jcalc

Python module to calculate vicinal coupling constant from Molecular Dynamics. A Jupyter Notebook with a quickstart example and adding hydrogens example shows how to use JCalc.

Getting started

Installing jcalc

• Install GROMACS
• Install obabel

Install locally

pip install jcalc

Install by docker

docker pull jlmeirelles/jcalc:latest

Running jcalc

Running on simulation (XTC and TPR file)

jcalc -x sim.xtc -t sim.tpr -n j_input.tsv

Running on directory with steps as PDB files

jcalc -i pdb_dir -n j_input.tsv

Running on single PDB file

jcalc -p file.pdb -i j_input.tsv

Running on docker

docker run -v $(pwd):/home/data jlmeirelles/jcalc -x sim.xtc \
-t sim.tpr -n j_input.tsv