README.md

PURPOSE OF CODE

This project is used to attach molecules to crystals, using avogadro .xyz files.

REQUIRMENTS

To run this project, one needs python3 and the module numpy.

HOW TO RUN

To replace a set amount of atoms

1. Design your crystal and molecule in avogadro and put attachment sites on both the crystal and molecule. You can put as many attachment sites on the crystal, but the molecule only needs one. The attachment sites have to be different from the other atoms.
2. In the MoleculeAttacher folder navigate to the input folder and put in your molecule in the molecule folder and the crystal in the crystal folder.
3. In your command prompt, move to the molcule attacher folder: $cd MoleculeAttacher
4. Run the GUI.py file by typing: $python -m src.GUI
5. An interface will open where you can put in your chosen atoms. Don't use quotation marks.
6. Press generate. The generated crystal with the molecules will be located in the output folder.# AvogadroMoleculeAttacher

To replace a percentage of hydrogen atoms on a crystal

1. Design your crystal in avogadro and add hydrogen on top of the crystal
2. In the MoleculeAttacher folder navigate to the input folder and put in your molecule in the molecule folder and the crystal in the crystal folder.
3. In your command prompt, move to the molcule attacher folder: $cd MoleculeAttacher
4. Run the spread.py file by typing: $python -m src.spread
5. Fill in the interface. Don't use quotation marks.
6. Press generate. The file is in the output folder.
7. Enjoy.