How to install

Recommended steps:

1 - Download the latest stable copy of UCSF Chimera and install it with the .dmg file (macOS) or with the following command (Linux):

chmod +x chimera-*.bin && sudo ./chimera-*.bin

Tip

When Chimera installer asks about Install symbolic link to chimera executable?, we recommend to choose option /usr/bin, so GaudiMM will find Chimera installation without problem.

2 - Download Miniconda Python 2.7 Distribution for your platform and install it with:

bash Miniconda2*.sh

3 - Install gpathfinder with conda in a new environment called gpathfinder (or whatever name you prefer after the -n flag), using these custom channels (-c flags):

conda create -n gpathfinder -c omnia -c conda-forge -c bioconda -c josan_bcn gpathfinder

4 - Activate the new environment as proposed:

conda activate gpathfinder

or

source activate gpathfinder

5 - Run it!

gpath

Check everything is OK

If everything went OK, you will get the usage screen:

Usage: gpath [OPTIONS] COMMAND [ARGS]...

  GPathFinder: Indentification of ligand pathways by a multi-objective
  genetic algorithm

  (C) 2019, InsiliChem
  https://github.com/insilichem/gpathfinder

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  prepare  Create or edit a GPATH input file.
  run      Launch a GPATH input file.
  view     Analyze the results in a GPATH output file.

OS Compatibility

GPathFinder is compatible with Linux and macOS. This installation procedure has been checked with Chimera v.1.13.1 and the following distributions:

• macOS Mojave 10.14
• Mint 19.1
• Debian 9.9.0
• Ubuntu 16.04 and 18.04
• OpenSUSE Leap 15.1
• Manjaro 18.0.4

If you find some difficulties when installing it in a concrete distribution, please use the issues page to report them.