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Datamol Changelogs

v0.7.12

Fixed:

  • Fix minor typos in tutorials

Authors:

  • Hadrien Mary
  • michelml

v0.7.11

Added:

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

v0.7.10

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

v0.7.9

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

v0.7.8

Fixed:

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

Authors:

  • Cas
  • Hadrien Mary

v0.7.7

Added:

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

Fixed:

  • Fix the API doc.

Authors:

  • Hadrien Mary

v0.7.6

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

v0.7.5

Added:

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

Authors:

  • Hadrien Mary

v0.7.4

Changed:

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

Authors:

  • Hadrien Mary

v0.7.3

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

v0.7.2

Changed:

  • allow_r_groups option in dm.align.auto_align_many

Removed:

  • should_align

Authors:

  • Hadrien Mary
  • michelml

v0.7.1

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

v0.7.0

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

v0.6.9

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

v0.6.8

Changed:

  • Add remove_hs flag in dm.read_sdf().

Authors:

  • Hadrien Mary

v0.6.7

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

v0.6.6

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

v0.6.5

Fixed:

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

Authors:

  • Hadrien Mary

v0.6.4

Changed:

  • Expose the clean_it flag when enumerating stereoisomers.

Authors:

  • Hadrien Mary
  • Julien Horwood

v0.6.3

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

v0.6.2

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

v0.6.1

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

v0.6.0

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

v0.5.0

Changed:

  • The default git branch is now main
  • appdirs is now an hard dep.
  • Change CI to use rdkit [2021.03, 2021.09] and add the info the readme and doc.

Fixed:

  • Test related to SELFIES to make it work with the latest 2.0 version.
  • dm.to_mol accept mol as input but the specified type was only str.

Authors:

  • Hadrien Mary

v0.4.11

Fixed:

  • Force the input value(s) of dm.molar.log_to_molar to be a float since power of integers are not allowed.

Authors:

  • Hadrien Mary

v0.4.10

Removed:

  • py.typed file that seems unused beside confusing static analyzer tools.

Authors:

  • Hadrien Mary

v0.4.9

Added:

  • to_smarts for exporting molecule objects as SMARTS
  • from_smarts for reading molecule from SMARTS string

Changed:

  • Allow exporting smiles in kekule representaiton
  • to_smarts is properly renamed into smiles_as_smarts

Authors:

  • Emmanuel Noutahi

v0.4.8

Removed:

  • Revert batch_size fix to use default joblib instead

Fixed:

  • Issue #58: sequence bug in parallel.

Authors:

  • Emmanuel Noutahi

v0.4.7

Added:

  • Add a new function to measure execution time dm.utils.perf.watch_duration.

Changed:

  • Add a batch_size option to dm.utils.parallelized. The default behaviour batch_size=None is unchanged and so 100% backward compatible.

Authors:

  • Hadrien Mary

v0.4.6

Changed:

  • get_protocol is more general

Fixed:

  • Bug in fs.glob due to protocol being a list

Authors:

  • Emmanuel Noutahi

v0.4.5

Added:

  • Add missing appdirs dependency
  • Add missing appdirs dependency

Fixed:

  • Propagate tqdm_kwargs for parallel (was only done for sequential)

Authors:

  • Hadrien Mary

v0.4.4

Added:

  • Add tqdm_kwargs to dm.utils.JobRunner()
  • Add tqdm_kwargs to dm.utils.parallelized()

Changed:

  • Propagate job_kwargs to dm.utils.parallelized()`

Authors:

  • Hadrien Mary

v0.4.3

Added:

  • Add a DOI so datamol can get properly cited.
  • Better doc about compat and CI
  • Add a datamol Mol type: dm.Mol identical to Chem.rdchem.Mol

Changed:

  • Bump test coverage from 70% to 80%.

Authors:

  • DeepSource Bot
  • Hadrien Mary
  • deepsource-autofix[bot]

v0.4.2

Added:

  • More tests for the dm.similarity modules + check against RDKit equivalent methods.
  • dm.same_mol(mol1, mol2) to check whether 2 molecules are the same based on their InChiKey.

Changed:

  • use scipy in dm.similarity.pdist().
  • Raise an error when a molecule is invalid in dm.similarity.pdist/cdist.

Deprecated:

  • dm.similarity.pdist() nows returns only the dist matrix without the valid_idx vector.

Fixed:

  • A bug returning an inconsistent dist matrix with dm.similarity.pdist().

Authors:

  • Hadrien Mary

v0.4.1

Changed:

  • A better and manually curated API documentation.

Authors:

  • Hadrien Mary

v0.4.0

Added:

  • Add support for more fingerprint types.
  • Two utility functions for molar concentration conversion: dm.molar_to_log() and dm.log_to_molar().
  • Add the dm.utils.fs module to work with any type of paths (remote or local).

Authors:

  • Hadrien Mary

v0.3.9

Added:

  • Add a sanitize flag to from_df.
  • Automatically detect the mol column in from_df.
  • Add add_hs arg to sanitize_mol.

Changed:

  • Allow input a single molecule to dm.to_sdf instead of a list of mol.
  • Preserve mol properties and the frist conformer in dm.sanitize_mol.
  • Display a warning message when input mol has multiple conformers in dm.sanitize_mol.

Fixed:

  • Remove call to sanitize_mol in read_sdf, instead use sanitize=True from RDKit.
  • Remove the mol column from the mol properties in from_df. It also fixes to_sdf.

Authors:

  • Hadrien Mary

v0.3.8

Changed:

  • Propagate sanitize and strict_parsing to dm.read_sdf.

Authors:

  • Hadrien Mary
  • Ishan Kumar
  • michelml

v0.3.7

Fixed:

  • Fix again and hopefully the last time google analytics.

Authors:

  • Hadrien Mary

v0.3.6

Changed:

  • Add s3fs and gcsfs as hard dep

Authors:

  • Hadrien Mary

v0.3.5

Authors:

  • Hadrien Mary
  • michelml

v0.3.4

Authors:

  • Hadrien Mary

v0.3.3

Changed:

  • New logo.

Authors:

  • Hadrien Mary

v0.3.2

Fixed:

  • Fixed typo in readme

Authors:

  • Emmanuel Noutahi
  • Hadrien Mary

v0.3.1

Authors:

  • Hadrien Mary

v0.3.0

Added:

  • dm.copy_mol
  • dm.set_mol_props
  • dm.copy_mol_props
  • dm.conformers.get_coords
  • dm.conformers.center_of_mass
  • dm.conformers.translate
  • dm.enumerate_stereoisomers
  • dm.enumerate_tautomers
  • dm.atom_indices_to_mol

Changed:

  • rdkit fp to numpy array conversion is purely numpy-based now (x4 faster).
  • Cleaning of various docstrings (removing explicit types).
  • Clean various types.
  • Allow dm.to_image instead of dm.viz.to_image
  • Add atom indices drawing option to dm.to_image
  • Allow to smiles to fail (default is to not fail but return None as before).
  • Add CXSmiles bool flag to to_smiles.
  • Rename utils.paths to utils.fs
  • Integrate pandatools into dm.to_df.
  • Build a mol column from smiles in read_csv and read_excel
  • Rename dm.sanitize_best to dm.sanitize_first

Fixed:

  • Scaffold tests for new rdkit version
  • Conformer cluster tests for new rdkit version

Authors:

  • Hadrien Mary
  • Therence1
  • michelml
  • mike

v0.2.12

Fixed:

  • Tqdm progress bar update on completion of job and not submission

Authors:

  • Emmanuel Noutahi

v0.2.11

Changed:

  • Make ipywidgets an optional dep.

Authors:

  • Hadrien Mary

v0.2.10

Changed:

  • Propagate more options to dm.reorder_atoms.

Authors:

  • Hadrien Mary

v0.2.9

Added:

  • dm.pick_centroids for picking a set of centroid molecules using various algorithm
  • dm.assign_to_centroids for clustering molecules based on precomputed centroids.

Changed:

  • Make add_hs optional in conformers.generate and removed them when add_hs is True. Explicit hydrogens will be lost.

Fixed:

  • Doc string of dm.pick_diverse

Authors:

  • Emmanuel Noutahi
  • Hadrien Mary

v0.2.8

Added:

  • Added outfile to viz.to_image

Changed:

  • Replace ete3 by networkx due to GPL licensing.
  • Fix some typos in docs.

Fixed:

  • Null pointer exception during conformers generation.

Authors:

  • Emmanuel Noutahi
  • Hadrien Mary
  • Honoré Hounwanou
  • michelml

v0.2.7

Added:

  • Add a test to monitor datamol import duration.

Changed:

  • Add rms cutoff option during conformers generation.
  • Refactor conformer cluster function.

Authors:

  • Hadrien Mary

v0.2.6

Added:

  • Include stub files for rdkit generated using stubgen from mypy.

Authors:

  • Hadrien Mary

v0.2.5

Added:

  • Add to_smi and from_smi in the IO module.
  • Support filelike object in io module.
  • Add kekulization to to_mol

Changed:

  • Switch tests of the IO module to regular functions.

Deprecated:

  • In the IO module, use urlpath instead of file_uri to follow fsspec conventions.

Fixed:

  • Fix bug in read_excel where sheet_name wasnt being used.

Authors:

  • Emmanuel Noutahi
  • Hadrien Mary

v0.2.4

Changed:

  • Constraint rdkit to 2020.09 to get rdBase.LogStatus()

Authors:

  • Hadrien Mary

v0.2.3

Changed:

  • Better rdkit log disable/enable.

Authors:

  • Hadrien Mary

v0.2.2

Added:

  • Test that execute the notebooks.

Fixed:

  • Force rdkit >=2020.03.6 to avoid thread-related bug in rdMolStandardize

Authors:

  • Hadrien Mary

v0.2.1

Added:

  • Add cdist function to compute tanimoto sim between two list of molecules.

Fixed:

  • Fix a bug in dm.from_df when the dataframe has a size of zero.

Authors:

  • Hadrien Mary

v0.2.0

Added:

  • Add all the common sanitize functions.
  • Add the 2_Preprocessing_Molecules notebook.
  • Add fragment module.
  • Add scaffold module.
  • Add cluster module.
  • Add assemble module.
  • Add actions module.
  • Add reactions module.
  • Add dm.viz.circle_grid function
  • Add doc with mkdocs

Authors:

  • Hadrien Mary

v0.1.2

Authors:

  • Hadrien Mary

v0.1.1

Authors:

v0.1.0

Added:

  • first release!

Authors: