Requirements for Provis

Provis is based on the idea of not to reinvent the wheel, so quite a few third party packages and binaries are required to run it.

Binaries

Binaries are 3rd party, ready to use programs, that are provided to the user as is. Here is a list of the required external programs and installation instructions.

OpenBabel

Easiest to install on Linux is by calling:

sudo apt install openbabel

Alterantively: http://openbabel.org/wiki/Main_Page

OpenBabel is needed to create the mol.2 files. These files store the bond information.

PDB2PQR

Download from: https://www.poissonboltzmann.org/

Pdb2pqr is required for the surface feature plotting. If creates the .pqr file needed for the feature information calculation.

MSMS

MSMS is optional but highly suggested. It is used to compute the surface, but a native method for the surface computation also exists in provis (and while it is fast, it is chemically less accurate).

Download MSMS form: https://ccsb.scripps.edu/mgltools/downloads/

This tutorial might help: http://biskit.pasteur.fr/install/applications/deprecated/msms

Pip

If provis was downloaded via pip (and not from the github) then all of the following packages should be installed.

If not, then run the following command in the root directory of provis:

python3 setup.py develop

This should pip install everything, including the provis package.

Here is a list of provis’ pip dependencies:

• BioPython

• Trimesh

• PyVista

• Biopandas

• Torch

• Pyvtk

• Open3d

• rTree

• Panel

• Imageio-ffmpeg