Function gen_species_type has a Cognitive Complexity of 108 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_species_type(self, kb_species_type, extra_compartment_ids=None):
        """ Generate a model species type and species

        Args:
            kb_species_type (:obj:`wc_kb.SpeciesType`): knowledge base species type

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File initialize_model.py has 861 lines of code (exceeds 250 allowed). Consider refactoring.

Open

""" Initialize the construction of wc_lang-encoded models from wc_kb-encoded knowledge base.

:Author: Yin Hoon Chew <yinhoon.chew@mssm.edu>
:Date: 2019-01-09
:Copyright: 2019, Karr Lab

Function gen_distribution_init_concentrations has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_distribution_init_concentrations(self):
        """ Generate concentrations for the model from knowledge base """
        kb = self.knowledge_base
        model = self.model
        media = self.options['media']

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Function gen_kb_reactions has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_kb_reactions(self):
        """ Generate reactions encoded within KB
        """

        kb = self.knowledge_base

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Function gen_kb_rate_laws has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_kb_rate_laws(self):
        """ Generate the rate laws for reactions encoded in the knowledge base """
        kb = self.knowledge_base
        model = self.model

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Function gen_parameters has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_parameters(self):
        """ Generate parameters for the model from knowledge base """
        kb = self.knowledge_base
        model = self.model

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Function clean_and_validate_options has 71 lines of code (exceeds 25 allowed). Consider refactoring.

Open

    def clean_and_validate_options(self):
        """ Apply default options and validate options """
        options = self.options

        culture_volume = options.get('culture_volume', 1.)

Function determine_protein_structure_from_aa has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def determine_protein_structure_from_aa(self, 
            polymer_id, count):
        """ Determine the empirical formula, molecular weight and charge of
            a protein based on the structural information of its metabolite
            amino acid monomers to ensure consistency with the pH

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Function run has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

    def run(self):
        """ Run all the components for initializing model from knowledge base """
        self.clean_and_validate_options()
        options = self.options

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Avoid deeply nested control flow statements.

Open

                        if subunit.species_type.transcript.gene.id in selenoproteome:
                            processed_seq = raw_seq[:-1] if raw_seq.endswith('*') else raw_seq
                            protein_seq = ''.join(i if i!='*' else 'U' for i in processed_seq)
                        else:                                            
                            protein_seq = ''.join(i for i in raw_seq if i!='*')

Avoid deeply nested control flow statements.

Open

                        if proton_participant:
                            proton_coef = [i for i in model_rxn.participants if i.species.species_type==proton_species_type][0]
                            model_rxn.participants.discard(proton_coef)
                            model_rxn.participants.add(
                                proton_coef.species.species_coefficients.get_or_create(coefficient=proton_coef.coefficient-delta_charge))

Avoid deeply nested control flow statements.

Open

                        if model_compartment.init_density.function_expressions:
                            volume = model_compartment.init_density.function_expressions[0].function
                            unit_adjusted_term = '{} * {} * {}'.format(param.id, Avogadro.id, volume.id)
                        else:
                            volume = model_compartment.init_volume.mean    

Avoid deeply nested control flow statements.

Open

                        if not determined:
                            formula += subunit.species_type.get_empirical_formula(seq_input=protein_seq) * coef
                            charge += subunit.species_type.get_charge(seq_input=protein_seq) * coef
                            weight += subunit.species_type.get_mol_wt(seq_input=protein_seq) * coef
                        else:

Avoid deeply nested control flow statements.

Open

                        if subunit_id not in gvar.transcript_ntp_usage:
                            seq = subunit.species_type.get_seq()
                            gvar.transcript_ntp_usage[subunit.species_type.id] = {
                                'A': seq.upper().count('A'),
                                'C': seq.upper().count('C'),

Function gen_compartments has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

Open

    def gen_compartments(self):
        """ Generate compartments for the model from knowledge base """
        kb = self.knowledge_base
        model = self.model

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