<jupyter_start><jupyter_text>Main starts here<jupyter_code>nbin = 27
dx = 0.1
dt = 1.0 ## always 1 because real time unit is used in the program
xlow=-0.35
lagstep =400
## plotting loglikelihood
L = np.loadtxt('loglike.out')
plot_loglike(L)
## plotting PMF                                                                                                                                                  
F = np.loadtxt('pmf.out')
plot_pmf_las(F,nbin,dx,xlow,'pmf_las.eps')
plot_pmf_error(F,nbin,dx,xlow,'pmf_av.eps')
## plotting D                                                                                                        
D = np.loadtxt('diffcoef.out')
Dlas = plot_d(D,dx,dt,'diffcoef.eps')
Dav,Dsd = plot_d_error(D,dx,dt); print('Dav=',Dav,'Dsd=',Dsd);
R=np.loadtxt('rate.out')
plot_rate(R)<jupyter_output><empty_output><jupyter_text>Plot trajectories<jupyter_code>dt0 = 0.000001
for itraj in range(30):
    print('itraj=',itraj)
    filehmm = 'hmmpd_prob_traj'+str(itraj)+'.out'
    filetraj = '../traj/trajectory_burnt-bridge_traj'+str(itraj)+'.out'
    A = np.loadtxt(filehmm)
    B = np.loadtxt(filetraj)
    fileeps = 'hmmpd_prob_traj'+str(itraj)+'.eps'
    plt.plot(B[:,0],B[:,1],'-')
    plt.plot(B[:,0],B[:,2],'-')
    plt.plot(np.linspace(0.0,dt0*lagstep*(len(A[:,0])-1),len(A[:,0])),A[:,0])
    plt.plot(np.linspace(0.0,dt0*lagstep*(len(A[:,0])-1),len(A[:,0])),A[:,1])
    plt.xlabel('Time')
    plt.ylabel('Position')
    Size = plt.gcf().get_size_inches()                                                                                                                       
    plt.gcf().set_size_inches(0.6*Size[0],0.6*Size[1])                                                                                                       
    plt.tight_layout()                                                                                                                                       
    plt.savefig(fileeps)
    plt.show()<jupyter_output>itraj= 0
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