Installation¶

Supported System¶

ChemTools is available on Linux and MacOS with Python 2.7. In the future release, we will support Windows 10 and Python 3.6+.

Source Code¶

The latest code can be obtained through Github (private at present),

$ git clone https://github.com/theochem/chemtools.git chemtools

Dependencies¶

The following dependencies will be necessary for ChemTools to build properly,

Python >= 2.7, < 3.0: http://www.python.org/ (Also install development files.)
PIP >= 7.0: https://pip.pypa.io/ (Not required in some scenarios but never bad to have.)
SciPy >= 0.11.0: http://www.scipy.org/
NumPy >= 1.9.1: http://www.numpy.org/
SymPy >= 0.7.1: http://code.google.com/p/sympy/
Matplotlib >= 1.0: http://matplotlib.org/
Nosetests >= 1.1.2: http://readthedocs.org/docs/nose/en/latest/
HORTON >= 2.0.1: http://theochem.github.io/horton/2.0.1/index.html
Git-LFS >= 2.0.1: https://git-lfs.github.com/

See Documentation Dependencies for the dependencies required for building the documentations. All dependencies are recommanded to install through Conda.

Conda¶

For Linux and MacOS users, you can download miniconda to manage the dependencies. Either version (2.7 or 3.7) will work.

To activate conda base in system:

$ conda activate

To create a virtual environment for ChemTools:

$ conda create -n chemtools python=2.7

To activate ChemTools virtual environment:

$ conda activate chemtools

To install HORTON and Git-LFS:

$ conda install -c theochem horton
$ conda install git-lfs

To deactivate the virtual environment:

$ conda deactivate

Installation¶

Before installing ChemTools, make sure you are in the chemtools conda environment. To install ChemTools to your system, run:

$ pip install .

Or, to install ChemTools inplace as an editable package, run:

$ pip install -e .

Testing¶

To ensure that all the parts of ChemTools working properly, nosetests can be used to run ChemTool’s automatic tests:

$ nosetests -v chemtools

At this stage, some UserWarning messages are printed in between tests which is expected. However, no test should fail.

Uninstallation¶

To remove ChemTools from your system, run:

$ pip uninstall chemtools

Intro to VMD¶

Go to VMD , select the link based on your system OS. Then you will be brought to the registration page. Shortly after it’s done, install the download file to the proper position on your laptop.

For macOS and Linux user, you can add the path to your bash profile (.bashrc on Linux, or .bash_profile on macOS) at your home directory for quick access if it’s not on your path.

alias vmd="The/path/to/vmd/command/in/your/system"

Usages¶

To visualize in VMD:

$ vmd -e script.vmd

To save the state, you can click File > Save Visualizaiton State.
If you’d like to save the picture during the visualization, you can click File > Render > Filename > Start Rendering