RINRUS

Residue Interaction Network-based ResidUe Selector (RINRUS) is a QM-cluster model building tool. Starting from a raw PDB file, after running a series of preparation tasks, the tool will

select important residues for chemical reactions, and
generate trimmed PDB files with the corresponding quantum chemical inputs.

Installation

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

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

Python dependencies

Python >= 3.x
NumPy
pymol
- If installing via conda, it's under -c conda-forge pymol-open-source.
openbabel (required for Arpeggio)

For certain scripts (optional),

matplotlib
BioPython

External dependencies

probe - version 2.16.130520 is packaged with RINRUS
reduce - version 3.23 is packaged with RINRUS
arpeggio

Currently, a precompiled copy of each is present in bin/.

which require

CMake >= 3.10
Any C/C++ compiler suite with C++11 support

Currently, RINRUS can generate appropriate QM-cluster model input files for
-Gaussian09/Gaussian16
-the Gaussian-xTB wrapper developed by the Asparu-Guzik group (https://github.com/aspuru-guzik-group/xtb-gaussian)
-Q-Chem 5.x/6.x

TODO:
-write QM/MM input files with RINRUS-designed QM regions
-write I/FSAPT input files in PSI4 (scripts to process PSI4 FSAPT calculations and build QM-cluster models of enzymes with non-covalently bonded substrates are available)
-write ORCA and TURBOMOLE QM-cluster model input files
-automated network graph visualization of RINRUS models

Current production-level use cases are described in bin/ with tutorials in bin/README.md
The first public release (version 0.2) includes examples 1 and 2 only! Examples 3 - 5 will be available soon.

Usage example 1 - generating a single or a few input files with probe interaction count ranking

Usage example 2 - generating a single or a few input files with distance-based ranking

Usage example 3 - generating a single or a few input files with arpeggio interaction-type ranking

Usage example 4 - generating a single or a few input files with manual ranking (from SAPT, ML, or from some scheme that doesn't yet interface with RINRUS automatically)

GENERATE ALL THE THINGS!!! Combinatorial model building from arpeggio or probe

Usage example 5a - Combinatorial model building from arpeggio

Usage example 5b - Combinatorial model building from probe

Contributors

This code has been developed by the DeYonker group at the University of Memphis Department of Chemistry.
Dr. Qianyi Cheng is the primary coder, assisted by Prof. Nathan DeYonker, Dr. Thomas Summers (University of Nevada-Reno), Donatus Agbaglo, Tejas Suhagia, and Dr. Eric Berquist (Q-Chem, Inc.)

tsantaloci/RINRUS