Functions

def com_traj(ftraj, nfrs, nmon, massarr):
    
    '''converts a formatted trajectory of monomers from the output of 
    LE4DNA.format_traj() into a trajectory of the center of mass of each monomer.
    
    args:
    
    ftraj (numpy array) : output of LE4DNA.format_traj(), trajectory of monomers
    nfrs (int) : np.shape(ftraj)[1], number of frames in trajectory
    nmon (int) : np.shape(ftraj)[0]/(3*len(massarr)), number of monomers in molecule
    massarr (numpy array) : masses of atoms in each monomer. i.e. massarr[i] = mass
    of ith atom in the monomer.
    '''
    
    import numpy as np
     
    monsize = len(massarr)
    
    totalM = massarr.sum()
    
    com_traj = np.zeros( ( 3*nmon , nfrs ) )
    
    for i in range(0, 3*nmon, 3):
        
        for j in range(monsize):
            
            com_traj[i] += massarr[j]*ftraj[3*j + monsize*i] #xij
            
            com_traj[i+1] += massarr[j]*ftraj[3*j + monsize*i + 1] #yij
            
            com_traj[i+2] += massarr[j]*ftraj[3*j + monsize*i + 2] #zij
            
    com_traj *= 1/totalM
    
    return com_traj
    
    
    
def save_ftraj_g96style(filename, ftraj):
    
    import numpy as np
    
    atomsxyz = np.shape(ftraj)[0]
    
    frames = np.shape(ftraj)[1]
    
    atoms = int(atomsxyz/3)
    
    output_trajarray = np.array([ ftraj[i:i+3] for i in range(0,atomsxyz,3)])
    
    np.savetxt(filename,np.reshape(np.swapaxes(np.swapaxes(output_trajarray,1,2),0,1),(atoms*frames,3)))
    
    return output_trajarray