A Python toolkit to facilitate working with Molaris-XG.

Author: Mikolaj Feliks <[email protected]>

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.

MolarisTools are actively developed and new features are added as they are needed. Major changes to the code can happen anytime. Bugs are inevitable - please report if you have found one.