Installation

Try pytraj online:

http://mybinder.org/assets/images/logo.svg

Note

For Linux user, we highly recommend install pytraj via conda

Requires

  • numpy

  • (optional) cython, >= 0.23. Cython is only required if installing development version:

    pip install cython --upgrade

# conda install cython

Install

from conda (Linux, OX)

We higly recommend install pytraj by conda

# install latest version
conda install -c ambermd pytraj

# install specific version
conda install -c ambermd pytraj==1.0.8

This takes only less than 30 seconds.

If you don’t want to read long description about installing conda, just copy and paste below script to your terminal (for Linux). For Mac user, you need to follow conda website.

$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh

From pip (Linux, OSX)

# latest version
pip install pytraj

# specific version
pip install pytraj==1.0.8

From source code (easy way: Linux, OSX)

git clone https://github.com/Amber-MD/pytraj
cd pytraj

# linux
python ./setup.py install

# osx:
python setup.py install

# note: pytraj will automatically install cpptraj first.

Depend on your machine, the fresh installation (libcpptraj + pytraj) could take 2 to 4 minutes.

From source code (hard way - expert only)

Sometimes you want to install libcpptraj.so by yourself.

  • First, download cpptraj:

    git clone https://github.com/Amber-MD/cpptraj
cd cpptraj
bash configure -shared -openmp gnu

# if you are AMBER user, you can add -amberlib
bash configure -shared -openmp -amberlib gnu
make libcpptraj -j4

# please check bash configure --full-help for other options.
# check: https://github.com/Amber-MD/cpptraj too
export CPPTRAJHOME=`pwd`

  • Then, install pytraj

    # cd to any folder you want to store pytraj code
# then
git clone https://github.com/Amber-MD/pytraj
cd pytraj
python ./setup.py install

From AMBER distribution (Linux, OSX)

pytraj is included in AMBER (version >= 16): ambermd.org

Update pytraj

Rule of thumb: using the same tool to install/update (upgrade)

From conda

If you install pytraj by conda, you can update it easily

conda update -c ambermd pytraj --force

From pip

pip install --upgrade pytraj

From github

if you install from source code and want to update the development code in github, you need to update both libcpptraj and pytraj

$ cd /to/pytraj/root/folder
$ cd cpptraj
$ git pull
$ make libcpptraj -j8

then

$ cd /to/pytraj/root/folder
$ git pull
$ python ./setup.py install

Update to AMBERHOME

  • From release version
rm $AMBERHOME/lib/libcpptraj.so # if using Macos, using "libcpptraj.dylib"
rm -rf $AMBERHOME/lib/python2.7/site-packages/pytraj* # replace "python2.7" by your own version (e.g: python3.6)
amber.pip install pytraj --prefix=$AMBERHOME
# if you don't have amber.pip, just use pip
  • From github development version
rm $AMBERHOME/lib/libcpptraj.so # if using Macos, using "libcpptraj.dylib"
rm -rf $AMBERHOME/lib/python2.7/site-packages/pytraj* # replace "python2.7" by your own version (e.g: python3.6)
# (which will be installed by pytraj itself)

cd /to/your/favorite/dir
git clone https://github.com/Amber-MD/pytraj
cd pytraj

# if there's no git
# wget https://github.com/Amber-MD/pytraj/archive/master.zip
# unzip master
# cd pytraj-master

python setup.py install --prefix=$AMBERHOME
  • From github development version with existing pytraj folder
rm $AMBERHOME/lib/libcpptraj.so # if using Macos, using "libcpptraj.dylib"
rm -rf $AMBERHOME/lib/python2.7/site-packages/pytraj* # replace "python2.7" by your own version (e.g: python3.6)

cd /to/your/pytraj/folder
git clean -fdx .
git pull # update newest code
cd cpptraj
git clean -fdx .
git pull
cd ../

python setup.py install --prefix=$AMBERHOME

Uninstall

Rule of thumb: using the same tool to install/uninstall

From conda

$ conda remove pytraj libcpptraj

From pip

$ pip uninstall pytraj

Troubleshooting

Permission denied

python setup.py install is standard process to install a new Python package. But if you are new to Python and got permission denied error, try to install pytraj in your home folder.

# install pytraj in $HOME/.local
python ./setup.py install --user

# or install pytraj in ``your_favorite_dir``
python ./setup.py install --prefix=your_favorite_dir
# if you do this, make sure to add ``your_favorite_dir`` to $PYTHONPATH
export PYTHONPATH=your_favorite_dir:$PYTHONPATH

If you want to see further options, check python setup.py install --help

Install ipython and its notebook for interactive data exploration

ipython and its notebook is great program for interactive exloration of MD data. Curious about how the notebook looks like? check out our pairwise rmsd tutorial

If you are using anaconda, just type ipython notebook. If you have not haved ipython and its notebook, try conda install ipython For further instruction and information about ipython-notebook, please check its website.

Install anaconda for all python packages

we highly recommend to install anaconda that has all good python packages (cython, numpy, sklearn, pandas, ...). Anaconda is totally free.

  • go to its website, choose your platform and python version. It’s better to pick up Python3
  • download file: For example, we downloaded Anaconda3-2.1.0-Linux-x86_64.sh (Python3 version)
  • just run bash Anaconda3-2.1.0-Linux-x86_64.sh and follow instruction. That’s it, you have a Python eco-system here.

install and run jupyter noteook

# install
conda install notebook

# run
jupyter notebook

# or run
jupyter notebook {your_notebook_name}.ipynb

If you want to run Jupyter notebook remotely, check Use Jupyter notebook remotely