chembl-downloader

What's Changed

• Added max_phase as an option by @jhylin in https://github.com/cthoyt/chembl-downloader/pull/13

New Contributors

• @jhylin made their first contribution in https://github.com/cthoyt/chembl-downloader/pull/13

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.4.4...v0.4.5

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.4.3...v0.4.4

What's Changed

• Refresh datasets from Cortés-Ciriano by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/9
• Update README.md by @YojanaGadiya in https://github.com/cthoyt/chembl-downloader/pull/5
• Update cortes-ciriano-refresh.ipynb by @rflameiro in https://github.com/cthoyt/chembl-downloader/pull/12

New Contributors

• @YojanaGadiya made their first contribution in https://github.com/cthoyt/chembl-downloader/pull/5
• @rflameiro made their first contribution in https://github.com/cthoyt/chembl-downloader/pull/12

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.4.2...v0.4.3

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.4.1...v0.4.2

What's Changed

• Add SQL for getting activities by target by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/8
• Improve ChEBI mapping notebook by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/10
• Add UniProt target mapping functions by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/11

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.4.0...v0.4.1

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

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.

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.

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: https://github.com/cthoyt/chembl-downloader/compare/v0.1.2...v0.1.3

• Add get_assay_sql() function

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.1.1...v0.1.2

Add more top-level imports for download_sdf(), download_sqlite(), and latest()

• rename download() to download_extract_sqlite() to make room for other download functions
• added supplier() function for loading the SDF dump through RDKit

• Update pandas backend for query() function
• Improve CLI

Add query() function for automatically generating pandas DataFrames from a given SQL query

• Fix bug when version not given
• Fix bug where different chembl versions' different folder structures causes problem

Initial release has a download(), connect(), and cursor() function.