Add some trajectory analysis scripts

trajectory_analysis/4-rmsf.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python3
+
+from prody import *
+from pylab import *
+import matplotlib.pyplot as plt
+import itertools
+import os
+import glob
+import re
+ion()
+prody.confProDy(auto_show=False)
+
+# set output dir
+out_dir = os.path.splitext(os.path.basename(sys.argv[0]))[0]
+out_file = out_dir + "/combined"
+
+# create output dir
+if not os.path.exists(out_dir):
+    os.makedirs(out_dir)
+
+# create palette
+colors = itertools.cycle(["red", "blue", "green", "orange"])
+
+# parse files
+in_files=os.listdir("1-concat/eda/")
+out_files=os.listdir(out_dir)
+systems = []
+get_systems=os.listdir("1-concat/combined/")
+for filename in get_systems:
+  if filename.endswith(".pdb"):
+     systems.append(re.sub('-.*','',filename))
+my_pdb=glob.glob("1-concat/eda/combined*.pdb")
+
+# if system_names file is present, set names from there
+if os.path.exists('system_names'):
+  exec(open('system_names').read())
+else:
+  systems=sorted(systems)
+
+# load pdb
+structure = parsePDB(my_pdb[0])
+
+# load trajectory
+if os.path.exists(out_file + '_prody.dcd'):
+  trajectory = parseDCD(out_file + '_prody.dcd')
+  trajectory.setCoords(structure)
+  trajectory.setAtoms(structure.all)
+else:
+  dcd = glob.glob('1-concat/eda/combined-*.dcd')
+  trajectory = parseDCD(dcd[0])
+  trajectory.setCoords(structure)
+  trajectory.setAtoms(structure.all)
+  trajectory.superpose()
+  # save aligned dcd
+  writeDCD(out_file + '_prody.dcd', trajectory)
+
+# calculate frame increments
+num_frames = DCDFile.numFrames(trajectory)
+num_systems = len(systems)
+frame_incr = int(num_frames / num_systems - 1)
+res_nums = AtomGroup.getResnums(structure)
+first_res = res_nums[0]
+last_res = res_nums[-1]
+
+# create rmsf figure
+first_frame = 0
+last_frame = frame_incr
+plt.figure(figsize=(12, 6))
+for system in systems:
+  rmsf = calcRMSF(trajectory[first_frame:last_frame])
+  print(rmsf)
+  plt.plot(res_nums, rmsf, label=system, color=next(colors), linewidth=1.5)
+  first_frame = last_frame + 1
+  last_frame = first_frame + frame_incr
+title('RMSF', size=20)
+plt.xlabel('Residue #', size=16)
+plt.ylabel('Angstroms', size=16)
+plt.xlim([first_res,last_res])
+ax = subplot(1,1,1)
+handles, labels = ax.get_legend_handles_labels()
+labels, handles = zip(*sorted(zip(labels, handles), key=lambda t: t[0]))
+plt.legend(handles, labels, loc='upper left')
+ax.grid(True)
+plt.savefig(out_file + '_rmsf.png', dpi=300, format='png')
+plt.close('all[')
+
+
+
+