Protein folding via Reinforcement Learning (PfRL)
- Python 3
- AmberTools 16
conda install -c ambermd ambertools
source ~/amber/bin/amber.sh
When called, the class performs some priliminary functions to get started from pdb. The sequence from pdb file is taken out and a straight chain for the protein is made. The straight chain is minimized for VanDerWallas interactions etc. The force field ff14fb is applied for making topology files and energy calculations.
E.g. p = protein('1mzi.pdb')
gives the initial coordinates of the straight chain of protein atoms, shape = (-1,3)
gives the atomic number of each of the atoms, shape = (-1)
args = coordinates of shape (-1,3)], returns Potential energy of the coordinates provided