1#!/usr/bin/env python
2# coding: utf-8
3
4# # Pairwise RMSD (2D-RMSD)
5import os
6import sys
7from glob import glob
8import numpy as np
9import pandas as pd
10import matplotlib.pyplot as plt
11# plt.style.use('~/Scripts/bin/v.mplstyle')
12
13import pytraj as pt
14
15# Load trajectory and topology files
16# relativbe path tooooo
17traj = pt.iterload('../1leader/4ntds/prod00.nc', top='../1leader/4ntds/step3_pbcsetup_1264.parm7')
18traj # Same as print(traj)
19
20
21data = pt.pairwise_rmsd(traj, mask='@CA')
22
23im = plt.imshow(data)
24
25plt.colorbar(im, label='2D-RMSD (Å)')
26plt.gca().invert_yaxis() # invert y-axis
27plt.xlabel('Frame Number')
28plt.ylabel('Frame Number')
29
30os.makedirs('img', exist_ok=True)
31# plt.savefig('img/2drmsd-4ntds.png') # uncomment to save
32
33
