Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of chembl-downloader

chembl-downloader - v0.5.2

This is the version that corresponds to the JOSS publication

What's Changed

  • Add paper and update notebooks by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/19
  • Add shortcut for querying for a scalar by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/23
  • Get version from HTTPS instead of FTP by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/24
  • Improve handling of versions by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/22
  • Replace internal removeprefix function by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/25
  • Switch downloads to HTTPS by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/27
  • Refactor logic for extracting SQLite database from a TAR archive by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/28
  • Enable passing version info by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/29
  • Automate generating temporal summaries by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/26
  • Extend historical analysis by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/30
  • Fix analysis on ChEMBL v9 by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/31

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.5.1...v0.5.2

- Jupyter Notebook
Published by cthoyt 9 months ago

chembl-downloader - v0.5.1

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.5.0...v0.5.1

- Jupyter Notebook
Published by cthoyt 10 months ago

chembl-downloader - v0.5.0

What's Changed

  • Update cruft by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/15
  • Update typing by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/17
  • Load fingerprints w/ NumPy by @cthoyt in https://github.com/cthoyt/chembl-downloader/pull/16

Full Changelog: https://github.com/cthoyt/chembl-downloader/compare/v0.4.5...v0.5.0

- Jupyter Notebook
Published by cthoyt over 1 year ago

chembl-downloader - v0.4.5

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

- Jupyter Notebook
Published by cthoyt over 2 years ago

chembl-downloader - v0.4.4

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

- Jupyter Notebook
Published by cthoyt over 2 years ago

chembl-downloader - v0.4.3

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

- Jupyter Notebook
Published by cthoyt over 2 years ago

chembl-downloader - v0.4.2

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

- Jupyter Notebook
Published by cthoyt over 2 years ago

chembl-downloader - New notebooks and uniprot mapping function

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

- Jupyter Notebook
Published by cthoyt over 3 years ago

chembl-downloader - 🧪⚗️🧪 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

- Jupyter Notebook
Published by cthoyt over 3 years ago

chembl-downloader - 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/chembl30monomer_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.

- Jupyter Notebook
Published by cthoyt about 4 years ago

chembl-downloader - 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.

- Jupyter Notebook
Published by cthoyt over 4 years ago

chembl-downloader - 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:

```python from rdkit import Chem

import chembl_downloader

library = chembldownloader.getsubstructure_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

- Jupyter Notebook
Published by cthoyt over 4 years ago

chembl-downloader - v0.1.2

  • Add get_assay_sql() function

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

- Jupyter Notebook
Published by cthoyt over 4 years ago

chembl-downloader -

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

- Jupyter Notebook
Published by cthoyt almost 5 years ago

chembl-downloader -

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

- Jupyter Notebook
Published by cthoyt almost 5 years ago

chembl-downloader -

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

- Jupyter Notebook
Published by cthoyt almost 5 years ago

chembl-downloader -

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

- Jupyter Notebook
Published by cthoyt almost 5 years ago

chembl-downloader -

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

- Jupyter Notebook
Published by cthoyt almost 5 years ago

chembl-downloader -

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

- Jupyter Notebook
Published by cthoyt almost 5 years ago