0.8.0

Added:

• dm.Atom and dm.Bond types.
• Add RDKit as a pypi dep.
• Add datamol.hash_mol() based on rdkit.Chem.RegistrationHash.

Changed:

• RDKit 2022.09: use Draw.shouldKekulize instead of Draw._okToKekulizeMol.
• RDKit 2022.09: don't use dm.convert._ChangeMoleculeRendering for RDKit >=2022.09.

Authors:

• Hadrien Mary

0.7.18

Added:

• Added argument product_index in select_reaction_output. It allows to return all products and a product of interest by the index.
• Updated unit tests.

Authors:

• Lu Zhu

0.7.17

Added:

• Added a new chemical reaction module for rdkit chemical reactions and attachment manipulations.

Fixed:

Authors:

• Hadrien Mary
• Lu Zhu

0.7.16

Changed:

• Bump upstream GH actions versions.
• dm.fs.copy_dir now uses the internal fsspec copy when the two source and destination fs are the same. It makes the copy much faster.

Fixed:

• Use os.PathLike to recognize a broader range of string-based path inputs in the dm.fs module. It prevents file objects such as py._path.local.LocalPath not being recognized as path.

Authors:

• Hadrien Mary

0.7.15

Fixed:

• Missing header in the fragment tutorial.

Authors:

• Hadrien Mary
• Valence-JonnyHsu

0.7.14

Added:

• Add with_atom_indices to dm.to_smiles. If enable, atom indices will be added to the SMILES.

Changed:

• Changed the default for dm.fs.is_file() from True`` to False`.
• Refactor the API doc to breakdown all the submodules in individual doc. Thanks to @MichelML for the suggestion.
• Re-enable pipy activity in rever.

Fixed:

• Minor typo in the documentation of dm.conformers.generate()

Authors:

• Cas
• Hadrien Mary
• Valence-JonnyHsu

0.7.13

Added:

• New aligning tutorials.

Removed:

• rdkit dep from pypi (the dep is only on the conda forge package)

Fixed:

• Grammar in tutorials.

Authors:

• Hadrien Mary
• Valence-JonnyHsu

0.7.12

Fixed:

• Fix minor typos in tutorials

Authors:

• Hadrien Mary
• michelml

0.7.11

Added:

• Add configurations for dev containers based on the micromamba Docker image. More informations about dev container at https://docs.github.com/en/codespaces/setting-up-your-project-for-codespaces/introduction-to-dev-containers.
• support for two additional forcefields: MMFF94s with and without electrostatic component
• energies output along with delta-energy to lowest energy conformer

Changed:

• API of dm.conformers.generate() to support choice of forcefield. In addition ewindow and eratio flags added to reject high energy conformers, either on absoute scale, or as ratio to rotatable bonds
• Revamped all the datamol tutorials and add new tutorials. Huge thanks to @Valence-JonnyHsu for leading the refactoring of the datamol tutorials.
• Improve documentation for dm.standardize_mol()
• Multiple various docstring and typing improvments.
• Embed the cdk2.sdf and solubility_*.sdf files within the datamol package to prevent issue with the RDKit config dir.
• Enable strict mode on the documentation to prevent any issues and inconsistency with the types and docstrings of datamol.
• Refactor micromamba CI to use latest and simplify it.

Removed:

• Remove unused and unmaintained dm.actions and dm.reactions module.
• Remove copy args from add_hs and remove_hs (RDKit already returns copies).

Fixed:

• Errors in ECFP fingerprints that computes FCFP instead of ECFP.

Authors:

• Emmanuel Noutahi
• Hadrien Mary
• Matt

0.7.10

Added:

• New possibilities for ambiguous matching of molecules in the function reorder_mol_from_template

Changed:

• Replaced allow_ambiguous_hs_only by the option "hs_only" for the ambiguous_match_mode parameter
• ambiguous_match_mode is now a String, no longer a bool.

Deprecated:

• allow_ambiguous_hs_only is no longer deprecated, but without warning since the feature is brand new.
• Same for ambiguous_match_mode being a bool.

Authors:

• DomInvivo
• Hadrien Mary