def main():
parser = OptionParser()
parser.add_option("-f", "--use-flat", action="store_true", dest="use_flat_flag", default=False,
help="load plot data from flat files")
parser.add_option("-n", "--nonpolar-timeseries", action="store_true", dest="run_nonpolar_flag", default=False,
help="run nonpolar timeseries analysis and plot")
parser.add_option("-p", "--hb-timeseries", action="store_true",
dest="run_polar_flag", default=False,
help="run polar timeseries analysis and plot")
parser.add_option("-c", "--cluster", action="store_true", dest="run_cluster", default=False,
help="process and plot cluster size analysis")
(options, args) = parser.parse_args()
# print options
# print args
if len(args) < 1:
parser.error("Please specify a .h5 input file")
filename = args[0]
# option = sys.argv[2]
# use_flat_flag = False
h5file = tables.openFile(filename)
ratio,ext = os.path.splitext(filename)
# binding.nonpolar_residue(h5file, ratio)
# binding.intersection(h5file, ratio)
# dssp.run(h5file)
config.configure_plot()
if options.run_polar_flag:
timeseries_hb.run(h5file, ratio, use_flat_files=options.use_flat_flag)
if options.run_nonpolar_flag:
timeseries_nonpolar.run(h5file, ratio, use_flat_files=options.use_flat_flag)
if options.run_cluster:
cluster.run(h5file, ratio, use_flat_files=options.use_flat_flag)
def plot(datalist, labellist, ratio, use_flat_files=False):
if use_flat_files == True:
print "using flat files ... "
datalist,labellist = create_datalist(ratio)
assert len(datalist) == 3, "%s data lists, expecting 3 for scyllo, chiro, water" % `len(datalist)`
config.configure_plot()
fig1 = pylab.figure(num=1)
fig2 = pylab.figure(num=2)
ax1 = fig1.add_subplot(111)
ax2 = fig2.add_subplot(111)
print "plotting data"
for i in range(0,len(datalist)):
parts = labellist[i].split()
isomer = parts[0]
print "plotting", isomer
if isomer == "water":
labellist[i] = "no inositol"
# print "Test: time column for", labellist[i], datalist[i][:,0]
nrows, ncols = datalist[i].shape
assert nrows > ncols, "Number of cols greater than rows!"
time = datalist[i][:,0]/1000
ax1.fill_between(time,
(datalist[i][:,1] - datalist[i][:,2])/config.NMOLECULES,
(datalist[i][:,1] + datalist[i][:,2])/config.NMOLECULES,
alpha=0.5,
facecolor=config.SHADED_COLOR[isomer],
edgecolor=config.SHADED_COLOR[isomer],
lw=0.5)
ax2.fill_between(time,
(datalist[i][:,3] - datalist[i][:,4])/config.NMOLECULES,
(datalist[i][:,3] + datalist[i][:,4])/config.NMOLECULES,
alpha=0.5,
facecolor=config.SHADED_COLOR[isomer],
edgecolor=config.SHADED_COLOR[isomer],
lw=0.5)
ax1.plot(time, datalist[i][:,1]/config.NMOLECULES, color=config.LINE_COLOR[isomer], label=labellist[i])
ax2.plot(time, datalist[i][:,3]/config.NMOLECULES, color=config.LINE_COLOR[isomer], label=labellist[i])
# print "using line color for", isomer, config.LINE_COLOR[isomer]
ax2.set_xlabel('Time (ns)')
ax1.set_ylabel('Intermolecular Hydrogen Bonds per peptide')
ax2.set_ylabel('Intramolecular Hydrogen Bonds per peptide')
ax1.grid(True); ax2.grid(True)
ax1.set_xlim(0, config.RUNTIME_NS); ax2.set_xlim(0, config.RUNTIME_NS)
ax1.set_ylim(0, 3); ax2.set_ylim(0, 3)
ax1.legend(loc='upper right', ncol=1, columnspacing=0.5, borderaxespad=0.)
ax2.legend(loc='upper right', ncol=1, columnspacing=0.5, borderaxespad=0.)
#frame = leg.get_frame()
#frame.set_linewidth(0.5)
print "Saving figure..."
#this produces a small image of this size, but everything else is way too big
#need to adjust rcParams for font size and legend size
# fig1.set_size_inches((3.25,3.5))
# fig2.set_size_inches((3.25,3.5))
print "Polar figure 1 size", fig1.get_size_inches()
print "Polar figure 2 size", fig2.get_size_inches()
fig1.savefig('inter_%(ratio)s.png' % vars())
fig2.savefig('intra_%(ratio)s.png' % vars())