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Category: Other Tips

Other tips or tutorials

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Macinchem Blog Other Tips

An AutoDock Vina script

8 December 20231 January 2024 chris

Another script from the fantastic MayaChemTools collection created by Manish Sud. A new command line script named VinaPerformDocking.py. The script relies on the presence of AutoDock Vina, Meeko,

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Macinchem Blog Other Tips Science Apps

REINVENT4

7 November 20237 November 2023 chris

REINVENT is a molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design, molecule optimization, and other small molecule design tasks. At

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Macinchem Blog Other Tips Science Apps

Parallel docking using EasyDock

5 November 20235 November 2023 chris

As virtual libraries get ever larger the challenges of virtual screening get larger. Whilst docking into a target protein is a very popular and successful

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Macinchem Blog Other Tips

Excel update helps scientists

23 October 202323 October 2023 chris

Whilst Excel is widely regarded as ubiquitous I avoid using it for many reasons. In particular, the “helpful” automatic formatting of data. However it sounds

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Macinchem Blog Other Tips

Important notice for BBEdit users

26 September 202326 September 2023 chris

I just got a message about my favourite text editor. They also updated the macOS compatibility page on the web site with this information. BBEdit is a

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Macinchem Blog Other Tips

New PyMOL script

31 July 202331 July 2023 chris

I just got details of a new script for PyMOL. The script PyMOLVisualizeFpockets.py relies on the presence of PyMOL in your environment and provides functionality to

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Macinchem Blog Other Tips

Using GitHub Copilot within Xcode

5 May 20235 May 2023 chris

GitHub Copilot uses the OpenAI Codex to suggest code and entire functions in real-time, right from your editor. https://github.com/features/copilot Whilst I’m hoping that Apple will

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Hints and Tutorials Jupyter Notebook Other Tips

Structure-based searching SQLite database

12 April 202318 February 2025 chris

The previous couple of pages described creating a SQLite database using the Terminal https://macinchem.co.uk/2023/04/12/using-sqlite-for-exact-search/ and then running exact searches from a Jupyter notebook, python script or ChemDraw

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Applescript Hints and Tutorials Other Tips

Other ways of using the exact search

12 April 202315 February 2025 chris

A Python Script At the end of the previous page on setting up and accessing a Sqlite datasets from a Jupyter notebook there was and example of

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Hints and Tutorials Other Tips Science Apps

Using sqlite for exact search

12 April 202312 April 2023 chris

Whilst on most occasions chemical searches involve substructure or similarity searches there are occasions when a simple exact match of a compound identifier (or list

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    Use the Foundation Models framework to access the on-device LLM that powers Apple Intelligence.

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    BindFlow

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