def write_plots (self, plot_file_base, out, show_labels=True, point_style='bo') :
"""
Write a set of six PNG images representing the plots for each residue type.
:param plot_file_base: file name prefix
:param out: log filehandle
"""
print >> out, ""
print >> out, "Creating images of plots..."
for pos in range(6) :
stats = utils.get_rotarama_data(
pos_type=res_types[pos],
convert_to_numpy_array=True)
file_label = res_type_labels[pos].replace("/", "_")
plot_file_name = plot_file_base + "_rama_%s.png" % file_label
points, coords = self.get_plot_data(position_type=pos)
draw_ramachandran_plot(
points=points,
rotarama_data=stats,
position_type=pos,
title=format_ramachandran_plot_title(pos, '*'),
file_name=plot_file_name,
show_labels=show_labels,
point_style=point_style)
print >> out, " wrote %s" % plot_file_name
def get_plots(self,
show_labels=True,
point_style='bo',
markersize=10,
markeredgecolor="black",
dpi=100,
markerfacecolor="white",
show_filling=True,
show_contours=True):
"""
Create a dictionary of six PNG images representing the plots for each residue type.
:param out: log filehandle
"""
result = {}
for pos in range(6):
stats = utils.get_rotarama_data(pos_type=res_types[pos],
convert_to_numpy_array=True)
points, coords = self.get_plot_data(position_type=pos)
result[pos] = draw_ramachandran_plot(
points=points,
rotarama_data=stats,
position_type=pos,
title=format_ramachandran_plot_title(pos, '*'),
show_labels=show_labels,
markeredgecolor=markeredgecolor,
markerfacecolor=markerfacecolor,
show_filling=show_filling,
show_contours=show_contours,
point_style=point_style,
markersize=markersize)
return result
def draw_plot(self):
stats = utils.get_rotarama_data(pos_type='general', convert_to_numpy_array=True)
residue_name = 'GLN'
points, coords = graphics.get_residue_rotamer_data(rotalyze_data=self.rotalyze_data,
residue_name=self.residue_name,
point_type=self.point_type)
self.plot.draw_plot(
stats=stats,
title="Chi1-Chi2 plot for %s" % self.residue_name,
points=points,
xyz=coords,
colormap="Blues",
contours=None)
if self.canvas is not None:
self.canvas.draw()
def draw_plot(self):
stats = utils.get_rotarama_data(pos_type='general', convert_to_numpy_array=True)
points, coords = graphics.get_residue_ramachandran_data(ramalyze_data=self.ramalyze_data,
position_type=self.pos_type,
residue_name=self.residue_name,
point_type=self.point_type)
title = graphics.format_ramachandran_plot_title(self.pos_type, self.residue_name)
self.plot.draw_plot(
stats=stats,
title=title,
points=points,
xyz=coords,
colormap="Blues",
contours=[0.1495, 0.376])
if self.canvas is not None:
self.canvas.draw()
def write_plots (self, plot_file_base, out) :
"""
Write a set of six PNG images representing the plots for each residue type.
:param plot_file_base: file name prefix
:param out: log filehandle
"""
print >> out, ""
print >> out, "Creating images of plots..."
for pos in range(6) :
stats = utils.get_rotarama_data(
pos_type=res_types[pos],
convert_to_numpy_array=True)
file_label = res_type_labels[pos].replace("/", "_")
plot_file_name = plot_file_base + "_rama_%s.png" % file_label
points, coords = self.get_plot_data(position_type=pos)
draw_ramachandran_plot(
points=points,
rotarama_data=stats,
position_type=pos,
title=format_ramachandran_plot_title(pos, '*'),
file_name=plot_file_name)
print >> out, " wrote %s" % plot_file_name
def get_plots(self):
'''
Draw plots from data in pickle file
'''
if self.json_data['success_composition'] is False:
return
make_sub_header('Making plots', out=self.logger)
self.save_json()
success = True
root = os.path.join(self.dest_dir)
# B factor histogram
print('Plotting B-factor histogram.', file=self.logger)
bfactor_hist_fn = os.path.join(root, self.pdb_code + '_bfactor_hist.svg')
try:
rerefine_plots.plot_b_histogram(
histogram = self.pickle_data.adp_hist,
r_histogram = self.pickle_data.r_adp_hist,
filename = bfactor_hist_fn,
log = self.logger)
except Exception as e:
success = False
msg = traceback.format_exc()
print(msg, file=self.logger)
if (os.path.isfile(bfactor_hist_fn)):
self.json_data['plot_bfactor_hist'] = bfactor_hist_fn
else:
print('\tNo B-factor plot generated.', file=self.logger)
# FSC plots
d_inv = self.pickle_data.d_inv
fsc_model = self.pickle_data.fsc_model
r_d_inv = self.pickle_data.r_d_inv
r_fsc_model = self.pickle_data.r_fsc_model
min_reso = self.pickle_data.min_reso
d_inv_half = self.pickle_data.d_inv_half
fsc_half = self.pickle_data.fsc_half
print('Plotting FSC halfmaps', file=self.logger)
filename = os.path.join(root, self.pdb_code + '_fsc_halfmaps.svg')
try:
rerefine_plots.plot_fsc(
x1 = d_inv_half,
y1 = fsc_half,
x2 = None,
y2 = None,
figure_title = 'Fourier Shell Correlation (from half maps)',
filename = filename,
resolution = min_reso)
except Exception as e:
success = False
msg = traceback.format_exc()
print(msg, file=self.logger)
if (os.path.isfile(filename)):
self.json_data['plot_fsc_halfmaps'] = filename
else:
print('\tNo FSC halfmaps plot generated.', file=self.logger)
print('Plotting FSC model', file=self.logger)
filename = os.path.join(root, self.pdb_code + '_fsc_model.svg')
try:
rerefine_plots.plot_fsc(
x1 = d_inv,
y1 = fsc_model,
x2 = r_d_inv,
y2 = r_fsc_model,
figure_title = 'Fourier Shell Correlation (Model vs Map)',
filename = filename,
resolution = min_reso,
label1 = 'initial model',
label2 = 'refined model')
except Exception as e:
success = False
msg = traceback.format_exc()
print(msg, file=self.logger)
if (os.path.isfile(filename)):
self.json_data['plot_fsc_model'] = filename
else:
print('\tNo FSC model plot generated', file=self.logger)
# CC per chain
print('Plotting CC per chain', file=self.logger)
cc_per_chain_fn = os.path.join(root, self.pdb_code + '_cc_per_chain.svg')
chains, chain_ccs, r_chains, r_chain_ccs = None, None, None, None
if (self.pickle_data.cc_per_chain):
chains, chain_ccs = [], []
for arg1 in self.pickle_data.cc_per_chain:
chains.append(arg1.chain_id)
chain_ccs.append(arg1.cc)
if (self.pickle_data.r_cc_per_chain):
r_chains, r_chain_ccs = [], []
for arg2 in self.pickle_data.r_cc_per_chain:
r_chains.append(arg2.chain_id)
r_chain_ccs.append(arg2.cc)
try:
rerefine_plots.plot_cc_chain(
x1 = chains,
y1 = chain_ccs,
x2 = r_chains,
y2 = r_chain_ccs,
filename = cc_per_chain_fn)
except Exception as e:
success = False
msg = traceback.format_exc()
print(msg, file=self.logger)
if (os.path.isfile(cc_per_chain_fn)):
self.json_data['plot_cc_chain'] = cc_per_chain_fn
else:
print('\tNo CC per chain plot generated', file=self.logger)
# CC per residue
print('Saving ngl color scheme.', file=self.logger)
if (self.pickle_data.cc_per_residue):
self.ngl_color_scheme(
property_list = self.pickle_data.cc_per_residue,
json_key = 'cc_color_scheme')
if (self.pickle_data.r_cc_per_residue):
self.ngl_color_scheme(
property_list = self.pickle_data.r_cc_per_residue,
json_key = 'r_cc_color_scheme')
file_list = []
print('Plotting CC per residue.', file=self.logger)
for chain in self.pickle_data.chain_dict:
res, cc, r_res, r_cc = [], [], [], []
if self.pickle_data.cc_per_residue:
for item in self.pickle_data.cc_per_residue:
if item.chain_id != chain: continue
res.append(int(item.resseq))
cc.append(item.cc)
if self.pickle_data.r_cc_per_residue:
for item in self.pickle_data.r_cc_per_residue:
if item.chain_id != chain: continue
r_res.append(int(item.resseq))
r_cc.append(item.cc)
filename = os.path.join(root, 'cc_per_residue_chain_' + chain + '.svg')
#filename = 'cc_per_residue_chain_' + chain + '.png'
title = 'CC per residue - chain %s' % chain
print('Chain: ', chain, file=self.logger)
try:
rerefine_plots.plot_cc_residue(
x1 = res,
y1 = cc,
x2 = r_res,
y2 = r_cc,
chain = chain,
filename = filename,
title = title)
except Exception as e:
success = False
msg = traceback.format_exc()
print(msg, file=self.logger)
if (os.path.isfile(filename)):
file_list.append(filename)
self.json_data['plot_cc_residue'] = file_list
if not file_list:
print('\tNo CC per residue plots generated', file=self.logger)
# Ramachandran plots
print('Making Ramachandran plot', file=self.logger)
for p, rl in zip(['', 'r_'],
[self.pickle_data.ramalyze, self.pickle_data.r_ramalyze]):
if rl is None: continue
rama_fn = os.path.join(root, self.pdb_code + '_' +p + 'rama.png')
rama_plot = ramachandran_plot()
# Just copy from ramalyze etc. but where do these numbers come from?
contours = [0.1495, 0.376]
# stats = utils.get_rotarama_data(
# pos_type='general',
# convert_to_numpy_array=True)
# # position type 0 is "general"
# points, coords = rl.get_plot_data(position_type=0)
# rama_plot.draw_plot(stats = stats,
# points = points,
# show_labels = False,
# title = "Ramachandran plot for all non-Pro/Gly residues",
# colormap = "Blues",
# contours = contours)
# rama_plot.save_image(
# file_name = rama_fn,
# dpi = 72)
# if (os.path.isfile(rama_fn)):
# self.json_data['plot_' + p+'rama'] = rama_fn
# else:
# print('\tNo Ramachandran plot generated', file=self.logger)
res_types = ["general", "glycine", "cis-proline", "trans-proline",
"pre-proline", "isoleucine or valine"]
positions = range(6)
titles = ["general", "glycine", "cis_pro", "trans_pro", "pre_pro", "ile_val"]
for res_type, pos, title in zip(res_types, positions, titles):
stats = utils.get_rotarama_data(
pos_type=res_type,
convert_to_numpy_array=True)
points, coords = rl.get_plot_data(position_type=pos)
rama_plot.draw_plot(stats = stats,
points = points,
show_labels = False,
title = "Ramachandran plot for all %s residues" % res_type,
colormap = "Blues",
contours = contours)
if pos == 0:
rama_fn = os.path.join(root, self.pdb_code + '_' +p + 'rama.png')
else:
rama_fn = os.path.join(root, self.pdb_code + '_' +p + 'rama_' + title + '.png')
rama_plot.save_image(file_name = rama_fn, dpi = 150)
if (os.path.isfile(rama_fn)):
if pos == 0:
self.json_data['plot_' + p +'rama'] = rama_fn
else:
self.json_data['plot_' + p +'rama_' + title] = rama_fn
else:
print('\tNo Ramachandran plot generated', file=self.logger)
self.json_data['success_plots'] = success