Dominique Sydow dominiquesydow

## search_my_gist.md

      
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              April 15, 2019 09:59
            
              
                How to search my gists
              
          
    How to search my gists

Search my gist by tags via:
user:myusername #tag

For example:
user:dominiquesydow #gist


## bash_cheatsheet.md

      
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                dominiquesydow
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              May 3, 2019 12:39
            
              
                Bash cheat sheet
              
          
    Useful bash commands

My notes.
File/path/directory naming conventions

path=/home/dom/test.txt
dirname=/home/dom/
filename=test.txt


## extract_lig_from_pdb.ipynb

      
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                dominiquesydow
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              Created
              April 16, 2019 16:33
            
              
                Extract ligand from PDB file
              
          
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## jupyter_nbconvert_execute.sh
# Run Jupyter notebooks via the console
# Here: TeachOpenCADD talktorials on https://github.com/volkamerlab/TeachOpenCADD

# Change to TeachOpenCADD directory
#cd /path/to/TeachOpenCADD

# Activate TeachOpenCADD conda environment
#conda activate teachopencadd

# Install kernelspec teachopencadd

## NGLviewer_add_labels.ipynb

      
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                dominiquesydow
                / NGLviewer_add_labels.ipynb
            
            
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              October 28, 2019 12:16
            
              
                NGLviewer: Attempt to add text labels to selection
              
          
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## mol2_pdb_tests.ipynb
{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Mol2 to PDB conversion"
   ]
  },
  {

## jupyterlab_extensions.sh
# Jeremy Tuloup - A tour of JupyterLab extensions
# https://mybinder.org/v2/gh/jtpio/a-tour-of-jupyterlab-extensions/master?urlpath=lab%2Ftree%2Fpresentation.ipynb

# 1. jupyterlab-git
# https://github.com/jupyterlab/jupyterlab-git
jupyter labextension install @jupyterlab/git

# 2. nbdime
# https://github.com/jupyter/nbdime
pip install nbdime

## chembl_activity.ipynb

      
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                dominiquesydow
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              February 6, 2020 09:39
            
              
                Transform activity ChEMBL query results to DataFrame - first element twice?
              
          
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## rdkit_combine_multiple_molecules.ipynb

      
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                dominiquesydow
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              Created
              March 19, 2020 11:00
            
              
                Combine multiple molecules in RDKit
              
          
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## check_sdf_dummy_atoms.ipynb

      
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                dominiquesydow
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              Created
              June 8, 2020 11:13
            
          
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	# Run Jupyter notebooks via the console
	# Here: TeachOpenCADD talktorials on https://github.com/volkamerlab/TeachOpenCADD

	# Change to TeachOpenCADD directory
	#cd /path/to/TeachOpenCADD

	# Activate TeachOpenCADD conda environment
	#conda activate teachopencadd

	# Install kernelspec teachopencadd
	{
	"cells": [
	{
	"cell_type": "markdown",
	"metadata": {},
	"source": [
	"# Mol2 to PDB conversion"
	]
	},
	{
	# Jeremy Tuloup - A tour of JupyterLab extensions
	# https://mybinder.org/v2/gh/jtpio/a-tour-of-jupyterlab-extensions/master?urlpath=lab%2Ftree%2Fpresentation.ipynb

	# 1. jupyterlab-git
	# https://github.com/jupyterlab/jupyterlab-git
	jupyter labextension install @jupyterlab/git

	# 2. nbdime
	# https://github.com/jupyter/nbdime
	pip install nbdime