def handle_residue_line(self, line):
'''
Handle a base line, creates an instance of |Monosaccharide|
and adds it to :attr:`graph` at the given index.
Called by :meth:`parse`
'''
_, ix, residue_str = re.split(r"^(\d+)b", line, maxsplit=1)
residue_dict = res_pattern.search(residue_str).groupdict()
mods = residue_dict.pop("modifications")
modifications = OrderedMultiMap()
if mods is not None:
for p, mod in modification_pattern.findall(mods):
modifications[try_int(p)] = modification_map[mod]
residue_dict["modifications"] = modifications
is_reduced = "aldi" in modifications[1]
if is_reduced:
modifications.pop(1, "aldi")
residue_dict['reduced'] = True
conf_stem = residue_dict.pop("conf_stem")
if conf_stem is not None:
config, stem = zip(*conf_stem_pattern.findall(conf_stem))
else:
config = ('x',)
stem = ('x',)
residue_dict['stem'] = stem
residue_dict['configuration'] = config
residue_dict["ring_start"], residue_dict["ring_end"] = list(map(
try_int, residue_dict.pop("indices").split(":")))
residue_dict['anomer'] = anomer_map[residue_dict['anomer']]
residue_dict['superclass'] = superclass_map[residue_dict['superclass']]
residue = monosaccharide.Monosaccharide(**residue_dict)
if self.in_repeat:
graph = self.current_repeat.graph
else:
graph = self.graph
graph[ix] = residue
residue.id = int(ix)
if self.root is None:
if self.in_repeat:
self.root = self.current_repeat
else:
self.root = residue
def parse(self):
for evt, entity in ET.iterparse(self.handle, ("start", "end")):
if evt != "end":
if entity.tag == "sugar":
self.state = START
elif entity.tag == 'residues':
if self.state == START:
self.state = RES
else:
raise GlycoCTXMLError("<residues> not the first section encountered")
elif entity.tag == 'linkages':
if self.state != RES:
raise GlycoCTXMLError("<linkages> not following <residues>")
elif entity.tag in {'repeat'}:
raise GlycoCTXMLSectionUnsupported("<{}> section is not supported".format(entity.tag))
continue
if entity.tag == "stemtype":
self.buffer['stem'].append(entity.attrib['type'][1:])
self.buffer['configuration'].append(entity.attrib['type'][0])
elif entity.tag == "modification":
self.buffer['modification'].append(
(entity.attrib['type'], try_int(entity.attrib['pos_one'])))
elif entity.tag == "basetype":
id, anomer, superclass, ring_start, ring_end = basetype_unpacker(entity.attrib)
superclass = superclass_map[superclass.upper()]
anomer = anomer_map[anomer]
id = int(id)
modifications = OrderedMultiMap()
mods = self.buffer.pop("modification", None)
if mods is not None:
for mod, pos in mods:
modifications[pos] = modification_map[mod]
is_reduced = "aldi" in modifications[1]
if is_reduced:
modifications.pop(1, "aldi")
residue = monosaccharide.Monosaccharide(
anomer=anomer, superclass=superclass, stem=self.buffer.pop('stem'),
configuration=self.buffer.pop("configuration"), ring_start=ring_start,
ring_end=ring_end, modifications=modifications, reduced=is_reduced, id=id)
self.graph[id] = residue
if self.root is None:
self.root = residue
elif entity.tag == "substituent":
substituent_obj = substituent.Substituent(entity.attrib['name'])
self.graph[int(entity.attrib['id'])] = substituent_obj
elif entity.tag == "connection":
parent_id = try_int(entity.attrib['parent'])
child_id = try_int(entity.attrib['child'])
parent_node = self.graph[parent_id]
child_node = self.graph[child_id]
link.Link(
parent_node, child_node, parent_position=self.buffer.pop("parent_position"),
child_position=self.buffer.pop("child_position"),
parent_loss=self.buffer.pop('parent_loss'), child_loss=self.buffer.pop('child_loss'),
id=self.buffer.pop('id'))
elif entity.tag == "parent":
self.buffer['parent_position'] = int(entity.attrib['pos'])
elif entity.tag == "child":
self.buffer['child_position'] = int(entity.attrib['pos'])
elif entity.tag == "linkage":
self.buffer["id"] = int(entity.attrib['id'])
self.buffer["parent_loss"] = link_replacement_composition_map[entity.attrib['parentType']]
self.buffer["child_loss"] = link_replacement_composition_map[entity.attrib['childType']]
elif entity.tag == 'sugar':
if self.root is not None:
yield glycan.Glycan(self.root)
self._reset()
