def parse_group_sbml(groups_sbml, chebi):
doc = libsbml.SBMLReader().readSBMLFromFile(groups_sbml)
groups_model = doc.getModel()
groups_plugin = groups_model.getPlugin("groups")
r_id2g_id, s_id2gr_id, ub_sps = {}, {}, set()
if groups_plugin:
for group in groups_plugin.getListOfGroups():
gr_members = [it.getIdRef() for it in group.getListOfMembers()]
gr_id, gr_name = group.getId(), group.getName()
gr_sbo = group.getSBOTermID()
gr_type = next(get_annotations(group, libsbml.BQB_IS_DESCRIBED_BY), None)
if not gr_type:
continue
if SBO_BIOCHEMICAL_REACTION == gr_sbo:
if GROUP_TYPE_EQUIV == gr_type:
for r_id in gr_members:
r_id2g_id[r_id] = gr_id, gr_name, len(gr_members)
elif SBO_CHEMICAL_MACROMOLECULE == gr_sbo:
if GROUP_TYPE_UBIQUITOUS == gr_type:
ub_sps = set(gr_members)
elif GROUP_TYPE_EQUIV == gr_type:
for s_id in gr_members:
term = get_chebi_term_by_annotation(group, chebi)
s_id2gr_id[s_id] = gr_id, term if term else gr_name, len(gr_members)
else:
raise GrPlError()
return r_id2g_id, s_id2gr_id, ub_sps
def parse_group_sbml(groups_sbml, chebi):
doc = libsbml.SBMLReader().readSBMLFromFile(groups_sbml)
groups_model = doc.getModel()
groups_plugin = groups_model.getPlugin("groups")
r_id2g_id, s_id2gr_id, ub_sps = {}, {}, set()
if groups_plugin:
for group in groups_plugin.getListOfGroups():
gr_members = [it.getIdRef() for it in group.getListOfMembers()]
gr_id, gr_name = group.getId(), group.getName()
gr_sbo = group.getSBOTermID()
gr_type = next(get_annotations(group, libsbml.BQB_IS_DESCRIBED_BY), None)
if not gr_type:
continue
if SBO_BIOCHEMICAL_REACTION == gr_sbo:
if GROUP_TYPE_EQUIV == gr_type:
for r_id in gr_members:
r_id2g_id[r_id] = gr_id, gr_name, len(gr_members)
elif SBO_CHEMICAL_MACROMOLECULE == gr_sbo:
if GROUP_TYPE_UBIQUITOUS == gr_type:
ub_sps = set(gr_members)
elif GROUP_TYPE_EQUIV == gr_type:
for s_id in gr_members:
term = get_chebi_term_by_annotation(group, chebi)
s_id2gr_id[s_id] = gr_id, term if term else gr_name, len(gr_members)
else:
raise GrPlError()
return r_id2g_id, s_id2gr_id, ub_sps
def check_for_groups(groups_sbml, sbo_term, group_type):
doc = libsbml.SBMLReader().readSBMLFromFile(groups_sbml)
groups_plugin = doc.getModel().getPlugin("groups")
if groups_plugin:
for group in groups_plugin.getListOfGroups():
gr_sbo = group.getSBOTermID()
gr_type = next(get_annotations(group, libsbml.BQB_IS_DESCRIBED_BY), None)
if sbo_term == gr_sbo and group_type == gr_type:
return True
return False
def check_for_groups(groups_sbml, sbo_term, group_type):
doc = libsbml.SBMLReader().readSBMLFromFile(groups_sbml)
groups_plugin = doc.getModel().getPlugin("groups")
if groups_plugin:
for group in groups_plugin.getListOfGroups():
gr_sbo = group.getSBOTermID()
gr_type = next(get_annotations(group, libsbml.BQB_IS_DESCRIBED_BY), None)
if sbo_term == gr_sbo and group_type == gr_type:
return True
return False
