Installation

Clone the repository, then add bin to your PATH and library code under lib3 to your PYTHONPATH. For example, to install in ~/git:

cd ~/git
git clone https://github.com/natedey/RINRUS.git
export PATH="~/git/RINRUS/bin:$PATH"
export PYTHONPATH="~/git/RINRUS/lib3:$PYTHONPATH"

Python dependencies

  • Python >= 3.x
  • NumPy
  • Pandas
  • PyMOL
    • If installing via conda, it’s under -c conda-forge pymol-open-source.
  • OpenBabel (required for Arpeggio)
  • BioPython (required for Arpeggio)

External dependencies

Precompiled binaries of Probe, Reduce, and Arpeggio are present in bin/.

  • Probe - version 2.16.130520 is packaged with RINRUS
  • Reduce - version 3.23 is packaged with RINRUS
  • Arpeggio - packaged with RINRUS

These require:

  • obabel version = openbabel/2.4.1
  • CMake >= 3.10
  • Any C/C++ compiler suite with C++11 support

PDB HET groups (some ligands and noncanonical amino acids) can be protonated by Reduce. The connectivity table file is included with RINRUS: bin/reduce_wwPDB_het_dict.txt You must set a shell environment variable to allow reduce to use the reduce_wwPDB_het_dict file, as the default location is /local:

setenv REDUCE_HET_DICT /home/$USER/git/RINRUS/bin/reduce_wwPDB_het_dict.txt

or

export REDUCE_HET_DICT=/home/$USER/git/RINRUS/bin/reduce_wwPDB_het_dict.txt