def cfg_plot(record):
if "svg_plot" in record.report_data:
return base64.decodestring(record.report_data["svg_plot"])
s = record.structure.clone()
composition_transform.strip_derivatization(s)
dtree, ax = plot.plot(s, orientation='h', squeeze=1.4, scale=.135)
fmap = {f.name: f for f in record.fragments}
for match in record.matches:
match_key = match.match_key.split(":")[0]
order = len(match_key.split("-"))
if order == 1:
dtree.draw_cleavage(ax=ax, fragment=fmap[match_key], color='red', label=True)
else:
for key in match_key.split("-"):
dtree.draw_cleavage(fragment=fmap[key], ax=ax, color='orange', label=True)
ax.axis('off')
fig = ax.get_figure()
fig.tight_layout(pad=0.2)
img_buffer = StringIO()
fig.savefig(img_buffer, format="svg")
plt.close(fig)
root, ids = ET.XMLID(img_buffer.getvalue())
root.set("id", dtree.uuid)
svg = ET.tostring(root)
record.report_data["svg_plot"] = base64.encodestring(svg)
record.update()
return svg
def spectrum_plot(precursor_spectrum):
fig = spectrum_model.plot_observed_spectra(precursor_spectrum, annotation_source=None)
img_buffer = StringIO()
fig.savefig(img_buffer, format='svg')
plt.close(fig)
root, ids = ET.XMLID(img_buffer.getvalue())
svg = ET.tostring(root)
return svg
def simple_plot(record):
dtree, ax = plot.plot(record, orientation='h', squeeze=1.4, scale=.135)
ax.axis('off')
fig = ax.get_figure()
fig.tight_layout(pad=0.2)
img_buffer = StringIO()
fig.savefig(img_buffer, format="svg")
plt.close(fig)
root, ids = ET.XMLID(img_buffer.getvalue())
root.set("id", dtree.uuid)
svg = ET.tostring(root)
return svg
def __str__(self): # pragma: no cover
rep = StringIO()
fmt = "{0}\n{1}\n{2}\n\n"
for k, v in self.items():
rep.write(fmt.format(k, v.to_glycoct(), v.mass(True)))
return rep.getvalue()
def to_glycoct(self, buffer=None, close=False):
'''
Serialize the |Glycan| graph object into condensed GlycoCT, using
`buffer` to store the result. If `buffer` is |None|, then the
function will operate on a newly created :class:`~glypy.utils.StringIO` object.
Parameters
----------
buffer: file-like or None
The stream to write the serialized structure to. If |None|, uses an instance
of `StringIO`
close: bool
Whether or not to close the stream in `buffer` after writing is done
Returns
-------
file-like or str if ``buffer`` is :const:`None`
'''
is_stringio = False
if buffer is None:
buffer = StringIO()
is_stringio = True
buffer.write("RES\n")
res_counter = make_counter()
lin_counter = make_counter()
# Look-ups for mapping RES nodes to objects by section index and id,
# respectively
index_to_residue = {}
residue_to_index = {}
# Accumulator for linkage indices and mapping linkage indices to
# dependent RES indices
lin_accumulator = []
dependencies = defaultdict(dict)
# Detect cycles and avoid including the same residue twice
visited = set()
for node in (self):
if node.id in visited:
continue
visited.add(node.id)
try:
res, lin, index = node.to_glycoct(
res_counter, lin_counter, complete=False)
lin_accumulator.append((index, lin))
residue_to_index[node.id] = index
index_to_residue[index] = node
for pos, link in node.links.items():
if link.is_child(node):
continue
dependencies[link.child.id][node.id] = ((lin_counter(), link))
for line in res:
buffer.write(line + '\n')
except:
pass
buffer.write("LIN\n")
for res_ix, links in lin_accumulator:
for line in links:
buffer.write(line + '\n')
residue = index_to_residue[res_ix]
for pos, link in residue.links.items():
if link.is_child(residue):
continue
child_res = link.child
ix, link = dependencies[child_res.id][residue.id]
buffer.write(
link.to_glycoct(ix, res_ix, residue_to_index[child_res.id]) + "\n")
if is_stringio:
return buffer.getvalue()
else: # pragma: no cover
if close:
buffer.close()
return buffer