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Published February 28, 2025 | Version Release_2024_09_6
Software Open

rdkit/rdkit: 2024_09_6 (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. Schrodinger
  • 11. Fraunhofer ITMP (Hamburg)

Description

Release_2024.09.6

(Changes relative to Release_2024.09.5)

Backwards incompatible changes

  • The colors of annotations on atoms and bonds in drawings are now controlled by the drawing options atomNoteColour and bondNoteColour instead of the general annotationColour.

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)

Andrey Alekseenko, Martin Buttenschoen, David Cosgrove, Tad Hurst, Gareth Jones, Brian Kelley, Niels Maeder, Jeremy Monat, Jan Oboril, Yakov Pechersky, Ricardo Rodriguez, Wonseok Shin, Paolo Tosco, Mike Trzaska, Riccardo Vianello, JessJKitty, laurenreid1,

New Features and Enhancements:

  • export the targets with a python dependency to a different config file (github pull #7914 from rvianello)
  • Option to put padding round elements of reaction. (github pull #8216 from DavidACosgrove)
  • Add property to track reactant index in reaction products (github issue #8222 from bp-kelley)
  • Rascal: Add option to specify minimum clique size directly. (github pull #8248 from DavidACosgrove)
  • MolDraw2D: add separate colors for atom and bond annotations (github pull #8249 from greglandrum)
  • Restore functionality of the MinimalLib Dockerfile and improve exception handling performance (github pull #8267 from ptosco)
  • Option to preserve default text colors when highlighting atoms. (github issue #8271 from JessJKitty)
  • Tweak mol fragmenter (github pull #8277 from DavidACosgrove)
  • Expose basinThresh to the python layer (github pull #8283 from nmaeder)
  • bump InChI version to 1.07.3 (github pull #8300 from greglandrum)

Bug Fixes:

  • UFF optimization leads to overlapping atoms (github issue #7901 from oboril)
  • Generating inchi for chiral phosphates raises a warning (github issue #8238 from pechersky)
  • Chiral phosphates no longer generate distinct inchi (github issue #8239 from pechersky)
  • RascalMCES.FindMCES Produces Incorrect SMARTS Output (github issue #8246 from gratus907)
  • Segmentation fault in EmbedMultipleConfs (github issue #8250 from maabuu)
  • Rascal - Missing atoms in MCESs (github issue #8255 from laurenreid1)
  • PR #8192 breaks AdjustQueryProperties / aromatizeIfPossible for some molecules. (github issue #8256 from ricrogz)
  • MolBlocks should fail to write when given coordinates that are too large (github issue #8265 from bp-kelley)
  • trimethylcyclohexane chirality error (github pull #8272 from tadhurst-cdd)
  • Some mem fixes. (github pull #8276 from ricrogz)
  • Fix buffer size in pickersCLI.cpp (github pull #8282 from al42and)
  • Another mem leak fix to the InChI conversion (github pull #8291 from ricrogz)
  • Fix memory leaks in MolStandardize SWIG Wrapper (github pull #8298 from jones-gareth)

Files

rdkit/rdkit-Release_2024_09_6.zip

Files (85.2 MB)

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md5:25aaee8c110f3f43ed969e64c478da14
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Additional details

Related works

Is supplement to
Software: https://github.com/rdkit/rdkit/tree/Release_2024_09_6 (URL)

Software

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