def calculate_peaks(ringer,threshold):
"""
Checks if something is greater than either of its neighbors (including
wrapping) and returns if true and if above a threshold)
"""
new_peaks=Peaklist()
list = ringer._angles[1].densities
for i in range(len(list)):
if (list[i]==max(list) and list[i]>threshold):
new_peaks.add_new(ringer.resname, ringer.resid, ringer.chain_id, 1, i, list[i])
return new_peaks
def calculate_peaks(ringer,threshold):
"""
Checks if something is greater than either of its neighbors (including
wrapping) and returns if true and if above a threshold)
"""
new_peaks=Peaklist()
list = ringer._angles[1].densities
for i in range(len(list)):
if (list[i]==max(list) and list[i]>threshold):
new_peaks.add_new(ringer.resname, ringer.resid, ringer.chain_id, 1, i, list[i])
return new_peaks
def __init__(self,
file_name,
ringer_result=None,
sampling_angle=5,
out_dir=None,
out=sys.stdout,
quiet=False):
self.threshold = waves = None
if (ringer_result is not None):
waves, self.thresholds = process_raw_results(ringer_result, out=out)
else :
assert (file_name is not None)
waves, self.thresholds = parse_pickle(file_name, out=out)
if not quiet:
assert (out_dir is None) or os.path.isdir(out_dir)
if (out_dir is None) and (not quiet):
out_dir = file_name + ".output"
if (not os.path.isdir(out_dir)):
os.makedirs(file_name+'.output')
Weird_residues=OrderedDict()
self.peak_count={}
residue_peak_count={}
rotamer_ratios_residues={}
zscores_residues={}
for i in Residue_codes:
residue_peak_count[i]={}
rotamer_ratios_residues[i]=[]
zscores_residues[i]=[]
binned_peaks={}
n_angles = iceil(360.0 / sampling_angle)
self.zscores=[]
self.rotamer_ratios=[]
self.non_zero_thresholds=[]
self.length = len(waves)
self.peaks=OrderedDict()
# calculate peaks and histogram
for threshold in self.thresholds:
if (not quiet):
print >>out, ""
print >>out, "===== Calculating Statistics for Threshold %.3f =====" %\
threshold
self.peaks[threshold]=Peaklist()
Weird_residues[threshold]=Peaklist()
self.peak_count[threshold] = [0]*n_angles
for i in Residue_codes:
residue_peak_count[i][threshold]=[0]*n_angles
for i in waves:
self.peaks[threshold].append_lists(calculate_peaks(i, threshold))
for peak in self.peaks[threshold].get_peaks():
self.peak_count[threshold][peak.chi_value] += 1
residue_peak_count[peak.resname][threshold][peak.chi_value]+=1
if ((peak.chi_value<6) or (peak.chi_value>18 and peak.chi_value<30) or (peak.chi_value>42 and peak.chi_value<54) or (peak.chi_value>66)):
Weird_residues[threshold].peaks.append(peak)
# Calculate the binned peaks and ratios
binned_peaks[threshold] = calculate_binned_counts(self.peak_count[threshold], 60)
# print "For threshold %.3f" % threshold
# print "Sample size = %d" % sum(binned_peaks[threshold])
zscore_n, rotamer_ratio_n = statistic(binned_peaks[threshold], n_angles)
if rotamer_ratio_n==0:
break
for i in Residue_codes:
rotamer_ratios_residues_n, zscores_n = calc_ratio(residue_peak_count[i][threshold], sampling_angle)
rotamer_ratios_residues[i].append(rotamer_ratios_residues_n)
zscores_residues[i].append(zscores_n)
self.non_zero_thresholds.append(threshold)
self.zscores.append(zscore_n)
self.rotamer_ratios.append(rotamer_ratio_n)
if (not quiet):
print >> out, "===== Plotting Histogram for Threshold %.3f =====" % \
threshold
out_file = os.path.join(out_dir, "%.3f.histogram.png" % threshold)
plot_peaks(
peak_count=self.peak_count[threshold],
file_name=out_file,
threshold=threshold,
first=60,
title=RMSD_statistic(self.peaks[threshold].peaks),
n_angles=n_angles)
print >> out, "Saved plot to %s" % out_file
# plot_rotamers(binned_peaks[threshold], file, threshold, args.first_rotamer)
# print "Outliers at threshold %.2f: %s" % (threshold, str(Weird_residues[threshold]))
if len(self.zscores) == 0:
raise Sorry("""No scores could be calculated at any threshold for this map. This could be because the
map is not sufficiently featured, or because of data corruption in the map.""")
if (not quiet):
print >> out, ""
print >> out, "===== Plotting Statistics Across Thresholds ====="
out_file = os.path.join(out_dir, "Total.threshold_scan.png")
plot_progression(
non_zero_thresholds=self.non_zero_thresholds,
rotamer_ratios=self.rotamer_ratios,
file_name=out_file,
zscores=self.all_scores)
print >> out, "Saved plot to %s" % out_file
# for i in Residue_codes:
# plot_progression(non_zero_thresholds, rotamer_ratios_residues[i], file, zscores_residues[i], i)
print >> out, ""
print >> out, "===== Writing Pickles Out ====="
easy_pickle.dump(out_dir + '/Outliers.pkl',Weird_residues)
print >> out, 'Wrote ' + out_dir + '/Outliers.pkl'
easy_pickle.dump(out_dir + '/rotamer_ratios.pkl', self.rotamer_ratios)
print >> out, 'Wrote ' + out_dir + '/rotamer_ratios.pkl'
easy_pickle.dump(out_dir + '/zscores.pkl', self.zscores)
print >> out, 'Wrote ' + out_dir + '/zscores.pkl'
easy_pickle.dump(out_dir + '/emringer_scores.pkl', self.all_scores)
print >> out, 'Wrote ' + out_dir + '/emringer_scores.pkl'
easy_pickle.dump(out_dir + '/thresholds.pkl', self.thresholds)
print >> out, 'Wrote ' + out_dir + '/thresholds.pkl'
easy_pickle.dump(out_dir + '/peak_counts.pkl', self.peak_count)
print >> out, 'Wrote ' + out_dir + '/peak_counts.pkl'
self.zscore_max = max(self.zscores)
self._zscore_max_index = self.zscores.index(self.zscore_max)