162 lines
5.1 KiB
Python
Executable File
162 lines
5.1 KiB
Python
Executable File
#!/usr/bin/env python3
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from prody import *
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from pylab import *
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import matplotlib.pyplot as plt
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import itertools
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import os
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import glob
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import re
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ion()
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prody.confProDy(auto_show=False)
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#######################################################################################
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## ADJUSTABLE PARAMETERS ##
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#######################################################################################
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# set specific system names to visualize
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#visualize=[]
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#show=["ALL", "no_PHQ"]
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#######################################################################################
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## JOB CONTROL ##
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#######################################################################################
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# set output dir
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out_dir = os.path.splitext(os.path.basename(sys.argv[0]))[0]
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out_file = out_dir + "/combined"
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# create palette
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colors = itertools.cycle(["red", "blue", "green", "orange"])
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# create output dir
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if not os.path.exists(out_dir):
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os.makedirs(out_dir)
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# parse files
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in_files=os.listdir("1-concat/eda/")
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out_files=os.listdir(out_dir)
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systems = []
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get_systems=os.listdir("1-concat/combined/")
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for filename in get_systems:
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if filename.endswith(".pdb"):
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systems.append(re.sub('-.*','',filename))
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my_pdb=glob.glob("1-concat/eda/combined*.pdb")
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# if system_names file is present, set names from there
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if os.path.exists('system_names'):
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exec(open('system_names').read())
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else:
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systems=sorted(systems)
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# load pdb
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structure = parsePDB(my_pdb[0])
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structure_select = structure.select("resnum 88:203")
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# load trajectory
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if os.path.exists(out_file + '_prody.dcd'):
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trajectory = parseDCD(out_file + '_prody.dcd')
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trajectory.setCoords(structure_select)
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trajectory.setAtoms(structure_select)
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else:
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combined_dcd = glob.glob('1-concat/eda/combined-*.dcd')
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trajectory = parseDCD(combined_dcd[0])
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trajectory.setCoords(structure)
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trajectory.setAtoms(structure_select)
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trajectory.superpose()
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# save aligned dcd
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writeDCD(out_file + '_prody.dcd', trajectory)
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# calculate frame increments
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num_frames = DCDFile.numFrames(trajectory)
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num_systems = len(systems)
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frame_incr = int(num_frames / num_systems - 1)
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res_nums = structure_select.getResnums()
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first_res = res_nums[0]
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last_res = res_nums[-1]
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# calculate covariance and modes
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if os.path.exists(out_file + '.eda.npz'):
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eda_trajectory = loadModel(out_file + '.eda.npz')
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else:
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eda_trajectory = EDA(combined_dcd[0])
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eda_trajectory.buildCovariance(trajectory, aligned=True)
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eda_trajectory.calcModes(n_modes=10)
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saveModel(eda_trajectory, filename=out_file)
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for mode in eda_trajectory[:4]:
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print(calcFractVariance(mode))
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# write VMD files
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writeNMD(out_file, eda_trajectory[:10], structure_select)
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# create EDA rmsf figures
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def my_showSqFlucts(modes, *args, **kwargs):
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"""Show square fluctuations using :func:`~matplotlib.pyplot.plot`. See
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also :func:`.calcSqFlucts`."""
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import matplotlib.pyplot as plt
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sqf = calcSqFlucts(modes)
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if not 'label' in kwargs:
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kwargs['label'] = str(modes)
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show = plt.plot(res_nums,sqf, *args, **kwargs)
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plt.xlabel('Residue #')
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plt.ylabel('Square fluctuations')
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plt.xlim([first_res,last_res])
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plt.title(str(modes))
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return show
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for i in range(0, 4):
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j = i + 1
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plt.figure(figsize=(8, 6))
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my_showSqFlucts(eda_trajectory[i])
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title('RMSF (EDA Mode ' + str(j) + ')')
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plt.savefig(out_file + '_rmsf_mode_' + str(j) + '.png', dpi=300, format='png')
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plt.close('all[')
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# create cross-corr figure
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def my_showCrossCorr(modes, *args, **kwargs):
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import matplotlib.pyplot as plt
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arange = np.arange(first_res - 1 ,last_res)
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cross_correlations = np.zeros((arange[-1]+2, arange[-1]+2))
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cross_correlations[arange[0]+1:,
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arange[0]+1:] = calcCrossCorr(modes)
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kwargs['interpolation'] = 'bilinear'
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kwargs['origin'] = 'lower'
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show = plt.imshow(cross_correlations, *args, **kwargs), plt.colorbar()
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plt.axis([arange[0]+0.5, arange[-1]+1.5, arange[0]+0.5, arange[-1]+1.5])
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plt.title('Cross-correlations for {0}'.format(str(modes)))
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plt.xlabel('Residue')
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plt.ylabel('Residue')
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return show
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plt.figure(figsize=(8, 6))
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my_showCrossCorr(eda_trajectory)
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title('Cross-correlation matrix')
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plt.savefig(out_file + '_corr.png', dpi=300, format='png')
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plt.close('all')
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# create projection figures
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plt.figure(figsize=(8, 6))
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showProjection(trajectory[:frame_incr], eda_trajectory[0,1], color='red', marker='.', label=systems[0])
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showProjection(trajectory[frame_incr + 1:frame_incr * 2 + 1], eda_trajectory[0,1], color='green', marker='.', label=systems[1]);
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legend(markerscale=2, numpoints=1, handletextpad=0.25)
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title('EDA')
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plt.savefig(out_file + '_proj1_2.png', dpi=300, format='png')
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plt.close('all')
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plt.figure(figsize=(8, 6))
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showProjection(trajectory[:frame_incr], eda_trajectory[2,3], color='red', marker='.', label=systems[0])
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showProjection(trajectory[frame_incr + 1:frame_incr * 2 + 1], eda_trajectory[2,3], color='green', marker='.', label=systems[1]);
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legend(markerscale=2, numpoints=1, handletextpad=0.25)
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title('EDA')
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plt.savefig(out_file + '_proj3_4.png', dpi=300, format='png')
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plt.close('all')
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