Install

Step 1 - Download ChemFlow sources.

The sources for ChemFlow can be downloaded from the Github repo.

# Clone ChemFlow to the install location of your choice:
git clone https://github.com/IFMlab/ChemFlow.git

Step 2 - Install miniconda.

Download and install the latest version of miniconda for python 3.x https://docs.conda.io/en/latest/miniconda.html

# Download the latest version of miniconda for python 3.x
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

# Install miniconda
chmod +x  Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

#Create an environment for ChemFlow
conda create -n chemflow

# Activate chemflow environment
conda activate chemflow

Step 3 - Install the software dependencies.

# rdkit
conda install -c rdkit rdkit

# AmberTools (use Amber18 if you have a licence)
conda install -c ambermd ambertools

# AutoDockTools (required for Vina)
Download and install from: http://mgltools.scripps.edu/downloads

# Autodock Vina
Download and install from: http://vina.scripps.edu

# PLANTS ( Requires free registration )
Download and install from: http://www.tcd.uni-konstanz.de/plants_download/

# Amber18 (Optional, licence is required)
Download and install from: http://ambermd.org

# Gaussian (Optional, licence is required. Required for RESP charges)
Download and install from: https://gaussian.com

Step 4 - Set PATHS

In addition to downloading the required software, you must be able to run then flawlessly. Set up the PATHS to their install locations, as following and add to your .bashrc.

# ChemFlow
export CHEMFLOW_HOME=~/software/ChemFlow/ChemFlow/
export PATH=${PATH}:${CHEMFLOW_HOME}/bin/

# MGLTools
export PATH="${PATH}:~/software/mgltools_x86_64Linux2_1.5.6/bin/"
export PATH="${PATH}:~/software/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/"

# Autodock Vina
export PATH="${PATH}:~/software/autodock_vina_1_1_2_linux_x86/bin/"

# PLANTS
export PATH="${PATH}:~/software/PLANTS/"

# Optional (paid software)

# Amber18 (Ambertools19 and Amber18)
source ~/software/amber18/amber.sh

# Gaussian 09
export g09root=~/software/
export GAUSS_SCRDIR=/tmp
source $g09root/g09/bsd/g09.profile

Additional software for the tutorial

To run the jupyter-notebook tutorial, you may also install some python modules.

conda install pandas seaborn