IMPORTANT NOTE

This is a legacy library that is only compatible with Python 2.
It is kept here solely for historical reasons.

MolarisTools

A Python toolkit to facilitate working with Molaris-XG.

Key features:

• QM/MM interface with electrostatic embedding to Gaussian, Mopac, GAMESS-US, ORCA, Q-Chem
• Parsing of Molaris files (input, log, gap, FVX, mol.in, evb.dat)
• Parsing of files from quantum chemical packages (Gaussian, Mopac, GAMESS-US, ORCA, Q-Chem)
• Parsing of geometry files (PDB, xyz, xyz trajectories)
• Reading and writing of Molaris libraries (amino-library, ENZYMIX \& EVB parameters)
• Handling of amino-components (calculation of partial charges, generation of angles and dihedrals, topology operations, merging)
• Conversion between Molaris and CHARMM topology formats
• Generation of tables for input files with EVB atoms \& bonds
• Automatic generation of amino-components from PDB files based on coordinates and distances
• Parsing of 1D \& 2D PES scans
• LRA calculations

Installation instructions:

MolarisTools is a stand-alone Python library and as such does not
need Molaris to be preinstalled. Nevertheless, a copy of Molaris can
be obtained from the Warshel Group.

To install MolarisTools, clone the repository from GitHub (assuming that you have
git installed on your computer):

git clone https://github.com/mfx9/MolarisTools.git

Or download and unpack the ZIP package from this website. In the next
step, adjust the PYTHONPATH variable so it points to the location
of MolarisTools, for example (in Bash):

export PYTHONPATH=${HOME}/MolarisTools:${PYTHONPATH}

Add the above line to your ~/.profile or ~/.bashrc file.