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VMD Alias (Mac OS X)

Put this alias in your .bash_rc or .profile :

alias vmd='/Applications/VMD\ 1.9.2.app/Contents/MacOS/VMD'

ChemTools on Google Colab

Run the 3-line commands below in one code block to get miniconda and install to /usr/local:

!wget -c https://repo.continuum.io/miniconda/Miniconda2-4.5.11-Linux-x86_64.sh

!chmod +x Miniconda2-4.5.11-Linux-x86_64.sh

!bash ./Miniconda2-4.5.11-Linux-x86_64.sh -b -f -p /usr/local

!conda install -y --prefix /usr/local -c theochem horton

!pip install --upgrade numpy

!pip install git+https://github.com/theochem/chemtools.git

import sys

sys.path.append('/usr/local/lib/python2.7/site-packages/')

!nosetests -v chemtools

import chemtools

Python

You are expected to be familiar with Python: https://www.python.org/

To refresh your mind on Python, you can take advantage of many tutorials, videos, blogs and courses on Python. We also recommend you to go through the Jupyter notebooks in the link below:

https://github.com/molmod/Tutorial/tree/master/python

You can download the notebooks and run the code block to get some hands-on experience.

For Windows Laptops

If you are running Windows on your laptop, we assume that you are using Windows 10. If so, please install "Windows Subsystem for Linux Installation" through the link below:

https://docs.microsoft.com/en-us/windows/wsl/install-win10

Git

We use Git for version control and hosting our code on GitHub. Please install it through:

https://git-scm.com/book/en/v2/Getting-Started-Installing-Git

ParaView

You should install ParaView and TTK prior to the session. You can either

• install it following this instructions: https://topology-tool-kit.github.io/installation.html
• download a virtual machine: https://topology-tool-kit.github.io/ieeeVisTutorial.html

Slides, data, demos, virtual machines and pre-installed software:

https://topology-tool-kit.github.io/ieeeVisTutorial.html

If you have any questions, please contact the ttk user email list: [1]