Analysis.py

Analysis of HIV systems using MDtraj

Currently supports various types of analysis for a specified simulation time(ns) and type of glycosylated protein (prot, nat or m9):

1. RMSD
2. RGYR of protein system no-H
3. RGYR of protein + glycan system no-H
4. RMSF env. plot wrt 0th frame of prot (divided into 3 chains)
5. RMSF env. plot wrt mean (divided into 3 chains)

To do:

6. RMSF error candle plots wrt. glycans BMA oxygen / sugar at the tip