PeptideMaker

Based on the given sequence, model it through PeptideBuilder, add hydrogen atoms and end-capping groups (ACE and NME), and then perform a short energy minimization in vacumm through Openmm
usage: python PeptideMaker.py -s <str> -o <str> [-helix] [-retain]
-s: the sequence of peptide you want to build
-o: specify a path for output (if the path do not exsit, it will be created)
-helix: optional flag, add this if you want the peptide be modelled into helix (otherwise it will be loop)
-retain: optional flag, add this if you want to retain all the files generated during the modelling process (otherwise they will be deleted)