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plot_backbone_rmsd.py
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plot_backbone_rmsd.py
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#!/usr/bin/env python
# encoding: utf-8
import argparse
import prody
import numpy
from matplotlib import pyplot
def get_traj_rmsds(reference, trajectory):
ref_backbone = reference.select('backbone or name OC2')
traj_backbone = trajectory.select('backbone or name OC2')
ensemble = prody.Ensemble('trajectory ensemble')
ensemble.setCoords( ref_backbone.getCoords() )
ensemble.addCoordset( traj_backbone.getCoordsets() )
ensemble.superpose()
return ensemble.getRMSDs()
def get_single_rmsd(reference, model):
ref_backbone = reference.select('backbone or name OC2')
mod_backbone = model.select('backbone or name OC2')
prody.superpose(mod_backbone, ref_backbone)
return prody.calcRMSD(mod_backbone, ref_backbone)
def parse_args():
parser = argparse.ArgumentParser(description='Perform cartesian average of trajectory.')
parser.add_argument('reference')
parser.add_argument('trajectory')
parser.add_argument('cart')
parser.add_argument('cart_min')
parser.add_argument('net')
parser.add_argument('net_min')
args = parser.parse_args()
return args
def main():
args = parse_args()
reference = prody.parsePDB(args.reference)
trajectory = prody.parsePDB(args.trajectory)
cart = prody.parsePDB(args.cart)
cart_min = prody.parsePDB(args.cart_min)
net = prody.parsePDB(args.net)
net_min = prody.parsePDB(args.net_min)
cart_rmsd = get_single_rmsd(reference, cart)
cart_min_rmsd = get_single_rmsd(reference, cart_min)
net_rmsd = get_single_rmsd(reference, net)
net_min_rmsd = get_single_rmsd(reference, net_min)
traj_rmsds = get_traj_rmsds(reference, trajectory)
pyplot.hist(traj_rmsds, range=(0, 5), bins=26, histtype='stepfilled',
color='lightgrey', normed=True, edgecolor='none')
pyplot.axvline(cart_rmsd, color='blue', linewidth=2, linestyle='--')
pyplot.axvline(cart_min_rmsd, color='blue', linewidth=2, linestyle='-')
pyplot.axvline(net_rmsd, color='orange', linewidth=2, linestyle='--')
pyplot.axvline(net_min_rmsd, color='orange', linewidth=2, linestyle='-')
pyplot.show()
if __name__ == '__main__':
main()