v0.4.5

What's Changed

• Added max_phase as an option by @jhylin in #13

New Contributors

• @jhylin made their first contribution in #13

Full Changelog: v0.4.4...v0.4.5

v0.4.4

Full Changelog: v0.4.3...v0.4.4

v0.4.3

What's Changed

• Refresh datasets from Cortés-Ciriano by @cthoyt in #9
• Update README.md by @YojanaGadiya in #5
• Update cortes-ciriano-refresh.ipynb by @rflameiro in #12

New Contributors

• @YojanaGadiya made their first contribution in #5
• @rflameiro made their first contribution in #12

Full Changelog: v0.4.2...v0.4.3

v0.4.2

Full Changelog: v0.4.1...v0.4.2

New notebooks and uniprot mapping function

What's Changed

• Add SQL for getting activities by target by @cthoyt in #8
• Improve ChEBI mapping notebook by @cthoyt in #10
• Add UniProt target mapping functions by @cthoyt in #11

Full Changelog: v0.4.0...v0.4.1

🧪⚗️🧪 Improve project skeleton and other tasty things

This PR does several things:

1. Removes dependency on bioversions and just implements the code locally
2. Adds a CLI for generating a statistics table for all versions of ChEMBL
3. Add proper project skeleton (documentation, unit tests, code quality assurance, CI)
4. Improve SQLite loading in case you delete the compressed data

Notebooks

1. Adds notebook about drug indications
2. Adds notebook about mapping to ChEBI

Add monomer library functionality 🧪🧪🧪

This release adds two new functions:

1. chembl_downloader.download_monomer_library which gets this file https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_30_monomer_library.xml for whatever version you specify
2. chembl_downloader.get_monomer_library_root which does the same as the downloader but also parses the XML for you

Thanks to @iwatobipen and his recent blog post for inspiring this.

Get fingerprints and chemical representations 🧪⚗️🧪

New Functions

• chembl_downloader.download_fps downloads the pre-computed Morgan fingerprint file
• chembl_downloader.download_chemreps downloads the chembl-smiles-inchi-inchikey map
• chembl_downloader.get_chemreps_df builds on chembl_downloader.download_chemreps and loads them in a pandas dataframe

Misc

• Add isort to code quality checking
• Enable many functions with return_version to make a tuple with the version, which is useful if you're having it infer the latest version.

v0.1.3

This release adds the get_substructure_library() for automating the generation of an RDKit substructure library as described in Greg Landrum's RDKit blog post, Some new features in the SubstructLibrary. The following example shows how it can be used to accomplish some of the first tasks presented in the post:

from rdkit import Chem

import chembl_downloader

library = chembl_downloader.get_substructure_library()
query = Chem.MolFromSmarts('[O,N]=C-c:1:c:c:n:c:c:1')
matches = library.GetMatches(query)

Full Changelog: v0.1.2...v0.1.3

v0.1.2

• Add get_assay_sql() function

Full Changelog: v0.1.1...v0.1.2