3.1.1.6.1.1. etfl.io.dict

Make the model serializable

3.1.1.6.1.1.1. Module Contents

3.1.1.6.1.1.1.1. Functions

metabolite_thermo_to_dict(metthermo)

expressed_gene_to_dict(gene)

coding_gene_to_dict(gene)

enzyme_to_dict(enzyme)

mrna_to_dict(mrna)

ribosome_to_dict(ribosome)

_single_ribosome_to_dict(ribosome)

rnap_to_dict(rnap)

_single_rnap_to_dict(rnap)

dna_to_dict(dna)

archive_variables(var_dict)

archive_constraints(cons_dict)

archive_compositions(compositions)

Turns a peptide compositions dict of the form:

_stoichiometry_to_dict(stoichiometric_dict)

Turns a stoichiometric compositions dict of the form:

archive_coupling_dict(coupling_dict)

Turns an enzyme coupling dict of the form:

archive_trna_dict(model)

Turns a tNA information dict of the form:

get_solver_string(model)

model_to_dict(model)

param model

_add_me_reaction_info(rxn, rxn_dict)

_add_thermo_reaction_info(rxn, rxn_dict)

_add_thermo_metabolite_info(met, met_dict)

model_from_dict(obj, solver=None)

prostprocess_me(new)

init_me_model_from_dict(new, obj)

init_thermo_model_from_dict(new, obj)

init_thermo_me_model_from_dict(new, obj)

rebuild_compositions(new, compositions_dict)

Performs the reverse operation of :func:archive_compositions

_rebuild_stoichiometry(new, stoich)

Performs the reverse operation of :func:_stoichiometry_to_dict

rebuild_coupling_dict(new, coupling_dict)

Performs the reverse operation of :func:archive_coupling_dict

enzyme_from_dict(obj)

mrna_from_dict(obj)

ribosome_from_dict(obj)

_single_ribosome_from_dict(obj)

rnap_from_dict(obj)

_single_rnap_from_dict(obj)

dna_from_dict(obj)

find_enzymatic_reactions_from_dict(new, obj)

find_translation_reactions_from_dict(new, obj)

find_transcription_reactions_from_dict(new, obj)

find_complexation_reactions_from_dict(new, obj)

link_enzyme_complexation(new, obj)

find_degradation_reactions_from_dict(new, obj)

find_dna_formation_reaction_from_dict(new, obj)

find_peptides_from_dict(new, obj)

find_rrna_from_dict(new, obj)

rebuild_trna(new, obj)

find_genes_from_dict(new, obj)

3.1.1.6.1.1.1.2. Attributes

SOLVER_DICT

MW_OVERRIDE_KEY

etfl.SOLVER_DICT
etfl.MW_OVERRIDE_KEY = molecular_weight_override
etfl.metabolite_thermo_to_dict(metthermo)
etfl.expressed_gene_to_dict(gene)
etfl.coding_gene_to_dict(gene)
etfl.enzyme_to_dict(enzyme)
etfl.mrna_to_dict(mrna)
etfl.ribosome_to_dict(ribosome)
etfl._single_ribosome_to_dict(ribosome)
etfl.rnap_to_dict(rnap)
etfl._single_rnap_to_dict(rnap)
etfl.dna_to_dict(dna)
etfl.archive_variables(var_dict)
etfl.archive_constraints(cons_dict)
etfl.archive_compositions(compositions)

Turns a peptide compositions dict of the form:

{ 'b3991': defaultdict(int,
         {<Metabolite ala__L_c at 0x7f7d25504f28>: -42,
          <Metabolite arg__L_c at 0x7f7d2550bcf8>: -11,
          <Metabolite asn__L_c at 0x7f7d2550beb8>: -6,
          ...}),
...}

to:

{ 'b3991': defaultdict(int,,
        {'ala__L_c': -42,
         'arg__L_c': -11,
         'asn__L_c': -6,
          ...}),
...}
Parameters

compositions –

Returns

etfl._stoichiometry_to_dict(stoichiometric_dict)

Turns a stoichiometric compositions dict of the form:

'b3991': defaultdict(int,
       {<Metabolite ala__L_c at 0x7f7d25504f28>: -42,
        <Metabolite arg__L_c at 0x7f7d2550bcf8>: -11,
        <Metabolite asn__L_c at 0x7f7d2550beb8>: -6,
        ...})

to:

'b3991': defaultdict(int,,
        {'ala__L_c': -42,
         'arg__L_c': -11,
         'asn__L_c': -6,
          ...})
etfl.archive_coupling_dict(coupling_dict)

Turns an enzyme coupling dict of the form:

{'AB6PGH': <Enzyme AB6PGH at 0x7f7d1371add8>,
 'ABTA': <Enzyme ABTA at 0x7f7d1371ae48>,
 'ACALD': <Enzyme ACALD at 0x7f7d1371aeb8>}

to:

{'AB6PGH': 'AB6PGH',
 'ABTA': 'ABTA',
 'ACALD': 'ACALD'
etfl.archive_trna_dict(model)

Turns a tNA information dict of the form:

{'ala__L_c': (<tRNA charged_tRNA_ala__L_c at 0x7f84c16d07b8>,
              <tRNA uncharged_tRNA_ala__L_c at 0x7f84c16d0be0>,
              <Reaction trna_ch_ala__L_c at 0x7f84c16d0978>),
 'arg__L_c': (<tRNA charged_tRNA_arg__L_c at 0x7f84c169b588>,
              <tRNA uncharged_tRNA_arg__L_c at 0x7f84c169b5f8>,
              <Reaction trna_ch_arg__L_c at 0x7f84c0563ef0>)}

to:

{'ala__L_c': ('charged_tRNA_ala__L_c',
              'uncharged_tRNA_ala__L_c',
              'trna_ch_ala__L_c'),
 'arg__L_c': ('charged_tRNA_arg__L_c',
              'uncharged_tRNA_arg__L_c',
              'trna_ch_arg__L_c')}
etfl.get_solver_string(model)
etfl.model_to_dict(model)
Parameters

model –

Returns

etfl._add_me_reaction_info(rxn, rxn_dict)
etfl._add_thermo_reaction_info(rxn, rxn_dict)
etfl._add_thermo_metabolite_info(met, met_dict)
etfl.model_from_dict(obj, solver=None)
etfl.prostprocess_me(new)
etfl.init_me_model_from_dict(new, obj)
etfl.init_thermo_model_from_dict(new, obj)
etfl.init_thermo_me_model_from_dict(new, obj)
etfl.rebuild_compositions(new, compositions_dict)

Performs the reverse operation of :func:archive_compositions

Parameters

  • new –

  • compositions_dict –

Returns

etfl._rebuild_stoichiometry(new, stoich)

Performs the reverse operation of :func:_stoichiometry_to_dict

Parameters

  • new –

  • stoich –

Returns

etfl.rebuild_coupling_dict(new, coupling_dict)

Performs the reverse operation of :func:archive_coupling_dict

Parameters

  • new –

  • coupling_dict –

Returns

etfl.enzyme_from_dict(obj)
etfl.mrna_from_dict(obj)
etfl.ribosome_from_dict(obj)
etfl._single_ribosome_from_dict(obj)
etfl.rnap_from_dict(obj)
etfl._single_rnap_from_dict(obj)
etfl.dna_from_dict(obj)
etfl.find_enzymatic_reactions_from_dict(new, obj)
etfl.find_translation_reactions_from_dict(new, obj)
etfl.find_transcription_reactions_from_dict(new, obj)
etfl.find_complexation_reactions_from_dict(new, obj)
etfl.find_degradation_reactions_from_dict(new, obj)
etfl.find_dna_formation_reaction_from_dict(new, obj)
etfl.find_peptides_from_dict(new, obj)
etfl.find_rrna_from_dict(new, obj)
etfl.rebuild_trna(new, obj)
etfl.find_genes_from_dict(new, obj)