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jcoupling_all.py
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jcoupling_all.py
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#!/usr/bin/python
from karplus import *
import mdtraj as md
import argparse
import os
import numpy as np
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-o',
'--output',
default = 'Data/J_coup_kalplus.dat',
help = "output file name for trajectory (default = Data/J_coup_kalplus.dat)"
)
parser.add_argument('-t',
'--trajectory',
default='trajectory',
help ='Path to the trajectory directory or project file (default=trajectory)'
)
parser.add_argument('-f',
'--function',
default = 'karp_function.dat',
help = "Function used to calculate Jcoupling default is karp_function.dat")
parser.add_argument('-d',
'--angle',
default = 'karp_angle.dat',
help = "angle used to calculate Jcoupling default is karp_angle.dat (phi first, psi second)")
args = parser.parse_args()
traj = md.load(os.path.join(os.getcwd(),args.trajectory,'traj.h5'))
function = np.loadtxt(args.function,dtype = str)
dispatcher = {'J3HNHa':J3HNHa,'J3HNC':J3HNC,'J3HaC':J3HaC,'J3CC':J3CC,'J3HNCb':J3HNCb,'J1NCa':J1NCa,'J2NCa':J2NCa,'J3HNCa':J3HNCa}
angles = np.loadtxt(args.angle,dtype = int)
phi = md.compute_phi(traj)[1] * 180.0 / np.pi
psi = md.compute_psi(traj)[1] * 180.0 / np.pi
snap=traj.n_frames
nj=len(function)
print 'There are '+str(nj)+' jcoupling and totally '+str(snap)+' snapshot'
J = np.zeros((snap, nj))
for i in range(nj):
print i
J[:,i] = map(dispatcher[function[i]],phi[:,angles[i,0]],psi[:,angles[i,1]])
if not os.path.isdir(os.path.dirname(args.output)):
os.mkdir(os.path.dirname(args.output))
np.savetxt(args.output,J,newline='\n',fmt='%f')
if __name__ == '__main__':
main()