class Gene(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(
verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(
verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
locus_name = obj_tables.StringAttribute(verbose_name='LocusName')
gene_product = obj_tables.StringAttribute(verbose_name='GeneProduct')
gene_product_s_b_m_l_species_id = obj_tables.StringAttribute(
verbose_name='GeneProduct:SBML:species:id')
operon = obj_tables.StringAttribute(verbose_name='Operon')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
s_b_m_l_fbc_i_d = obj_tables.StringAttribute(verbose_name='SBML:fbc:ID')
s_b_m_l_fbc_name = obj_tables.StringAttribute(verbose_name='SBML:fbc:Name')
s_b_m_l_fbc_gene_product = obj_tables.BooleanAttribute(
verbose_name='SBML:fbc:GeneProduct')
s_b_m_l_fbc_gene_association = obj_tables.BooleanAttribute(
verbose_name='SBML:fbc:GeneAssociation')
s_b_m_l_fbc_label = obj_tables.StringAttribute(
verbose_name='SBML:fbc:Label')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'locus_name',
'gene_product',
'gene_product_s_b_m_l_species_id',
'operon',
'identifiers',
's_b_m_l_fbc_i_d',
's_b_m_l_fbc_name',
's_b_m_l_fbc_gene_product',
's_b_m_l_fbc_gene_association',
's_b_m_l_fbc_label',
)
verbose_name = 'Gene'
verbose_name_plural = 'Gene'
class Relation(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(
verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
i_d = obj_tables.StringAttribute(verbose_name='ID')
from_object = obj_tables.StringAttribute(verbose_name='FromObject')
to_object = obj_tables.StringAttribute(verbose_name='ToObject')
is_symmetric = obj_tables.BooleanAttribute(verbose_name='IsSymmetric')
value_quantity_type = obj_tables.FloatAttribute(
verbose_name='Value:QuantityType')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'i_d',
'from_object',
'to_object',
'is_symmetric',
'value_quantity_type',
)
verbose_name = 'Relation'
verbose_name_plural = 'Relation'
class GeneLocus(core.PolymerLocus):
""" Knowledge of a gene
Attributes:
symbol (:obj:`str`): symbol
Related attributes:
proteins (:obj:`list` of :obj:`ProteinSpeciesType`): protein
"""
symbol = obj_tables.StringAttribute()
start = obj_tables.IntegerAttribute()
end = obj_tables.IntegerAttribute()
is_essential = obj_tables.BooleanAttribute()
proteins = obj_tables.OneToOneAttribute(ProteinSpeciesType,
related_name='gene')
homologs = obj_tables.LongStringAttribute()
evidence = obj_tables.OneToManyAttribute(core.Evidence,
related_name='genes')
cog = obj_tables.sci.onto.OntoTermAttribute(
kbOnt, terms=kbOnt['WC:COG'].subclasses(), none=True)
class Meta(obj_tables.Model.Meta):
verbose_name = 'Gene'
verbose_name_plural = 'Genes'
attribute_order = ('id', 'name', 'synonyms', 'symbol', 'polymer',
'start', 'end', 'cog', 'homologs', 'is_essential',
'proteins', 'evidence', 'identifiers', 'references',
'comments')
class FbcObjective(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
name = obj_tables.StringAttribute(verbose_name='Name')
s_b_m_l_fbc_type = obj_tables.StringAttribute(verbose_name='SBML:fbc:type')
s_b_m_l_fbc_active = obj_tables.BooleanAttribute(
verbose_name='SBML:fbc:active')
s_b_m_l_fbc_objective = obj_tables.StringAttribute(
verbose_name='SBML:fbc:objective')
s_b_m_l_fbc_reaction = obj_tables.StringAttribute(
verbose_name='SBML:fbc:reaction')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'name',
's_b_m_l_fbc_type',
's_b_m_l_fbc_active',
's_b_m_l_fbc_objective',
's_b_m_l_fbc_reaction',
)
verbose_name = 'FbcObjective'
verbose_name_plural = 'FbcObjective'
class Relationship(obj_tables.Model):
i_d = obj_tables.StringAttribute(verbose_name='ID')
from_object = obj_tables.StringAttribute(verbose_name='FromObject')
to_object = obj_tables.StringAttribute(verbose_name='ToObject')
value = obj_tables.IntegerAttribute(verbose_name='Value')
is_symmetric = obj_tables.BooleanAttribute(verbose_name='IsSymmetric')
sign = obj_tables.EnumAttribute(['+', '-', '0'],
default='0',
verbose_name='Sign')
relation = obj_tables.StringAttribute(verbose_name='Relation')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'i_d',
'from_object',
'to_object',
'value',
'is_symmetric',
'sign',
'relation',
)
verbose_name = 'Relationship'
verbose_name_plural = 'Relationship'
class Reaction(obj_tables.Model):
id = obj_tables.StringAttribute(primary=True, unique=True)
id_i_a_f1260 = obj_tables.StringAttribute(
none=True,
default=None,
default_cleaned_value=None,
verbose_name='Id (iAF1260 [Ref1])')
name = obj_tables.StringAttribute(none=True,
default=None,
default_cleaned_value=None)
equation = obj_tables.chem.ReactionEquationAttribute(
species_cls=Metabolite, compartment_cls=Compartment)
reversible = obj_tables.BooleanAttribute()
subsystem = obj_tables.StringAttribute(none=True,
default=None,
default_cleaned_value=None)
ec_number = obj_tables.RegexAttribute(pattern='\d+\.\d+\.\d+\.\d+',
none=True,
default=None,
default_cleaned_value=None,
verbose_name='EC number')
lower_bound = obj_tables.FloatAttribute()
upper_bound = obj_tables.FloatAttribute()
flux_acetate = obj_tables.FloatAttribute(
verbose_name='Flux (Acetate media, mmol * gCDW^-1 * h^-1)')
flux_acetate_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Acetate media, mmol * gCDW^-1 * h^-1)')
flux_fructose = obj_tables.FloatAttribute(
verbose_name='Flux (Fructose media, mmol * gCDW^-1 * h^-1)')
flux_fructose_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Fructose media, mmol * gCDW^-1 * h^-1)'
)
flux_galactose = obj_tables.FloatAttribute(
verbose_name='Flux (Galactose media, mmol * gCDW^-1 * h^-1)')
flux_galactose_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Galactose media, mmol * gCDW^-1 * h^-1)'
)
flux_glucose = obj_tables.FloatAttribute(
verbose_name='Flux (Glucose media, mmol * gCDW^-1 * h^-1)')
flux_glucose_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Glucose media, mmol * gCDW^-1 * h^-1)')
flux_glycerol = obj_tables.FloatAttribute(
verbose_name='Flux (Glycerol media, mmol * gCDW^-1 * h^-1)')
flux_glycerol_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Glycerol media, mmol * gCDW^-1 * h^-1)'
)
flux_gluconate = obj_tables.FloatAttribute(
verbose_name='Flux (Gluconate media, mmol * gCDW^-1 * h^-1)')
flux_gluconate_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Gluconate media, mmol * gCDW^-1 * h^-1)'
)
flux_pyruvate = obj_tables.FloatAttribute(
verbose_name='Flux (Pyruvate media, mmol * gCDW^-1 * h^-1)')
flux_pyruvate_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Pyruvate media, mmol * gCDW^-1 * h^-1)'
)
flux_succinate = obj_tables.FloatAttribute(
verbose_name='Flux (Succinate media, mmol * gCDW^-1 * h^-1)')
flux_succinate_uncertainty = obj_tables.FloatAttribute(
verbose_name='Flux uncertainty (Succinate media, mmol * gCDW^-1 * h^-1)'
)
delta_g_acetate = obj_tables.FloatAttribute(
verbose_name='ΔG (Acetate, kJ * mol^-1)')
delta_g_acetate_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Acetate, kJ * mol^-1)')
delta_g_fructose = obj_tables.FloatAttribute(
verbose_name='ΔG (Fructose, kJ * mol^-1)')
delta_g_fructose_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Fructose, kJ * mol^-1)')
delta_g_galactose = obj_tables.FloatAttribute(
verbose_name='ΔG (Galactose, kJ * mol^-1)')
delta_g_galactose_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Galactose, kJ * mol^-1)')
delta_g_glucose = obj_tables.FloatAttribute(
verbose_name='ΔG (Glucose, kJ * mol^-1)')
delta_g_glucose_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Glucose, kJ * mol^-1)')
delta_g_glycerol = obj_tables.FloatAttribute(
verbose_name='ΔG (Glycerol, kJ * mol^-1)')
delta_g_glycerol_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Glycerol, kJ * mol^-1)')
delta_g_gluconate = obj_tables.FloatAttribute(
verbose_name='ΔG (Gluconate, kJ * mol^-1)')
delta_g_gluconate_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Gluconate, kJ * mol^-1)')
delta_g_pyruvate = obj_tables.FloatAttribute(
verbose_name='ΔG (Pyruvate, kJ * mol^-1)')
delta_g_pyruvate_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Pyruvate, kJ * mol^-1)')
delta_g_succinate = obj_tables.FloatAttribute(
verbose_name='ΔG (Succinate, kJ * mol^-1)')
delta_g_succinate_uncertainty = obj_tables.FloatAttribute(
verbose_name='ΔG uncertainty (Succinate, kJ * mol^-1)')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'id',
'id_i_a_f1260',
'name',
'equation',
'reversible',
'subsystem',
'ec_number',
'lower_bound',
'upper_bound',
'flux_acetate',
'flux_acetate_uncertainty',
'flux_fructose',
'flux_fructose_uncertainty',
'flux_galactose',
'flux_galactose_uncertainty',
'flux_glucose',
'flux_glucose_uncertainty',
'flux_glycerol',
'flux_glycerol_uncertainty',
'flux_gluconate',
'flux_gluconate_uncertainty',
'flux_pyruvate',
'flux_pyruvate_uncertainty',
'flux_succinate',
'flux_succinate_uncertainty',
'delta_g_acetate',
'delta_g_acetate_uncertainty',
'delta_g_fructose',
'delta_g_fructose_uncertainty',
'delta_g_galactose',
'delta_g_galactose_uncertainty',
'delta_g_glucose',
'delta_g_glucose_uncertainty',
'delta_g_glycerol',
'delta_g_glycerol_uncertainty',
'delta_g_gluconate',
'delta_g_gluconate_uncertainty',
'delta_g_pyruvate',
'delta_g_pyruvate_uncertainty',
'delta_g_succinate',
'delta_g_succinate_uncertainty',
)
verbose_name = 'Reaction'
verbose_name_plural = 'Reactions'
class Quantity(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(
verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(
verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
quantity = obj_tables.StringAttribute(verbose_name='Quantity')
reference = obj_tables.StringAttribute(verbose_name='Reference')
quantity_name = obj_tables.StringAttribute(verbose_name='QuantityName')
quantity_type = obj_tables.StringAttribute(verbose_name='QuantityType')
value = obj_tables.FloatAttribute(verbose_name='Value')
mean = obj_tables.FloatAttribute(verbose_name='Mean')
std = obj_tables.FloatAttribute(verbose_name='Std')
min = obj_tables.FloatAttribute(verbose_name='Min')
max = obj_tables.FloatAttribute(verbose_name='Max')
median = obj_tables.FloatAttribute(verbose_name='Median')
geometric_mean = obj_tables.FloatAttribute(verbose_name='GeometricMean')
sign = obj_tables.EnumAttribute(['+', '-', '0'],
default='0',
verbose_name='Sign')
prob_dist = obj_tables.StringAttribute(verbose_name='ProbDist')
s_b_m_l_parameter_id = obj_tables.StringAttribute(
verbose_name='SBML:parameter:id')
unit = obj_tables.StringAttribute(verbose_name='Unit')
scale = obj_tables.StringAttribute(verbose_name='Scale')
time = obj_tables.FloatAttribute(verbose_name='Time')
time_point = obj_tables.StringAttribute(verbose_name='TimePoint')
condition = obj_tables.StringAttribute(verbose_name='Condition')
p_h = obj_tables.FloatAttribute(verbose_name='pH')
temperature = obj_tables.FloatAttribute(verbose_name='Temperature')
location = obj_tables.StringAttribute(verbose_name='Location')
location_s_b_m_l_compartment_id = obj_tables.StringAttribute(
verbose_name='Location:SBML:compartment:id')
compound = obj_tables.StringAttribute(verbose_name='Compound')
compound_s_b_m_l_species_id = obj_tables.StringAttribute(
verbose_name='Compound:SBML:species:id')
reaction = obj_tables.StringAttribute(verbose_name='Reaction')
reaction_s_b_m_l_reaction_id = obj_tables.StringAttribute(
verbose_name='Reaction:SBML:reaction:id')
enyzme = obj_tables.StringAttribute(verbose_name='Enyzme')
enyzme_s_b_m_l_species_id = obj_tables.StringAttribute(
verbose_name='Enyzme:SBML:species:id')
enyzme_s_b_m_l_parameter_id = obj_tables.StringAttribute(
verbose_name='Enyzme:SBML:parameter:id')
gene = obj_tables.StringAttribute(verbose_name='Gene')
organism = obj_tables.StringAttribute(verbose_name='Organism')
provenance = obj_tables.StringAttribute(verbose_name='Provenance')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_kegg_reaction = obj_tables.StringAttribute(
verbose_name='Identifiers:kegg.reaction')
identifiers_kegg_compound = obj_tables.StringAttribute(
verbose_name='Identifiers:kegg.compound')
identifiers_obo_chebi = obj_tables.StringAttribute(
verbose_name='Identifiers:obo.chebi')
reaction_identifiers_kegg_reaction = obj_tables.StringAttribute(
verbose_name='Reaction:Identifiers:kegg.reaction')
compound_identifiers_kegg_compound = obj_tables.StringAttribute(
verbose_name='Compound:Identifiers:kegg.compound')
biological_element = obj_tables.StringAttribute(
verbose_name='BiologicalElement')
mathematical_type = obj_tables.StringAttribute(
verbose_name='MathematicalType')
data_geometric_std = obj_tables.FloatAttribute(
verbose_name='DataGeometricStd')
prior_median = obj_tables.FloatAttribute(verbose_name='PriorMedian')
prior_std = obj_tables.FloatAttribute(verbose_name='PriorStd')
prior_geometric_std = obj_tables.FloatAttribute(
verbose_name='PriorGeometricStd')
lower_bound = obj_tables.FloatAttribute(verbose_name='LowerBound')
upper_bound = obj_tables.FloatAttribute(verbose_name='UpperBound')
data_std = obj_tables.FloatAttribute(verbose_name='DataStd')
physical_type = obj_tables.StringAttribute(verbose_name='PhysicalType')
dependence = obj_tables.StringAttribute(verbose_name='Dependence')
use_as_prior_information = obj_tables.BooleanAttribute(
verbose_name='UseAsPriorInformation')
s_b_m_l_element = obj_tables.StringAttribute(verbose_name='SBMLElement')
abbreviation = obj_tables.StringAttribute(verbose_name='Abbreviation')
matrix_info = obj_tables.StringAttribute(verbose_name='MatrixInfo')
s_b_o_equilibrium_constant = obj_tables.FloatAttribute(
verbose_name='SBO:equilibrium_constant')
s_b_o_identifiers_obo_sbo = obj_tables.StringAttribute(
verbose_name='SBO:Identifiers:obo.sbo')
s_b_o_concentration = obj_tables.FloatAttribute(
verbose_name='SBO:concentration')
s_b_o_concentration_m_m_log10_median = obj_tables.FloatAttribute(
verbose_name='SBO:concentration [mM:Log10]:Median')
value_type = obj_tables.StringAttribute(verbose_name='ValueType')
concentration_min = obj_tables.FloatAttribute(
verbose_name='Concentration:Min')
concentration_max = obj_tables.FloatAttribute(
verbose_name='Concentration:Max')
parameter_s_b_m_l_parameter_id = obj_tables.StringAttribute(
verbose_name='Parameter:SBML:parameter:id')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
'quantity',
'reference',
'quantity_name',
'quantity_type',
'value',
'mean',
'std',
'min',
'max',
'median',
'geometric_mean',
'sign',
'prob_dist',
's_b_m_l_parameter_id',
'unit',
'scale',
'time',
'time_point',
'condition',
'p_h',
'temperature',
'location',
'location_s_b_m_l_compartment_id',
'compound',
'compound_s_b_m_l_species_id',
'reaction',
'reaction_s_b_m_l_reaction_id',
'enyzme',
'enyzme_s_b_m_l_species_id',
'enyzme_s_b_m_l_parameter_id',
'gene',
'organism',
'provenance',
's_b_o_term',
'identifiers',
'identifiers_kegg_reaction',
'identifiers_kegg_compound',
'identifiers_obo_chebi',
'reaction_identifiers_kegg_reaction',
'compound_identifiers_kegg_compound',
'biological_element',
'mathematical_type',
'data_geometric_std',
'prior_median',
'prior_std',
'prior_geometric_std',
'lower_bound',
'upper_bound',
'data_std',
'physical_type',
'dependence',
'use_as_prior_information',
's_b_m_l_element',
'abbreviation',
'matrix_info',
's_b_o_equilibrium_constant',
's_b_o_identifiers_obo_sbo',
's_b_o_concentration',
's_b_o_concentration_m_m_log10_median',
'value_type',
'concentration_min',
'concentration_max',
'parameter_s_b_m_l_parameter_id',
)
verbose_name = 'Quantity'
verbose_name_plural = 'Quantity'
class Reaction(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(
verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
modifier = obj_tables.StringAttribute(verbose_name='Modifier')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(
verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
s_b_m_l_reaction_id = obj_tables.StringAttribute(
verbose_name='SBML:reaction:id')
reaction_formula = obj_tables.LongStringAttribute(
verbose_name='ReactionFormula')
location = obj_tables.StringAttribute(verbose_name='Location')
enzyme = obj_tables.StringAttribute(verbose_name='Enzyme')
model = obj_tables.StringAttribute(verbose_name='Model')
pathway = obj_tables.StringAttribute(verbose_name='Pathway')
subreaction_of = obj_tables.StringAttribute(verbose_name='SubreactionOf')
is_complete = obj_tables.BooleanAttribute(verbose_name='IsComplete')
is_reversible = obj_tables.BooleanAttribute(verbose_name='IsReversible')
is_in_equilibrium = obj_tables.BooleanAttribute(
verbose_name='IsInEquilibrium')
is_exchange_reaction = obj_tables.BooleanAttribute(
verbose_name='IsExchangeReaction')
flux = obj_tables.FloatAttribute(verbose_name='Flux')
is_non_enzymatic = obj_tables.BooleanAttribute(
verbose_name='IsNonEnzymatic')
kinetic_law = obj_tables.LongStringAttribute(verbose_name='KineticLaw')
kinetic_law_name = obj_tables.StringAttribute(
verbose_name='KineticLaw:Name')
kinetic_law_formula = obj_tables.StringAttribute(
verbose_name='KineticLaw:Formula')
gene = obj_tables.StringAttribute(verbose_name='Gene')
gene_symbol = obj_tables.StringAttribute(verbose_name='Gene:Symbol')
operon = obj_tables.StringAttribute(verbose_name='Operon')
enzyme_s_b_m_l_species_id = obj_tables.StringAttribute(
verbose_name='Enzyme:SBML:species:id')
enzyme_s_b_m_l_parameter_id = obj_tables.StringAttribute(
verbose_name='Enzyme:SBML:parameter:id')
build_reaction = obj_tables.BooleanAttribute(verbose_name='BuildReaction')
build_enzyme = obj_tables.BooleanAttribute(verbose_name='BuildEnzyme')
build_enzyme_production = obj_tables.BooleanAttribute(
verbose_name='BuildEnzymeProduction')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_kegg_reaction = obj_tables.StringAttribute(
verbose_name='Identifiers:kegg.reaction')
identifiers_obo_sbo = obj_tables.StringAttribute(
verbose_name='Identifiers:obo.sbo')
identifiers_ec_code = obj_tables.StringAttribute(
verbose_name='Identifiers:ec-code')
s_b_m_l_fbc_gene_association = obj_tables.LongStringAttribute(
verbose_name='SBML:fbc:GeneAssociation')
s_b_m_l_fbc_lower_bound = obj_tables.StringAttribute(
verbose_name='SBML:fbc:LowerBound')
s_b_m_l_fbc_upper_bound = obj_tables.StringAttribute(
verbose_name='SBML:fbc:UpperBound')
regulator = obj_tables.StringAttribute(verbose_name='Regulator')
name_for_plots = obj_tables.StringAttribute(verbose_name='NameForPlots')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'modifier',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
's_b_m_l_reaction_id',
'reaction_formula',
'location',
'enzyme',
'model',
'pathway',
'subreaction_of',
'is_complete',
'is_reversible',
'is_in_equilibrium',
'is_exchange_reaction',
'flux',
'is_non_enzymatic',
'kinetic_law',
'kinetic_law_name',
'kinetic_law_formula',
'gene',
'gene_symbol',
'operon',
'enzyme_s_b_m_l_species_id',
'enzyme_s_b_m_l_parameter_id',
'build_reaction',
'build_enzyme',
'build_enzyme_production',
's_b_o_term',
'identifiers',
'identifiers_kegg_reaction',
'identifiers_obo_sbo',
'identifiers_ec_code',
's_b_m_l_fbc_gene_association',
's_b_m_l_fbc_lower_bound',
's_b_m_l_fbc_upper_bound',
'regulator',
'name_for_plots',
)
verbose_name = 'Reaction'
verbose_name_plural = 'Reaction'
class Compound(obj_tables.Model):
comment = obj_tables.StringAttribute(verbose_name='Comment')
reference_name = obj_tables.StringAttribute(verbose_name='ReferenceName')
reference_pub_med = obj_tables.StringAttribute(
verbose_name='ReferencePubMed')
reference_d_o_i = obj_tables.StringAttribute(verbose_name='ReferenceDOI')
description = obj_tables.StringAttribute(verbose_name='Description')
name = obj_tables.StringAttribute(verbose_name='Name')
miriam_annotations = obj_tables.StringAttribute(
verbose_name='MiriamAnnotations')
type = obj_tables.StringAttribute(verbose_name='Type')
symbol = obj_tables.StringAttribute(verbose_name='Symbol')
position_x = obj_tables.FloatAttribute(verbose_name='PositionX')
position_y = obj_tables.FloatAttribute(verbose_name='PositionY')
i_d = obj_tables.StringAttribute(verbose_name='ID')
s_b_m_l_species_id = obj_tables.StringAttribute(
verbose_name='SBML:species:id')
s_b_m_l_speciestype_id = obj_tables.StringAttribute(
verbose_name='SBML:speciestype:id')
initial_value = obj_tables.FloatAttribute(verbose_name='InitialValue')
initial_concentration = obj_tables.FloatAttribute(
verbose_name='InitialConcentration')
unit = obj_tables.StringAttribute(verbose_name='Unit')
location = obj_tables.StringAttribute(verbose_name='Location')
state = obj_tables.StringAttribute(verbose_name='State')
compound_sum_formula = obj_tables.StringAttribute(
verbose_name='CompoundSumFormula')
structure_formula = obj_tables.StringAttribute(
verbose_name='StructureFormula')
charge = obj_tables.IntegerAttribute(verbose_name='Charge')
mass = obj_tables.FloatAttribute(verbose_name='Mass')
is_constant = obj_tables.BooleanAttribute(verbose_name='IsConstant')
enzyme_role = obj_tables.StringAttribute(verbose_name='EnzymeRole')
regulator_role = obj_tables.StringAttribute(verbose_name='RegulatorRole')
s_b_o_term = obj_tables.StringAttribute(verbose_name='SBOTerm')
identifiers = obj_tables.StringAttribute(verbose_name='Identifiers')
identifiers_sbo_kegg = obj_tables.StringAttribute(
verbose_name='Identifiers:sbo.kegg')
identifiers_kegg_compound = obj_tables.StringAttribute(
verbose_name='Identifiers:kegg.compound')
identifiers_obo_chebi = obj_tables.StringAttribute(
verbose_name='Identifiers:obo.chebi')
s_b_m_l_fbc_chemical_formula = obj_tables.StringAttribute(
verbose_name='SBML:fbc:ChemicalFormula')
s_b_m_l_fbc_charge = obj_tables.FloatAttribute(
verbose_name='SBML:fbc:Charge')
has_only_substance_units = obj_tables.BooleanAttribute(
verbose_name='HasOnlySubstanceUnits')
name_for_plots = obj_tables.StringAttribute(verbose_name='NameForPlots')
class Meta(obj_tables.Model.Meta):
table_format = obj_tables.TableFormat.row
attribute_order = (
'comment',
'reference_name',
'reference_pub_med',
'reference_d_o_i',
'description',
'name',
'miriam_annotations',
'type',
'symbol',
'position_x',
'position_y',
'i_d',
's_b_m_l_species_id',
's_b_m_l_speciestype_id',
'initial_value',
'initial_concentration',
'unit',
'location',
'state',
'compound_sum_formula',
'structure_formula',
'charge',
'mass',
'is_constant',
'enzyme_role',
'regulator_role',
's_b_o_term',
'identifiers',
'identifiers_sbo_kegg',
'identifiers_kegg_compound',
'identifiers_obo_chebi',
's_b_m_l_fbc_chemical_formula',
's_b_m_l_fbc_charge',
'has_only_substance_units',
'name_for_plots',
)
verbose_name = 'Compound'
verbose_name_plural = 'Compound'