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 test_strip_derivatize(self):
glycan = load("common_glycan")
glycan.reducing_end = ReducedEnd()
mass = glycan.mass()
composition_transform.derivatize(glycan, 'methyl')
self.assertNotEqual(mass, glycan.mass())
composition_transform.strip_derivatization(glycan)
self.assertAlmostEqual(glycan.mass(), mass, 3)
def is_dhex(residue):
try:
return is_a(
strip_derivatization(residue.clone(
monosaccharide_type=MonosaccharideResidue)), dhex)
except TypeError:
if not isinstance(residue, MonosaccharideResidue):
return False
else:
raise
def is_dhex(residue):
try:
return is_a(
strip_derivatization(
residue.clone(monosaccharide_type=MonosaccharideResidue)),
dhex)
except TypeError:
if not isinstance(residue, MonosaccharideResidue):
return False
else:
raise
def from_monosaccharide(cls, monosaccharide, configuration=False, stem=True, ring=False):
"""Construct an instance of :class:`MonosaccharideResidue` from an instance
of |Monosaccharide|. This function attempts to preserve derivatization if possible.
This function will create a *deep copy* of `monosaccharide`.
Parameters
----------
monosaccharide : Monosaccharide
The monosaccharide to be converted
configuration : bool, optional
Whether or not to preserve |Configuration|. Defaults to |False|
stem : bool, optional
Whether or not to preserve |Stem|. Defaults to |True|
ring : bool, optional
Whether or not to preserve |RingType|. Defaults to |False|
Returns
-------
MonosaccharideResidue
"""
residue = monosaccharide.clone(monosaccharide_type=cls)
premass = residue.mass()
deriv = has_derivatization(monosaccharide)
strip_derivatization(residue)
if _resolve_special_base_type(monosaccharide) is None:
if not configuration:
residue.configuration = (Configuration.x,)
if not stem:
residue.stem = (Stem.x,)
if not ring:
residue.ring_start = residue.ring_end = None
if deriv:
derivatize(residue, deriv)
if residue.mass() != premass and not deriv:
residue.composition += water_composition
return residue
def normalize_key(composition):
key_obj = composition.clone()
key_obj = composition_transform.strip_derivatization(key_obj)
return str(key_obj)
def normalize_key(composition):
key_obj = composition.clone()
key_obj = composition_transform.strip_derivatization(key_obj)
return str(key_obj)
def strip_derivatize_glycoct(record):
s = record.structure.clone()
composition_transform.strip_derivatization(s)
return(str(s))
