Discover MooersLab/jupyter-atom-pymolpysnips Open Source project

Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.

pymolsnips

Emacs version 29 profile for use with LaTeX in academic writing.

latex-emacs

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

jupyterlabpymolpysnips

Script to facilitate the making of horizontal scripts

EasyPyMOL

Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.

orgpymolpysnips

A collection of links to free and proprietary curve fitting software.

Curve-fitting-software

snippet-org-mode

Blaine's yasnippet snippets for org-mode.

*Document preparation with LATEX in Emacs*

BerlinEmacsAugust2022

LaTeX template for diary, log book, or lab notebook for 2023

diary2023inLaTeX

Brief introduction to functional programming in Emacs Lisp

EmacsATX4May2022

cctbxsnips-SublimeText3

snippets for CCTBX formatted for use with Sublime Text 3

colabpymolpysnips

Library of PyMOL Python snippets for Google Colab.

Beginner’s Guide to Doing Science on the OU Supercomputer

MooersLab

oscer-supercomputer-tutorial

jupyternbclassicpymolpysnips

PyMOL Python snippets for the Classic Jupyter Notebook.

JavaScript

vinacolab

Data Science class 2022

Webpage for the Mooers Lab, along with a blog.

mooerslab.github.io

JavaScript

cctbxsnips-Atom

pymolshortcuts4rna

An extended version of pymolshortcuts for working with RNA structures.

Transfer multiple files by scp without repeated manual password entry

org-structural-biology-snips

multipleFileTransfer

Protocol for making large scale images to be framed or for background images of posters.

PyMOLwallhangings

Quizzes about Emacs to aid learning the key-bindings

qemacs

dsd4xtals

Crystal improvement with Definitive Screening Designs (DSDs)

cctbxsnips-Ultisnips

cctbx-snips for the ultisnips package for Vim and NeoVim

manuscriptInOrg

Manuscript in org-mode

CCTBX snippets for neosnippets package for Vim and NeoVim

cctbxsnips-neosnippets

Python script to convert LaTeX glossaries entries to Typst gloassarium entries

latex-gloassaries-to-typst-gloassarium

Script to populate the folder for talk with the standard subfolders.

setup-talk

posterInLaTeX

Template for making compact poster in LaTeX

Code snippets for colab-notebooks running open-source PyMOL

colabOpenSourcePyMOLpySnips

PyMOL Python snippet library to edit live Jupyter notebook cells with vim or neovim using the ultisnips plugin and the browser plugin GhostText

jupyter-ultisnips-pymolpysnips

diary2022inLaTeX

Dairy for 2022 in LaTeX

Molecular Graphics links for the molecular graphics and structure analysis short course at OUHSC that ran from 2010 to 2019

MolecularGraphicsLinks

PyMOL Python snippet library to edit live Jupyter notebook cells with vim or neovim using the snipmate plugin and the browser plugin GhostText

jupyter-snipmate-pymolpysnips

Excel workbook to compute cryosolutions for the cryopreservation of protein crystals

cryosolution-generation

pymolpysnips

The pymolsnips rewritten in Python. This Python enables direct interaction with the pymol api from other Python environments like electronic notebooks (e.g. Jupyter Notebooks), IDEs, and literate programming documents (e.g., Rmarkdown, org-mode ).

Design of experiments related commands for Voice-In speech-to-text software

design-of-experiments-voice-in

jupyterlabcctbxsnips

jupyterlabcctbxsnipsplus

setup-book

Automated Expansions of English Contractions For Serenade

thewriterslaw

The Writer's Creed

serenade-contractions

JavaScript

emacs30macos13treesitter

Compile emacs30 on macOS 13.2 with support for using tree-sitter

timeSpent

Electronic workbook for tracking effort by project

Script for creating common subfolders in a folder for a manuscript. Also writes a AAAreadme.md file with a description of the role of the subfolders.

setup-manuscript

Blaine's user configuration for scimax

scimaxuserconfig

Template for making slideshows in LaTeX

slideshowTemplateLaTeX

Template for the first submission of a manuscript

manuscriptInLaTeX

PyMOL Python snippet library to edit live Jupyter notebook cells with Emacs using GhostText

jupyter-emacs-pymolpysnips

Landing page for a number of cctbx related snippet libraries.

cctbxsnips

jupyter-vsc-pymolpysnips

PyMOL Python snippet library to edit live Jupyter notebook cells with Visual Studio Code using GhostText

cctbxsnips-snipmate

TalonScript file of expansions for common contractions in English

talon-contractions

Talon

barebonesLaTeX

This is a bare bones LaTeX template document.

Expand English contractions automatically when using Voice In Plus for dictation.

voice-in-plus-contractions

snippet-fundamental-mode

yasnippets snippets for the fundamental-mode

Blaine's neovim init.vim file.

neovim-init-file

PyMOL Python snippet library to edit live Jupyter notebook cells with Sublime Text 3 using GhostText

cctbxsnips-VSC

jupyter-st3-pymolpysnips

rtd-tutorial

Read the docs tutorial

Blaine's pymolrc file, the configuration file for the molecular graphics program.

MooersLabWebpage

Mooers Lab website

pymolrc

snippet-latex-mode

Blaine's personal LaTeX snippets for the latex-mode in Emacs.

cctbxsnips for the Emacs yasnippet package

cctbxsnips-Emacs

Interactive quiz written in Python3 about the basic commands for the dictation plugin Voice In for Google Chrome.

voice-in-basics-quiz

LaTex dominated configuration for Emacs 30

latexemacs30

Writing accountability contract

writingContract

Code snippets to facilitate running several molecular graphics software packages in Colab notebooks.

polyglotmolviz

LaTeXsnippetsInWebpages

vimrc4oscer

dot vimrc file for OSCER

PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.

rstudiopymolpysnips

Emacs configuration file for Emacs on the University of Oklahoma Supercomputing Center

emacs4oscer

jupyterlabpymolpysnipsplus

PyMOL Python Script Writing with Code Templates in Jupyter notebooks with JupyterLab using the Elyra extension

taggedpymolpysnips

Workbook for tracking minutes spent and words written per day per writing project.

writingProgess2023

Blaine's current .vimrc file for his Macbook Pro

vimrc

Slides show presentation on August 3, 2021 at the American Crystallographic Association annual meeting.

ACA2021

cryoEMLinks

CryoEM weblinks and additional

Template in LaTeX for a writing log for thinking about writing projects.

writingLogTemplate

scipy21poster160

Links to journals of interest.

qvim

Quizzes about Vim.

JournalLinks

Slideshow to talk in August 2022 at 72nd Annual Meeting of the American Crystallographic Association

ACA2022

vimrc4ssrl

Template for writing.log in org-mode

writingLogTemplateInOrg

CCTBX code fragment library in colab snippet notebook.

colabcctbxsnips

bib2item3 converts a bib file into a txt file with bibitems.

bib2item3

Generate Voice In commands for a new writing project

new-writing-project-voice-in

Annotated bibliography template in LaTeX for specific writing projects

annotatedBibliography

Protocol to install emacs30 on ubuntu 22.04 LTS with tree-sitter support.

emacs30ubuntu22

latextips

Tips for greater productivity with LaTeX

SmallAngleScatteringWebpage

Small angle scattering webpage.

cctbxsnips library for Elyra-snippets extension for Jupyter Lab

taggedcctbxsnips

jointprob1D

Notes for the jointprob group

Bash functions to ease work on supercomputer using SLURM

bashFunctions4oscer

Blaine's configuration file for crafted-emacs--a smart framework on which to build

crafted-emacs-config

PyMOL Python snippet library to edit live Jupyter notebook cells with vim or neovim using GhostText

jupyter-neosnippets-pymolpysnips

100

snippet-pymol-mode

yasnippet snippets for pymol-mode