Installation - alexandrova-lab-ucla/phd3 GitHub Wiki

System Requirements

  • TURBOMOLE Version 6.6
  • piDMD
  • Openbabel Version 3.1.1
  • Chimera Version 1.6.0 or greater (1.15.0 or greater recommended)
  • Python Version 3.6 or greater (3.8 or greater recommended)

Python Package Dependencies

When phd3 is installed via pip, the following packages will also be installed if not already present on your system.

  • jinja2
  • sklearn
  • propka
  • numpy Version 1.20.0 or greater
  • hdbscan
  • scipy Version 1.1.0

Installation

First, clone this repository

git clone https://github.com/alexandrova-lab-ucla/phd3

Then, edit the phd_config.json file so that all of the paths in the PATHS section point to the correct directory. That is

  • TURBODIR points to the TURBOMOLE directory that contains basen, bin, TURBOTEST, Config_turbo_env, etc.
  • DMD_DIR points to the directory that holds the DMD binaries complex.linux, comples_m2p.linux, pdmd.linux, and repdmd.linux.
  • parameters points to the directory that holds the DMD parameters file allatom.par, DMD_NA_allatom.par, etc.
  • chimera points to the directory that holds the chimera executable. Note, this is not the path TO the chimera executable, but to the directory that contains the executable.

If you are using phd3 on a cluster with queuing, you can modify the QUEUING section as well. Next we make a directory in ~/.config and moves some files there as

mkdir ${HOME}/.config/phd3
mv phd_config.json logger_config.json ${HOME}/.config/phd3

Finally, we use pip3 to install

pip3 install ./

If you are having issues with 'sudo', add the --user option. Further, if you are developing, include the -e option as

pip3 install --user -e ./

Make sure that ~/.local/bin is in your PATH as this is where the executibles are installed with pip3.