Install

Content

Requirements

  • Python >= 3.7 (but python >= 3.8 is recommended because of deeptime)
  • PaCS-Toolkit currently supports 3 simulator

1. Install by pip

1.1 Install by conda and pip

conda create -n pacsmd "python>=3.8" -y
conda activate pacsmd
  • if using whole pacstk function
pip install "pacs[all] @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"
  • elif using "pacs mdrun" and analyzer == "mdtraj"
pip install "pacs[mdtraj] @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"
  • elif using "pacs mdrun" and analyzer == "gromacs"
pip install "pacs @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"
  • elif performing MSM
    • python >= 3.8 is recommended because of deeptime
pip install "pacs[msm] @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"

1.2. Install by pip

  • if using whole pacstk function
pip install "pacs[all] @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"
  • elif using "pacs mdrun" and analyzer == "mdtraj"
pip install "pacs[mdtraj] @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"
  • elif using "pacs mdrun" and analyzer == "gromacs"
pip install "pacs @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"
  • elif performing MSM
    • python >= 3.8 is recommended because of deeptime
pip install "pacs[msm] @ git+https://github.com/Kitaolab/PaCS-Toolkit.git"

2. Get source code from github

  • git clone
git clone https://github.com/Kitaolab/PaCS-Toolkit.git
cd pacsmd
  • get latest release
verion="x.x.x"
wget https://github.com/Kitaolab/PaCS-Toolkit/archive/refs/tags/${version}.tar.gz
tar -xvzf ${version}.tar.gz
cd pacsmd-${version}

2.1. Install by conda and pip locally

conda create -n pacsmd "python>=3.8" -y
conda activate pacsmd
  • if using whole pacstk function
    • python >= 3.8 is recommended because of deeptime
pip install -e ".[all]"
  • elif using "pacs mdrun" and analyzer == "mdtraj"
pip install -e ".[mdtraj]"
  • elif using "pacs mdrun" and analyzer == "gromacs"
pip install -e "."
  • elif using "pacs mdrun" and analyzer == "cpptraj"
pip install -e "."
  • elif performing MSM
pip install -e ".[msm]"

2.2. Install by pip locally

  • if using whole pacstk function
    • python >= 3.8 is recommended because of deeptime
pip install -e ".[all]"
  • elif using "pacs mdrun" and analyzer == "mdtraj"
pip install -e ".[mdtraj]"
  • elif using "pacs mdrun" and analyzer == "gromacs"
pip install -e "."
  • elif using "pacs mdrun" and analyzer == "cpptraj"
pip install -e "."
  • elif performing MSM
    • python >= 3.8 is recommended because of deeptime
pip install -e ".[msm]"