers.align_conformers() to align the conformers of a list of molecules.

Changed:

• New lower bound rdkit version to >=2021.09. See #81 for details.

Authors:

• Hadrien Mary

0.6.5

Fixed:

• Catch too long integer values in set_mol_props and switch to SetDoubleProp instead of SetIntProp

Authors:

• Hadrien Mary

0.6.4

Changed:

• Expose the clean_it flag when enumerating stereoisomers.

Authors:

• Hadrien Mary
• Julien Horwood

0.6.3

Added:

• Parameters allowing to customize or ignore failures when running the conformer generation.

Changed:

• When the conformer embedding fails, it will now optionally fall back to using random coordinates.

Authors:

• Hadrien Mary
• Julien Horwood

0.6.2

Added:

• Add a new total arg in dm.parallelized() (only useful when the progress is set to True)

Changed:

• Prevent tqdm_kwargs`` collision in dm.parallelized()`.

Authors:

• Hadrien Mary

0.6.1

Added:

• Add dm.to_inchi_non_standard() and dm.to_inchikey_non_standard() in order to generate InChi values that are sensitive to tautomerism as well as undefined stereoisomery.
• Add dm.unique_id to generate unique molecule identifiers based on dm.to_inchikey_non_standard

Changed:

• Add use_non_standard_inchikey flag argument to dm.same_mol.

Authors:

• Hadrien Mary

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