本文整理汇总了Python中cobra.Model.update方法的典型用法代码示例。如果您正苦于以下问题：Python Model.update方法的具体用法？Python Model.update怎么用？Python Model.update使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类cobra.Model的用法示例。
在下文中一共展示了Model.update方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: matlab_cobra_struct_to_python_cobra_object
# 需要导入模块: from cobra import Model [as 别名]
# 或者: from cobra.Model import update [as 别名]
#.........这里部分代码省略.........
the_csense = matlab_struct.csense
_constraint_sense = [the_csense[i] for i in range(len(the_csense))]
else:
_constraint_sense = matlab_cell_to_python_list(matlab_struct.csense)
else:
_constraint_sense = ['E']*len(cobra_metabolites)
if 'metFormulas' in struct_fields:
_metabolite_formulas = matlab_cell_to_python_list(matlab_struct.metFormulas)
else:
_metabolite_formulas = ['']*len(the_model.metabolites)
if 'metCharge' in struct_fields:
_metabolite_charges = matlab_struct.metCharge.flatten().tolist()
else:
_metabolite_charges = [None]*len(cobra_metabolites)
if 'metCASID' in struct_fields:
_metabolite_cas_id = matlab_cell_to_python_list(matlab_struct.metCASID)
else:
_metabolite_cas_id = [None]*len(cobra_metabolites)
if 'metKeggID' in struct_fields:
_metabolite_kegg_id = matlab_cell_to_python_list(matlab_struct.metKeggID)
else:
_metabolite_kegg_id = [None]*len(cobra_metabolites)
the_compartments = {}
for the_metabolite, b, n, c, f, ch, cas, kegg in zip(cobra_metabolites,
_b,
_metabolite_names,
_constraint_sense,
_metabolite_formulas,
_metabolite_charges,
_metabolite_cas_id,
_metabolite_kegg_id):
the_metabolite._bound = b[0]
the_metabolite.name = n
the_metabolite._constraint_sense = c
the_metabolite.formula = Formula(f)
the_metabolite.charge = int(ch)
the_compartments[the_metabolite.compartment] = the_metabolite.compartment
if ch is not None:
the_metabolite.notes['CHARGE'] = int(ch)
if cas is not None and cas != '':
the_metabolite.notes['CASID'] = cas
if kegg is not None and kegg != '':
the_metabolite.notes['KEGGID'] = kegg
metabolite_dict = dict([(x.id, x)
for x in cobra_metabolites])
#Reaction section
cobra_reactions = map(Reaction, matlab_cell_to_python_list(matlab_struct.rxns))
_objective_coefficients = deepcopy(matlab_struct.c).tolist()
_lower_bounds = deepcopy(matlab_struct.lb).tolist()
_upper_bounds = deepcopy(matlab_struct.ub).tolist()
_reversibility = deepcopy(matlab_struct.rev).tolist()
if 'rxnNames' in struct_fields:
_reaction_names = matlab_cell_to_python_list(matlab_struct.rxnNames)
else:
_reaction_names = ['']*len(the_model.reactions)
if 'grRules' in struct_fields:
_gene_reaction_rules = matlab_cell_to_python_list(matlab_struct.grRules)
else:
_gene_reaction_rules = ['']*len(the_model.reactions)
if 'subSystems' in struct_fields:
_subsystems = matlab_cell_to_python_list(matlab_struct.subSystems)
else:
_subsystems = ['']*len(the_model.reactions)
for the_reaction, o, l, u, n, r, s, rev in zip(cobra_reactions,
_objective_coefficients,
_lower_bounds,
_upper_bounds,
_reaction_names,
_gene_reaction_rules,
_subsystems, _reversibility ):
the_reaction.objective_coefficient = o[0]
the_reaction.lower_bound = l[0]
the_reaction.upper_bound = u[0]
the_reaction.name = n
the_reaction.gene_reaction_rule = r
the_reaction.subsystem = s
the_reaction.reversibility = rev[0]
the_reaction.parse_gene_association()
index_to_reaction = dict(zip(range(len(cobra_reactions)),
cobra_reactions))
index_to_metabolite = dict(zip(range(len(cobra_metabolites)),
cobra_metabolites))
for k, coefficient in _S_dok.items():
the_reaction = index_to_reaction[k[1]]
the_metabolite = index_to_metabolite[k[0]]
the_reaction.add_metabolites({the_metabolite: coefficient})
#solution needs to be redesigned from a matlab proxy.
#Now populate all of the reactions
#NOTE: Having a metabolite referenece here would be a good idea
compartment_dict = {'e': 'extracellular',
'c': 'cytosol',
'p': 'periplasm'}
for the_key in the_compartments:
if the_key in compartment_dict:
the_compartments[the_key] = compartment_dict[the_key]
the_model.add_reactions(cobra_reactions)
the_model.compartments = the_compartments
the_model.update()
return the_model