https://github.com/efliks/molaristools
Python scripts to facilitate working with Molaris-XG
https://github.com/efliks/molaristools
computational-chemistry proteins python
Last synced: over 1 year ago
JSON representation
Python scripts to facilitate working with Molaris-XG
- Host: GitHub
- URL: https://github.com/efliks/molaristools
- Owner: efliks
- License: gpl-3.0
- Created: 2015-10-01T01:24:46.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2021-07-03T09:37:11.000Z (about 5 years ago)
- Last Synced: 2023-10-25T19:39:34.460Z (almost 3 years ago)
- Topics: computational-chemistry, proteins, python
- Language: Python
- Homepage:
- Size: 1.54 MB
- Stars: 3
- Watchers: 2
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: COPYING
Awesome Lists containing this project
README
:warning: **IMPORTANT NOTE** :warning:
**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](http://laetro.usc.edu/software.html).
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.