cctbxsnips for the Atom text editor

CCTBX

CCTBX is the Computational Crystallography Toolbox. Its development is based at Lawrence-Berkeley National Laboratory. It provides code for computations with diffraction data and atomic coordinates of proteins and small molecules. It has C++ and Python ports. It is available in Anaconda in the conda-forge channel as cctbx-base for python3.8 through 3.11 for Windows, macOS, and Linux.

Blaine's cctbx install protocol

I assume that Anaconda has already been installed. We will create a conda env specifically for CCTBX. CCTBX has numerous dependencies. It is best kept in an isolated env. We also create the correpsonding Jupyter notebook kernel while we are at it.

Execute one line at a time: Wait for the execution to finish before executing the next line.

conda create --name cctbx39 python=3.9
conda activate cctbx39
conda install -c conda-forge cctbx-base -y
conda install ipykernel -y
python -m ipykernel install --user --name cctbx39 --display-name "cctbx python3.9"

The second to last command triggers the installation of Jupyter in the cctbx39 env. The last command creates and installs the Jupyter kernel in ~/Library/Jupyter/kernels/cctbx39 on the Mac. Select cctbx python3.9 from the list of kernels when opening a new notebook in Jupyter.

Replace the 3.9 or 39 above with whatever version of Python you want to use (between 3.8 and 3.11).

The problems that this repo addresses

Facilitation of code reuse. The use of code snippets can save time by reusing existing code. The presence of tab stops in code snippets can help ensure that all parameters that need customization to a new problem are considered. Thus, tab stops can reduce subsequent debugging.
Use of Atom to edit Jupyter and Colab code and markdown cells The existing snippet formats for Jupyter and Colab notebooks do not support tab triggers and tab stops: These are standard features of code snippet systems in most text editors. We can overcome these limitations by sending the active code cell to Atom via the GhostText extension for the browser.

Installation of the snippets

1. Install the snippets for Atom.

You will need the snippets package to be able to use the cctbx snippets in Atom. The package installer is very intuitive. Go to Packages → Settings View → Install packages/themes. Search for snippets and click the install button. It may already be installed, but you must make sure that the snippets package is enabled (green bar along the button).

The snippets for all programming languages are stored in a single coffeescript file that is called snippets.cson. The snippets for different languages are separated by the first line of a snippet library for a specific language. This line contains a specification of the scope--the kinds of script files to which a set of snippets applies. The snippets.cson file is stored in a hidden folder on your home directory called ~.atom/snippets.cson. You can concatenate the file of cctbx snippets for Atom to your existing snippets.cson file. To do this, Mac users enter: cp -a ~/cctbxsnips-Atom/cctbxsnippets.cson ~/.atom/snippets.cson.

2. Optional setup to edit live Jupyter and Colab cells.

If you want to use these snippets from Atom to edit live cells in Jupyter or Colab notebooks, install GhostText browser extension in your browser and the GhostText package for Atom. The GhostText package for Atom can be installed with Atom's command-line package manager (apm) by running the following command in your terminal: apm i GhostText/GhostText-for-Atom

Related repositories

cctbxsnips-Emacs CCTBX snippets for the yasnippet snippet system in for Emacs.
cctbxsnips-SublimeText3 CCTBX snippets for Sublime Text 3 (ST3).
cctbxsnips-VSC CCTBX snippets for Visual Studio Code (VSC).
cctbxsnips-UltiSnips CCTBX snippets for Vim or NeoVim via UltiSnips plugin.
cctbxsnips-neosnippets CCTBX snippets for Vim or NeoVim via neosnippets plugin.
cctbxsnips-Snipmate CCTBX snippets for Vim or NeoVim via snipmate plugin.
Jupyterlab cctbx snippets CCTBX snippets for JupyterLab with the jupyterlab-snippets extension or the jupyterlab-snippets-mutlimenus extension.
Jupyterlab cctbx plus snippets The variant of the jupyterlabcctbxsnips library with comments to guide editing of the snippets.
Colab cctbx snippets Colab snippets.