0.7.9

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

0.7.8

Fixed:

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

Authors:

• Cas
• Hadrien Mary

0.7.7

Added:

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

Fixed:

• Fix the API doc.

Authors:

• Hadrien Mary

0.7.6

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

0.7.5

Added:

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

Authors:

• Hadrien Mary

0.7.4

Changed:

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

Authors:

• Hadrien Mary

0.7.3

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

0.7.2

Changed:

• allow_r_groups option in dm.align.auto_align_many

Removed:

• should_align

Authors:

• Hadrien Mary
• michelml

0.7.1

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

0.7.0

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