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Published December 20, 2024 | Version Release_2024_09_4
Software Open

rdkit/rdkit: 2024_09_4 (Q3 2024) Release

Creators

  • 1. CozChemIx Limited
  • 2. Glysade LLC
  • 3. @schrodinger
  • 4. @DEShawResearch
  • 5. Google
  • 6. @merckgroup
  • 7. University of Alabama
  • 8. Schrödinger
  • 9. Wageningen University
  • 10. Fraunhofer ITMP (Hamburg)
  • 11. Company
  • 12. Schrodinger

Description

Release_2024.09.4

(Changes relative to Release_2024.09.3)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to see your contribution acknowledged with your name, please set your name in GitHub)

David Cosgrove, Jozef Fulop, Hussein Faara, Eisuke Kawashima, Brian Kelley, Radics Laszlo, Jeremy Monat, Dan Nealschneider, Rachael Pirie Ricardo Rodriguez, Nikitas Rontsis, Paolo Tosco, Marco Visani, JP,

New Features and Enhancements:

  • NumAmideBonds descriptor missing (github issue #1670 from malteseunderdog)
  • Make sure that loggers can be enabled, disabled, captured and tee'd from MinimalLib (github pull #7962 from ptosco)
  • Add Molecular Interaction Fields (github pull #7993 from greglandrum)
  • Resolve clashing atom labels in 2D drawing (github pull #8074 from DavidACosgrove)
  • Add drawMols3D() and improve documentation for IPythonConsole (github pull #8083 from greglandrum)
  • Allow fragments of aromatic rings to match in RascalMCES (github pull #8088 from DavidACosgrove)
  • SynthonSearch synth check (github pull #8109 from DavidACosgrove)
  • Avoid expensive matching in conformer generation if it's not needed. (github pull #8111 from nrontsis)
  • allow specified chiral features to SSS match unspecified features (github pull #8115 from greglandrum)

Documentation:

  • Getting Started with Contributing to RDKit (github pull #7813 from RPirie96)
  • Some documentation updates (github pull #8080 from greglandrum)
  • document H atoms in SMARTS (github pull #8081 from greglandrum)
  • Add section How to Build RDKit Documentation Locally (github pull #8120 from bertiewooster)

Bug Fixes:

  • Segmentation fault using None as property name in SetProp (github issue #4570 from bp-kelley)
  • MinimalLib and CFFI get_mol() will not remove Hs even when removeHs is set to true (github issue #8027 from ptosco)
  • segfault when parsing molecule with high coordination number (github issue #8060 from garaboncias)
  • Adding Hs to a linear molecule throws "Cannot normalize a zero length vector" (github issue #8065 from ricrogz)
  • Handle DOS files in SynthonSpaceSearch (github pull #8075 from DavidACosgrove)
  • reloading IPythonConsole breaks it (github issue #8082 from greglandrum)
  • Avoid that map::at() throws an exception in case atomColourPalette includes neither 6 nor -1 (github pull #8085 from ptosco)
  • Synthon search fp bug (github pull #8086 from DavidACosgrove)
  • rdDetermineBonds segfaults when called from readonly directory (github issue #8092 from bp-kelley)
  • Tanimoto score exceeds 1 for deuterium-containing molecules in rdShapeAlign.AlignMol() (github issue #8096 from fulopjoz)
  • Rascal returns empty results even when told not to (github issue #8098 from DavidACosgrove)
  • Use endian-aware read/write for length of string. (github pull #8105 from DavidACosgrove)
  • normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter (github pull #8107 from ptosco)

Cleanup work:

  • Remove warnings from npscorer.py (github issue #8052 from mvisani)
  • Minor MinimalLib cleanup (github pull #8112 from ptosco)

Files

rdkit/rdkit-Release_2024_09_4.zip

Files (85.1 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/rdkit/rdkit/tree/Release_2024_09_4 (URL)

Software

Repository URL
https://github.com/rdkit/rdkit