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Month: December 2024

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Hints and Tutorials Macinchem Blog Science Apps

STOUT V2.0: SMILES to IUPAC name conversion using transformer models

31 December 202431 December 2024 chris

An interesting publication, using the IUPAC rules for naming compounds can be a challenge for for complex systems. This paper describes a transformer-based model https://doi.org/10.1186/s13321-024-00941-x

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Macinchem Blog Science Apps

ChimeraX updated

16 December 202420 January 2025 chris

UCSF ChimeraX version 1.9 has been released! ChimeraX includes user documentation and is free for noncommercial use.Download for Windows, Linux, and MacOS from:https://www.rbvi.ucsf.edu/chimerax/download.html Updates since

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Macinchem Blog Science Apps

AlvaDesc updated

12 December 202412 December 2024 chris

AlvaDesc v3.0.0 has been updated, it has a few new features but for Mac users it is now fully compatible with Apple Silicon!! AlvaDesc is

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Hints and Tutorials Macinchem Blog

Using VMD and Gromacs on M4 Macs

4 December 202413 January 2025 chris

A reader asks about running VMD and installing Gromacs on M4 Macs. I don’t use either application and looking on the VMD website there is

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  • View post by on Bluesky

    @macinchem.bsky.social 23 hours

    Avogadro 2.0.0 released

    Avogadro is a free and open source molecular editor and visualization tool. The new release of Avogadro 2, is a major update, and includes major changes, a revised interface,...
  • View post by on Bluesky

    @macinchem.bsky.social 3 days

    Looking at mlxmolkit — GPU-accelerated molecular clustering on Apple Silicon

    I've written several posts on the various options for clustering molecules...

    https://macinchem.org/2026/04/03/looking-at-mlxmolkit-gpu-accelerated-molecular-clustering-on-apple-silicon/
  • View post by on Bluesky

    @macinchem.bsky.social 5 days

    RSC CICAG Chemical Structure Representations Meeting 2026 

    I've just signed up for the meeting, hope to see you there at Burlington House, London, UK Wednesday 8th April 2026 A one-day conference...

    https://macinchem.org/2026/04/01/rsc-cicag-chemical-structure-representations-meeting-2026-2/
  • View post by on Bluesky

    @macinchem.bsky.social 6 days

    Mole2D molecule drawing package

    Mole2D is a lightweight molecule drawing package written in Python and PyQt6. All code is on GitHub https://github.com/sfmlab/mole2d and it requires RDKit and PyQt6.. PubChem lookup...

    https://macinchem.org/2026/03/31/mole2d-molecule-drawing-package/
  • View post by on Bluesky

    @macinchem.bsky.social 1 week

    RDKit Updated

    An update to RDKit has been released 2026_03_1 (Q1 2026). Highlights A significant number of known SMILES canonicalization problems were resolved. It's now possible to provide your own matching...

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  • Looking at mlxmolkit — GPU-accelerated molecular clustering on Apple Silicon
  • RSC CICAG Chemical Structure Representations Meeting 2026 
  • Mole2D molecule drawing package
  • RDKit Updated
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