Datamol is a python library to work with molecules

Added:

• Add PDB read/writer functions: dm.to_pdbblock(), dm.read_pdbblock(), dm.read_pdbfile(), dm.to_pdbfile()

Changed:

• Improve output type in to_df.`

Authors:

• Hadrien Mary

Added:

• Add multiple utilities to work with mapped SMILES with hydrogens.
• Add dm.clear_atom_props() to remove atom's properties.
• Add dm.clear_atom_map_number() to remove the atom map number property.
• Add dm.get_atom_positions() to retrieve the atomic positions of a conformer of a molecule.
• Add dm.set_atom_positions() to add a new confomer to a molecule given a list of atomic positions.

Changed:

• Add new arguments to dm.to_mol: allow_cxsmiles, parse_name, remove_hs and strict_cxsmiles. Refers to the docstring for the details.
• Set copy to True by default to dm.atom_indices_to_mol().
• Allow to specify the property keys to clear in dm.clear_mol_props(). If not set, the original default beahviour is to clear everything.

Authors:

• Hadrien Mary

Fixed:

• Ensure rdkit 2021.03 works with latest datamol. The support is not "official" but only a single function must be adapted so it's ok.

Authors:

• Hadrien Mary

Added:

• Support for max_num_mols in dm.read_sdf(). Useful when files are large and debugging code.
• Support for returning the invalid molecules in dm.read_sdf. Useful when we need to know which one failed.
• Support for more compression formats when reading SDF files using fssep.open(..., compression="infer").
• Add CODEOWNERS file.
• Add dm.descriptors.n_spiro_atoms and dm.descriptors.n_stereo_centers_unspecified.

Changed:

• Overload output types for dm.read_sdf and dm.data.*.
• Reduce tests duration (especially in CI).

Authors:

• DomInvivo
• Hadrien Mary

Changed:

• Add a comment recommending to not use the SMI file format.

Fixed:

• Fix a bug when reading a remote file with dm.read_smi().

Authors:

• Hadrien Mary

Added:

• Parallelization to to_df for faster conversion to dataframe

Fixed:

• Error in docs

Authors:

• Emmanuel Noutahi

Fixed:

• Fix a typo in a tutorial.

Authors:

• Hadrien Mary
• Valence-JonnyHsu

Changed:

• Remove the rdkit dependency in the setup.py to prevent pip to always override the conda rdkit package. See https://github.com/rdkit/rdkit/pull/2690#issuecomment-1295375416 for context.

Authors:

• Hadrien Mary

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

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

Added:

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

Fixed:

Authors:

• Hadrien Mary
• Lu Zhu

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

Fixed:

• Missing header in the fragment tutorial.

Authors:

• Hadrien Mary
• Valence-JonnyHsu

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`` toFalse`.
• 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

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

Fixed:

• Fix minor typos in tutorials

Authors:

• Hadrien Mary
• michelml

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

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

Added:

• datamol.graph.match_molecular_graphs, with unit-tests
• datamol.graph.reorder_mol_from_template, with unit-tests

Changed:

• Typing in datamol.graph.py, changed rdkit.Chem.rdchem.Mol to dm.Mol

Deprecated:

• NOTHING

Removed:

• NOTHING

Fixed:

• NOTHING

Security:

• NOTHING

Authors:

• DomInvivo
• Emmanuel Noutahi

Fixed:

• Bug in dm.conformer.generate() when multiple conformers had equal energies
• Fix the documentation.

Authors:

• Cas
• Hadrien Mary

Added:

• Add dm.read_molblock() and dm.to_molblock() functions.
• Add dm.to_xlsx() function.

Fixed:

• Fix the API doc.

Authors:

• Hadrien Mary

Changed:

• Add joblib_batch_size in dm.parallelized_with_batches() to be able to control the joblib batch size (which is different than the dm.parallelized_with_batches batch size.
• Various small improvements for unit tests.

Authors:

• Hadrien Mary

Added:

• Add dm.parallelized_with_batches() to parallelize workload with a function that take a batch of inputs.

Authors:

• Hadrien Mary

Changed:

• Don't import sasscorer by default but only during the call to dm.descriptors.sas(mol)

Authors:

• Hadrien Mary

Changed:

• Use micromamba during CI.
• Add CI tests for RDKit=2022.03.
• Adapt a test to new rdkit version.

Fixed:

• typing for what is returned by dm.align.template_align

Authors:

• Hadrien Mary
• michelml

Changed:

• allow_r_groups option in dm.align.auto_align_many

Removed:

• should_align

Authors:

• Hadrien Mary
• michelml

Added:

• A new dm.align module with various functions to align a list of molecules. Use dm.align.template_align to align a molecule to a template and dm.align.auto_align_many to automatically partition and align a list of molecules.
• New descriptors: formal_charge
• New descriptors: refractivity
• New descriptors: n_rigid_bonds
• New descriptors: n_stereo_centers
• New descriptors: n_charged_atoms
• Add dm.clear_props to clear all the properties of a mol.
• Add a new dataset in addition to freesolv based on RDKit CDK2 at dm.cdk2().
• Add dm.strip_mol_to_core to remove all R groups from a molecule.
• Add dm.UNSPECIFIED_BOND
• dm.compute_ring_system to extract the ring systems from a molecule.

Changed:

• Improve typing.
• Improve relative imports coverage.
• Adapt dm.to_image to use the align module.

Removed:

• Remove a lot of # type: ignore as those can be error prone (hopefully the tests are here!)

Authors:

• Hadrien Mary

Added:

• Add dm.conformers.keep_conformers in order to only keep one or multiple conformers from a molecules.

Changed:

• Change the conformer generation arguments to use useRandomCoords=True by default.
• Start using explicit Optional instead of implicit Optional for typing.
• Start using relative imports instead of absolute ones.
• When conformers are not minimized, sort them by energy (can be turned to False).

Removed:

• Remove fallback_to_random_coords argument from generate_conformers.

Authors:

• Hadrien Mary

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

Changed:

• Add remove_hs flag in dm.read_sdf().

Authors:

• Hadrien Mary