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Installation

  • Essential: Fragmenstein
  • Optional: Pyrosetta or OpenMM, PLIP and OpenBabel

Fragmenstein and dependencies

Python 3.6 or above. It can be install from pipy

python -m pip install fragmenstein

Requires Pyrosetta

PyRosetta is optional, but it is required for full operations. Without it the pocket sidechains are not minimised, which requires a perfect receptor/template/protein.

⚠️ PyRosetta no longer runs on CentOS 7 due to old kernel headers (cf. blog post).

⚠️ PyRosetta is not available on Windows. For that you need to install Windows Subsystem for Linux (WSL) and install PyRosetta on the Linux subsystem.

Modern way

This no longer requires a password:

pip install pyrosetta-installer 
python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'

Details from former way

Pyrosetta used to require a password to be downloaded (academic licence) obtained by https://els2.comotion.uw.edu/product/pyrosetta. This is a different licence from the Rosetta one. The username of the Rosetta binaries is formatted variant of "academic user", while the PyRosetta is the name of a researcher whose name bares an important concept in protein folding, like boltzmann + constant (but is not that). Pyrosetta can be downloaded via a browser from http://www.pyrosetta.org/dow. Or in the terminal via:

curl -u 👾👾👾:👾👾👾https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python38.linux/PyRosetta4.Release.python38.linux.release-NNN.tar.bz2 -o a.tar.bz2
tar -xf a.tar.bz2
cd PyRosetta4.Release.python38.linux
sudo pip3 install .

or using conda

or using install_pyrosetta from the pyrosetta-help package.

pip install pyrosetta-help
PYROSETTA_USERNAME=👾👾👾 PYROSETTA_PASSWORD=👾👾👾 install_pyrosetta

The PYROSETTA_USERNAME and PYROSETTA_PASSWORD are environment variables, which should not be shared publicly (i.e. store them as private environmental variables in your target application).

PLIP

PLIP is used for the interactions and it is optional.

It is involved by Victor method get_plip_interactions and Laboratory will use it if it finds it.

To install PLIP, sometimes issues happen as openbabel is installed via conda, so I do this:

conda install -c conda-forge openbabel lxml
conda install -c conda-forge --no-deps plip