Install

Content

• Install
  • Requirements
  • 1. Install by pip
    • 1.1 Install by conda and pip
    • 1.2. Install by pip
  • 2. Get source code from github
    • 2.1. Install by conda and pip locally
    • 2.2. Install by pip locally

Requirements

• Python >= 3.7
• PaCS-ToolKit currently supports 3 simulator
  • Gromacs
  • Amber
  • Namd

1. Install by pip

1.1 Install by conda and pip

conda create -n pacsmd "python>=3.7" -y
conda activate pacsmd

• if using whole pacstk function

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git#egg=pacs[all]"
pip install pyemma

• elif using "pacs mdrun" and analyzer == "mdtraj"

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git#egg=pacs[mdtraj]"

• elif using "pacs mdrun" and analyzer == "gromacs"

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git"

• elif performing MSM

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git#egg=pacs[msm]"
pip install pyemma

1.2. Install by pip

• if using whole pacstk function

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git#egg=pacs[all]"

• elif using "pacs mdrun" and analyzer == "mdtraj"

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git#egg=pacs[mdtraj]"

• elif using "pacs mdrun" and analyzer == "gromacs"

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git"

• elif performing MSM

pip install "git+https://github.com/Kitaolab/PaCS-Toolkit.git#egg=pacs[msm]"
pip install pyemma

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>=3.7" -y
conda activate pacsmd

• if using whole pacstk function
  • pyemma does not recommend pip-install

pip install -e ".[all]"
conda install -c conda-forge pyemma

• 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
  • pyemma does not recommend pip-install

pip install -e ".[msm]"
conda install -c conda-forge pyemma

2.2. Install by pip locally

• if using whole pacstk function
  • pyemma does not work, conda is recommend

pip install -e ".[all]"
pip install pyemma

• 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
  • sometimes pyemma does not work, conda is recommend

pip install -e ".[msm]"
pip install pyemma