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#!/usr/bin/env python
# coding=utf-8
# Example script, part of MDAnalysis
"""
:Author: Joshua Adelman
:Year: 2011
:License: BSD 3-clause
Example code to demonstrate aligning a trajectory to a reference file and
calculating the rmsd using PyQCPROT
Requires MDAnalysis http://www.mdanalysis.org
"""
import numpy as np
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD, PDB_small
import MDAnalysis.lib.qcprot as qcp
ref = mda.Universe(PSF, PDB_small) # reference structure 1AKE
traj = mda.Universe(PSF, DCD) # trajectory of change 1AKE->4AKE
# align using the backbone atoms
select = 'backbone'
selections = {'reference': select, 'target': select}
frames = traj.trajectory
nframes = len(frames)
rmsd = np.zeros((nframes,))
# Setup writer to write aligned dcd file
writer = mda.coordinates.DCD.DCDWriter(
'rmsfit.dcd', frames.n_atoms,
frames.start_timestep,
frames.skip_timestep,
frames.delta,
remarks='RMS fitted trajectory to ref')
ref_atoms = ref.select_atoms(selections['reference'])
traj_atoms = traj.select_atoms(selections['target'])
natoms = traj_atoms.n_atoms
# if performing a mass-weighted alignment/rmsd calculation
# masses = ref_atoms.masses
# weight = masses/np.mean(masses)
# reference centre of mass system
ref_com = ref_atoms.center_of_mass()
ref_coordinates = ref_atoms.coordinates() - ref_com
# allocate the array for selection atom coords
traj_coordinates = traj_atoms.coordinates().copy()
# R: rotation matrix that aligns r-r_com, x~-x~com
# (x~: selected coordinates, x: all coordinates)
# Final transformed traj coordinates: x' = (x-x~_com)*R + ref_com
for k, ts in enumerate(frames):
# shift coordinates for rotation fitting
# selection is updated with the time frame
x_com = traj_atoms.center_of_mass()
traj_coordinates[:] = traj_atoms.coordinates() - x_com
R = np.zeros((9,), dtype=np.float64)
# Need to transpose coordinates such that the coordinate array is
# 3xN instead of Nx3. Also qcp requires that the dtype be float64
a = ref_coordinates.T.astype('float64')
b = traj_coordinates.T.astype('float64')
rmsd[k] = qcp.CalcRMSDRotationalMatrix(a, b, natoms, R, None)
R = np.matrix(R.reshape(3, 3))
# Transform each atom in the trajectory (use inplace ops to avoid copying
# arrays)
ts._pos -= x_com
ts._pos[:] = ts._pos * R # R acts to the left & is broadcasted N times.
ts._pos += ref_com
writer.write(traj.atoms) # write whole input trajectory system
np.savetxt('rmsd.out', rmsd)