To run our project first clone the project. Then from the root directory, launch the docker container through:
./interactive.sh
Then to build our C++ code run:
./clean.sh
./build.sh
To run the simulation code run:
./run.sh
The MMFF94 implementation code can also be experimented with. To output the data that I collected from varying the bond lengths and angles of a water molecule, you can run:
./run_water_plot_data.sh
This will write the energy data to the files data/angle_energies.txt and data/bond_energies.txt. Once those are populated, you can run ./install_python.sh to install the necessary Python packages and then run python rdkit_comp.py to see how I compared the RDKit implementation of MMFF94 to my own. This is how I generated the comparison plots also located in the data directory.
Additionally, you can simply calculate the energy of any of the molecules that are in the molecules directory, by running ./run_mol_energy.sh. Based on which molecule you want to get the energy for, you can change the file path in the run_mol_energy.sh file.
Note: If any scripts don't work, try chmod +x /path_to_script.sh to make sure they are executable first.