Generate an AFM simulation of a molecule from its Protein Data Bank (https://www.rcsb.org/) file. Required Libraries: mdtraj (https://www.mdtraj.org/1.9.8.dev0/index.html), numpy, matplotlib.
Download .pdb file of chosen molecule and add to pdb_files folder Required inputs: Protein Data Bank ID of molecule
Changeable settings: tip radius, cone angle, sampling (pix/nm), noise, xyz angles to rotate molecule, z threshold (membrane embedded fraction)