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#usage: python mdanalysis/res_specific_rmsd.py TOPFILE TRAJFILE REF_STRUCTURE OUT_NAME.DATZZ
import numpy as np
import os 
import MDAnalysis as mda
import MDAnalysis.analysis.rms
import sys
import argparse
#system_list=np.loadtxt("system_list",dtype=str)
parser = argparse.ArgumentParser()
cwd=os.getcwd()
parser.add_argument (topology,dest='topology',help='topology',required=True)
parser.add_argument (trajectory,dest='trajectory',help='trajectory',required=True)
parser.add_argument (stride,dest='stride',help='stride of trajectory, skip this many frames each jump.',required=True)
parser.add_argument (sel_list,dest='selection_list',help='list of selections to collect the rmsd for.',nargs="+",required=True)
parser.add_argument (ref_sel,dest='reference_seelection',help='list of selections to collect the rmsd for.',required=True)
parser.add_argument (ref_struct,dest='ref_struct',help='structure for reference')
parser.add_argument (o,dest='o',help='outfile')

#f=open('system_list','r')

#f1=f.readlines()


#os.chdir ('..')
#print (i)
#files=i.split()
#psf=files[0]
#xtc=files[1]
print(args.topology)
exit()
u = mda.Universe(args.topology,args.trajectory)
r = mda.Universe(args.topology,args.ref_struct)
R = MDAnalysis.analysis.rms.RMSD(u,r,select=args.reference_selection, groupselections=[args.selection_list], filename=args.o)
R.run()
np.savetxt(out_name, R.rmsd)