Core schema to represent a knowledge base to build models

Author:: Balazs Szigeti <balazs.szigeti@mssm.edu>
Author:: Jonathan Karr <karr@mssm.edu>
Author:: Bilal Shaikh <bilal.shaikh@columbia.edu>
Author:: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
Author:: Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:: 2018-02-07
Copyright:: 2018, Karr Lab
License:: MIT

3.2.3. Module Contents¶

3.2.3.1. Classes¶

`SubunitAttribute`	Subunits
`OneToOneSpeciesAttribute`	Species attribute
`IdentifierAttribute`	Identifier attribute
`ReactionParticipantAttribute`	Reaction participants
`Identifier`	Reference to an entity in an external namespace
`KnowledgeBaseObject`	Knowledge of a biological entity
`KnowledgeBase`	A knowledge base
`Cell`	Knowledge of a cell
`Reference`	Reference to the literature
`Compartment`	Knowledge of a subcellular compartment
`SpeciesType`	Knowledge of a molecular species
`Species`	Species (tuple of species type, compartment)
`Concentration`	Species concentration
`SpeciesTypeCoefficient`	A tuple of a species type and a coefficient
`SpeciesCoefficient`	A tuple of a species and a coefficient
`PolymerSpeciesType`	Knowledge of a polymer
`PolymerLocus`	Knowledge about a locus of a polymer
`ObservableExpression`	A mathematical expression of Observables and Species
`Observable`	Observable: a linear function of other Observables and Species
`Parameter`	Knowledge of parameters
`Validator`
`MetaboliteSpeciesType`	Knowledge of a metabolite
`DnaSpeciesType`	Knowledge of a DNA species
`ComplexSpeciesType`	Knowledge of a protein complex
`RateLawDirection`	Rate law directions
`RateLawExpression`	Rate law expression
`RateLaw`	Rate law
`Reaction`	Knowledge of reactions
`ChromosomeFeature`	Knowledge of chromosome features
`Evidence`	Represents the measurement / observation of a property
`Experiment`	Represents an experiment in which a property was measured
`SpeciesTypeProperty`	Knowledge of the properties of species types

3.2.3.2. Attributes¶

`PolymerStrand`
`PolymerDirection`

wc_kb.core.PolymerStrand[source]¶

wc_kb.core.PolymerDirection[source]¶

class wc_kb.core.SubunitAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.ManyToManyAttribute

Subunits

serialize(subunits, encoded=None)[source]¶

Serialize related object

Parameters:

subunits (list of SpeciesTypeCoefficient) – Python representation of subunits
encoded (dict, optional) – dictionary of objects that have already been encoded

Returns:

simple Python representation

Return type:

str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value

Parameters:

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model
decoded (dict, optional) – dictionary of objects that have already been decoded

Returns:

tuple of cleaned value and cleaning error

Return type:

tuple of object, InvalidAttribute or None

class wc_kb.core.OneToOneSpeciesAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.OneToOneAttribute

Species attribute

serialize(value, encoded=None)[source]¶

Serialize related object :param value: Python representation :type value: Model :param encoded: dictionary of objects that have already been encoded :type encoded: dict, optional

Returns:: simple Python representation
Return type:: str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value

Parameters:

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model
decoded (dict, optional) – dictionary of objects that have already been decoded

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of Species, InvalidAttribute or None

class wc_kb.core.IdentifierAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.ManyToManyAttribute

Identifier attribute

serialize(identifiers, encoded=None)[source]¶

Serialize related object :param identifiers: a list of instances of Identifier Python representation :type identifiers: list of Model :param encoded: dictionary of objects that have already been encoded :type encoded: dict, optional

Returns:: simple Python representation
Return type:: str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value :param value: String representation :type value: str :param objects: dictionary of objects, grouped by model :type objects: dict :param decoded: dictionary of objects that have already been decoded :type decoded: dict, optional

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of Identifier, InvalidAttribute or None

class wc_kb.core.ReactionParticipantAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.ManyToManyAttribute

Reaction participants

serialize(participants, encoded=None)[source]¶

Serialize related object

Parameters:

participants (list of SpeciesCoefficient) – Python representation of reaction participants
encoded (dict, optional) – dictionary of objects that have already been encoded

Returns:

simple Python representation

Return type:

str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value

Parameters:

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model
decoded (dict, optional) – dictionary of objects that have already been decoded

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of SpeciesCoefficient, InvalidAttribute or None

deserialize_side(direction, value, objects, global_comp)[source]¶

Deserialize the LHS or RHS of a reaction equation :param direction: -1. indicates LHS, +1. indicates RHS :type direction: float :param value: String representation :type value: str :param objects: dictionary of objects, grouped by model :type objects: dict :param global_comp: global compartment of the reaction :type global_comp: Compartment

Returns:

list of SpeciesCoefficient: list of species coefficients
list of Exception: list of errors

Return type:

tuple

class wc_kb.core.Identifier[source]¶

Bases: obj_tables.Model

Reference to an entity in an external namespace

namespace[source]¶

namespace

Type:: str

id[source]¶

identifier within the namespace

Type:: str

Related attributes:: compartments (list of Compartment): compartments species_types (list of SpeciesType): species_types concentrations (list of Concentration): concentrations loci (list of PolymerLocus): loci properties (list of SpeciesTypeProperty): species type properties reactions (list of Reaction): reactions rate_laws (list of RateLaw): rate_laws observables (list of Observable): observables

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('namespace', 'id')[source]¶

table_format[source]¶

ordering = ('namespace', 'id')[source]¶

namespace[source]¶

id[source]¶

static _serialize(namespace, id)[source]¶

Generate string representation

Parameters:

namespace (str) – namespace
id (str) – identifier within the namespace

Returns:

value of primary attribute

Return type:

str

serialize()[source]¶

Generate string representation

Returns:: value of primary attribute
Return type:: str

class wc_kb.core.KnowledgeBaseObject[source]¶

Bases: obj_tables.Model

Knowledge of a biological entity

id[source]¶

identifier

Type:: str

name[source]¶

name

Type:: str

synonyms[source]¶

synonyms

Type:: str

comments[source]¶

comments

Type:: str

id[source]¶

name[source]¶

synonyms[source]¶

comments[source]¶

get_nested_metadata()[source]¶

Returns a list of wc_kb.core.Reference / wc_kb.core.DatabaseReference / wc_kb.core.Comments objects that: appear in the object’s wc_kb.core.Evidence and the associated wc_kb.core.Experiment

Returns:: references
Return type:: id (list of Reference)

_parse_EviNExperiment(metadataObjs)[source]¶

_append_metadata_entries(key, metadataObjs)[source]¶

Appends wc_kb.core.Reference / wc_kb.core.DatabaseReference / wc_kb.core.Comments objects to metadataObjs list

Input:: obj(obj_tables.Model): model object

Returns:: list of metadata objects
Return type:: metadataObjs (list of Reference / Evidence / Comments)

class wc_kb.core.KnowledgeBase[source]¶

Bases: KnowledgeBaseObject

A knowledge base

version[source]¶

version

Type:: str

translation_table[source]¶

translation table

Type:: int

version[source]¶

version of the KB

Type:: str

url[source]¶

url of the KB Git repository

Type:: str

branch[source]¶

branch of the KB Git repository

Type:: str

revision[source]¶

revision of the KB Git repository

Type:: str

wc_kb_version[source]¶

version of wc_kb

Type:: str

Related attributes:: cell (Cell): cell

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'KB'[source]¶

description = 'Knowledge base'[source]¶

attribute_order = ('id', 'name', 'translation_table', 'version', 'url', 'branch', 'revision', 'wc_kb_version', 'comments')[source]¶

table_format[source]¶

translation_table[source]¶

version[source]¶

url[source]¶

branch[source]¶

revision[source]¶

wc_kb_version[source]¶

class wc_kb.core.Cell[source]¶

Bases: KnowledgeBaseObject

Knowledge of a cell

knowledge_base[source]¶

knowledge base

Type:: KnowledgeBase

taxon[source]¶

NCBI taxon identifier

Type:: int

Related attributes:: references (list of Reference): references compartments (list of Compartment): compartments species_types (list of SpeciesType): species types concentrations (list of Concentration): concentrations observables (list or Observable) : observables loci (list of PolymerLocus): locus reactions (list of Reaction): reactions

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'taxon', 'comments')[source]¶

table_format[source]¶

knowledge_base[source]¶

taxon[source]¶

class wc_kb.core.Reference[source]¶

Bases: obj_tables.Model

Reference to the literature

id[source]¶

identifier

Type:: str

name[source]¶

name

Type:: str

authors[source]¶

authors

Type:: str

title[source]¶

title

Type:: str

volume[source]¶

volume

Type:: str

issue[source]¶

issue

Type:: str

journal[source]¶

journal

Type:: str

pages (: obj:``str): pages

year[source]¶

year

Type:: int

cell[source]¶

cell

Type:: Cell

identifiers[source]¶

identifiers

Type:: list of Identifier

comments[source]¶

comments

Type:: str

type[source]¶

type of reference

Type:: pronto

Related attributes:: compartments (list of Compartment): compartments species_types (list of SpeciesType): species_types concentrations (list of Concentration): concentrations loci (list of PolymerLocus): loci properties (list of SpeciesTypeProperty): species type properties reactions (list of Reaction): reactions rate_laws (list of RateLaw): rate_laws observables (list of Observable): observables

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'type', 'title', 'authors', 'journal', 'volume', 'issue', 'pages', 'year',...[source]¶

id[source]¶

name[source]¶

authors[source]¶

title[source]¶

volume[source]¶

issue[source]¶

journal[source]¶

pages[source]¶

year[source]¶

cell[source]¶

identifiers[source]¶

comments[source]¶

type[source]¶

class wc_kb.core.Compartment[source]¶

Bases: KnowledgeBaseObject

Knowledge of a subcellular compartment

cell[source]¶

cell

Type:: Cell

volumetric_fraction[source]¶

average volumetric fraction relative to the cell volume

Type:: float

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

Related attributes:: reaction_participants (list of ReactionParticipant): reaction participants

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'volumetric_fraction', 'identifiers', 'references', 'comments')[source]¶

id[source]¶

cell[source]¶

volumetric_fraction[source]¶

references[source]¶

identifiers[source]¶

class wc_kb.core.SpeciesType[source]¶

Bases: KnowledgeBaseObject

Knowledge of a molecular species

cell[source]¶

cell

Type:: Cell

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

Related attributes:: reaction_participants (list of ReactionParticipant): reaction participants

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'comments', 'references', 'identifiers')[source]¶

id[source]¶

cell[source]¶

references[source]¶

identifiers[source]¶

abstract get_empirical_formula()[source]¶

Get the empirical formula

Returns:: empirical formula
Return type:: chem.EmpiricalFormula

abstract get_charge()[source]¶

Get the charge

Returns:: charge
Return type:: int

abstract get_mol_wt()[source]¶

Get the molecular weight

Returns:: molecular weight
Return type:: float

class wc_kb.core.Species[source]¶

Bases: obj_tables.Model

Species (tuple of species type, compartment)

species_type[source]¶

species type

Type:: SpeciesType

compartment[source]¶

compartment

Type:: Compartment

Related attributes:: concentration (Concentration): concentration species_coefficients (list of SpeciesCoefficient): participations in reactions rate_law_expressions (list of RateLawExpression): participations in the evaluation of rates observable_expressions (list of ObservableExpression): participations in observables

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'species_type', 'compartment')[source]¶

frozen_columns = 1[source]¶

table_format[source]¶

unique_together = (('species_type', 'compartment'),)[source]¶

ordering = ('species_type', 'compartment')[source]¶

expression_term_token_pattern = ()[source]¶

id[source]¶

species_type[source]¶

compartment[source]¶

static gen_id(species_type, compartment)[source]¶

Generate a Species’ primary identifier

Parameters:

species_type (object) – a SpeciesType, or its id
compartment (object) – a Compartment, or its id

Returns:

canonical identifier for a specie in a compartment, ‘species_type_id[compartment_id]’

Return type:

str

id()[source]¶

Provide a Species’ primary identifier

Returns:: canonical identifier for a specie in a compartment, ‘specie_id[compartment_id]’
Return type:: str

serialize()[source]¶

Provide a Species’ primary identifier

Returns:: canonical identifier for a specie in a compartment, ‘specie_id[compartment_id]’
Return type:: str

classmethod deserialize(attribute, value, objects)[source]¶

Deserialize value

Parameters:

attribute (Attribute) – attribute
value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns:

tuple of cleaned value and cleaning error

Return type:

tuple of object, InvalidAttribute or None

class wc_kb.core.Concentration[source]¶

Bases: KnowledgeBaseObject

Species concentration

cell[source]¶

cell

Type:: Cell

species[source]¶

species

Type:: Species

medium[source]¶

medium

Type:: str

value[source]¶

value

Type:: float

units[source]¶

units; default units is ‘M’

Type:: unit_registry.Unit

evidence[source]¶

evidence

Type:: list of Evidence

comments[source]¶

comments

Type:: str

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'species', 'value', 'units', 'evidence', 'identifiers', 'references', 'comments')[source]¶

unique_together = (('species',),)[source]¶

ordering = ('species',)[source]¶

frozen_columns = 1[source]¶

cell[source]¶

species[source]¶

medium[source]¶

value[source]¶

units[source]¶

evidence[source]¶

references[source]¶

identifiers[source]¶

serialize()[source]¶: Generate string representation :returns: value of primary attribute :rtype: str

class wc_kb.core.SpeciesTypeCoefficient[source]¶

Bases: obj_tables.Model

A tuple of a species type and a coefficient

species_type[source]¶

species_type

Type:: SpeciesType

coefficient[source]¶

coefficient

Type:: float

Related attributes:: complex (ComplexSpeciesType): complex

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('species_type', 'coefficient')[source]¶

frozen_columns = 1[source]¶

table_format[source]¶

ordering = ('species_type',)[source]¶

species_type[source]¶

coefficient[source]¶

serialize()[source]¶

Serialize related object

Returns:: string representation of a species type and a coefficient
Return type:: str

static _serialize(species_type, coefficient)[source]¶

Serialize values

Parameters:

species_type (SpeciesType) – species_type
coefficient (float) – coefficient

Returns:

string representation of a species type and a coefficient

Return type:

str

classmethod deserialize(attribute, value, objects)[source]¶

Deserialize value

Parameters:

attribute (Attribute) – attribute
value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of SpeciesTypeCoefficient, InvalidAttribute or None

class wc_kb.core.SpeciesCoefficient[source]¶

Bases: obj_tables.Model

A tuple of a species and a coefficient

species[source]¶

species

Type:: Species

coefficient[source]¶

coefficient

Type:: float

Related attributes:: reaction (Reaction): reaction

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('species', 'coefficient')[source]¶

frozen_columns = 1[source]¶

table_format[source]¶

ordering = ('species',)[source]¶

species[source]¶

coefficient[source]¶

serialize(show_compartment=True, show_coefficient_sign=True)[source]¶

Serialize related object

Parameters:

show_compartment (bool, optional) – if true, show compartment
show_coefficient_sign (bool, optional) – if true, show coefficient sign

Returns:

string representation of a species and a coefficient

Return type:

str

static _serialize(species, coefficient, show_compartment=True, show_coefficient_sign=True)[source]¶

Serialize values

Parameters:

species (Species) – species
coefficient (float) – coefficient
show_compartment (bool, optional) – if true, show compartment
show_coefficient_sign (bool, optional) – if true, show coefficient sign

Returns:

string representation of a species and a coefficient

Return type:

str

classmethod deserialize(attribute, value, objects, compartment=None)[source]¶

Deserialize value

Parameters:

attribute (Attribute) – attribute
value (str) – String representation
objects (dict) – dictionary of objects, grouped by model
compartment (Compartment, optional) – compartment

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of SpeciesCoefficient, InvalidAttribute or None

class wc_kb.core.PolymerSpeciesType[source]¶

Bases: SpeciesType

Knowledge of a polymer

circular[source]¶

is the polymer circular

Type:: bool

double_stranded[source]¶

is the polymer double stranded

Type:: bool

Related attributes:: loci (list of PolymerLocus): loci

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'circular', 'double_stranded', 'comments', 'references', 'identifiers')[source]¶

circular[source]¶

double_stranded[source]¶

abstract get_seq()[source]¶

Get the polymer sequence

Returns:: sequence
Return type:: Bio.Seq.Seq

get_len()[source]¶

Get the polymer length

Returns:: length
Return type:: int

get_subseq(start, end, strand=PolymerStrand.positive)[source]¶

Get a subsequence

Parameters:

start (int) – start coordinate (1-indexed)
end (int) – end coordinate (1-indexed)
strand (PolymerStrand, optional) – strand

Returns:

sequence

Return type:

Bio.Seq.Seq

Raises:

ValueError – if the polymer is linear and the start or end coordinates are less than 1 or greater than the length of the sequence

class wc_kb.core.PolymerLocus[source]¶

Bases: KnowledgeBaseObject

Knowledge about a locus of a polymer

polymer[source]¶

polymer

Type:: PolymerSpeciesType

start[source]¶

start position

Type:: int

end[source]¶

end position

Type:: int

strand[source]¶

strand

Type:: PolymerStrand

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'polymer', 'strand', 'start', 'end', 'identifiers', 'references', 'comments')[source]¶

cell[source]¶

polymer[source]¶

start[source]¶

end[source]¶

references[source]¶

identifiers[source]¶

strand[source]¶

get_seq()[source]¶

Get the sequence

Returns:: sequence
Return type:: Bio.Seq.Seq

get_len()[source]¶

Get the length

Returns:: length
Return type:: int

get_direction()[source]¶

Returns the direction of the polymer feature defind by its strand and start/end coordinate

Returns:

direction (in [‘forward’, ‘reverse’])

Return type:

PolymerDirection

Raises:

ValueError – start and end coordinate of chromosome feature can not be the same
Exception – strand is not member of PolymerStrand

class wc_kb.core.ObservableExpression[source]¶

Bases: obj_tables.Model, obj_tables.math.expression.Expression

A mathematical expression of Observables and Species

The expression used by a Observable.

expression[source]¶

mathematical expression for an Observable

Type:: str

species[source]¶

Species used by this Observable expression

Type:: list of Species

observables[source]¶

other Observables used by this Observable expression

Type:: list of Observable

Related attributes:: observable (Observable): observable

class Meta[source]¶

Bases: obj_tables.Model.Meta, obj_tables.math.expression.Expression.Meta

table_format[source]¶

expression_term_models = ('Species', 'Observable')[source]¶

expression_is_linear = True[source]¶

expression_unit_registry[source]¶

expression[source]¶

species[source]¶

observables[source]¶

serialize()[source]¶

Generate string representation

Returns:: string representation
Return type:: str

classmethod deserialize(value, objects)[source]¶

Deserialize value

Parameters:

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model

Returns:

tuple of cleaned value and cleaning error

Return type:

tuple of ObservableExpression, InvalidAttribute or None

class wc_kb.core.Observable[source]¶

Bases: KnowledgeBaseObject

Observable: a linear function of other Observables and Species

cell[source]¶

cell

Type:: Cell

expression[source]¶

mathematical expression for an Observable

Type:: ObservableExpression

units[source]¶

units of expression

Type:: unit_registry.Unit

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

Related attributes:: observable_expressions (list of ObservableExpression): observable expressions rate_law_expressions (list of RateLawExpression): rate law expressions

class Meta[source]¶

Bases: obj_tables.Model.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'name', 'expression', 'units', 'identifiers', 'references', 'comments')[source]¶

expression_term_model[source]¶

expression_term_units = 'units'[source]¶

cell[source]¶

expression[source]¶

units[source]¶

references[source]¶

identifiers[source]¶

deserialize(value, objects, decoded=None)[source]¶

Deserialize value

Parameters:

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model
decoded (dict, optional) – dictionary of objects that have already been decoded

Returns:

tuple of cleaned value and cleaning error

Return type:

tuple of ObservableExpression, InvalidAttribute or None

class wc_kb.core.Parameter[source]¶

Bases: KnowledgeBaseObject

Knowledge of parameters

cell[source]¶

cell

Type:: Cell

value[source]¶

value

Type:: float

error[source]¶

measurement error

Type:: float

units[source]¶

units of value

Type:: unit_registry.Unit

evidence[source]¶

evidence

Type:: list of Evidence

references[source]¶

references

Type:: list of Reference

identifierss[source]¶

reference in external namespaces

Type:: list of DatabaseReference

Related attributes:: rate_law_expressions (list of RateLawExpression): rate law expressions that use a Parameter

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'synonyms', 'value', 'units', 'evidence', 'identifiers', 'references', 'comments')[source]¶

expression_term_token_pattern = ()[source]¶

cell[source]¶

value[source]¶

error[source]¶

units[source]¶

references[source]¶

evidence[source]¶

identifiers[source]¶

class wc_kb.core.Validator[source]¶

Bases: obj_tables.Validator

run(knowledge_base, get_related=True)[source]¶

Validate a knowledge_base and return its errors

Parameters:

knowledge_base (KnowledgeBase) – knowledge base
get_related (bool, optional) – if true, get all related objects

Returns:

list of invalid objects/models and their errors

Return type:

InvalidObjectSet or None

class wc_kb.core.MetaboliteSpeciesType[source]¶

Bases: SpeciesType

Knowledge of a metabolite

synonyms[source]¶

synonyms

Type:: str

type[source]¶

type

Type:: pronto

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'Metabolite'[source]¶

attribute_order = ('id', 'name', 'synonyms', 'type', 'identifiers', 'references', 'comments')[source]¶

synonyms[source]¶

type[source]¶

get_structure()[source]¶

Get the structure

Returns:: InChI or SMILES structure
Return type:: str
Raises:: ValueError – if structure has not been provided

calc_structure(ph=7.4, major_tautomer=False, keep_hydrogens=False, dearomatize=False)[source]¶

Get the major microspecies

Parameters:

pH (float, optional) – pH, default is 7.4
major_tautomer (bool, optional) – if True, use the major tautomeric in the calculation
keep_hydrogens (bool, optional) – if True, keep explicity defined hydrogens
dearomatize (bool, optional) – if True, dearomatize molecule

Returns:

InChI-encoded structure

Return type:

str

to_openbabel_mol()[source]¶

Convert species type to an Open Babel molecule

Returns:: Open Babel molecule
Return type:: openbabel.OBMol

get_empirical_formula()[source]¶

Get the empirical formula

Returns:: empirical formula
Return type:: chem.EmpiricalFormula

calc_empirical_formula()[source]¶

Calculate the empirical formula

Returns:: empirical formula
Return type:: chem.EmpiricalFormula

get_charge()[source]¶

Get the charge

Returns:: charge
Return type:: int

calc_charge()[source]¶

Calculate the charge

Returns:: charge
Return type:: int

get_mol_wt()[source]¶

Get the molecular weight

Returns:: molecular weight
Return type:: float
Raises:: ValueError – if there is not enough information to calculate molecular weight

class wc_kb.core.DnaSpeciesType[source]¶

Bases: PolymerSpeciesType

Knowledge of a DNA species

seq_path[source]¶

path to sequence fasta file

Type:: str

ploidy[source]¶

ploidy

Type:: int

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'Chromosome'[source]¶

attribute_order = ('id', 'name', 'sequence_path', 'circular', 'double_stranded', 'ploidy', 'identifiers',...[source]¶

sequence_path[source]¶

ploidy[source]¶

get_seq(start=None, end=None)[source]¶

Get the sequence

Parameters:

start (int, optional) – start coordinate of the queried subsequence, default is the start of the full sequence
end (int, optional) – end coordinate of the queried subsequence, default is the end of the full sequence

Returns:

structure

Return type:

Bio.Seq.Seq

get_empirical_formula()[source]¶

Get the empirical formula for a DNA molecule with

5’ monophosphate (for linear molecules)
Deprotonated phosphate oxygens
Linear DNA

\(N_A * dAMP + N_C * dCMP + N_G * dGMP + N_T * dTMP - (L - 1) * OH\)
Circular DNA

\(N_A * dAMP + N_C * dCMP + N_G * dGMP + N_T * dTMP - L * OH\)

N’s in the sequence will be distributed into the four bases by preserving the original ratio

Returns:: empirical formula
Return type:: chem.EmpiricalFormula

get_charge()[source]¶

Get the charge for a DNA molecule with

5’ monophosphate (for linear molecules)
Deprotonated phosphate oxygens
Linear DNA

\(-L - 1\)
Circular DNA

\(-L\)

Returns:: charge
Return type:: int

get_mol_wt()[source]¶

Get the molecular weight for a DNA molecule with

5’ monophosphate (for linear molecules)
Deprotonated phosphate oxygens
Linear DNA

\(N_A * MW_{dAMP} + N_C * MW_{dCMP} + N_G * MW_{dGMP} + N_T * MW_{dTMP} - (L - 1) * MW_{OH}\)
Circular DNA

\(N_A * MW_{dAMP} + N_C * MW_{dCMP} + N_G * MW_{dGMP} + N_T * MW_{dTMP} - L * MW_{OH}\)

Returns:: molecular weight
Return type:: float

class wc_kb.core.ComplexSpeciesType[source]¶

Bases: SpeciesType

Knowledge of a protein complex

formation_process[source]¶

type of formation process

Type:: pronto

subunits[source]¶

subunits

Type:: list of SpeciesTypeCoefficient

type[source]¶

type of complex formation

Type:: pronto

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'Complex'[source]¶

attribute_order = ('id', 'name', 'synonyms', 'type', 'formation_process', 'subunits', 'identifiers', 'references',...[source]¶

subunits[source]¶

type[source]¶

formation_process[source]¶

get_empirical_formula()[source]¶

Get the empirical formula

Returns:: empirical formula
Return type:: chem.EmpiricalFormula

get_charge()[source]¶

Get the charge at physiological pH

Returns:: charge
Return type:: int

get_mol_wt()[source]¶

Get the molecular weight

Returns:: molecular weight
Return type:: float

class wc_kb.core.RateLawDirection[source]¶

Bases: int, wc_utils.util.enumerate.CaseInsensitiveEnum

Rate law directions

backward[source]¶

forward = 1[source]¶

class wc_kb.core.RateLawExpression[source]¶

Bases: obj_tables.Model, obj_tables.math.expression.Expression

Rate law expression

expression[source]¶

mathematical expression of the rate law

Type:: str

parameters[source]¶

parameters whose values are used in the rate law

Type:: list of Parameter

species[source]¶

species whose dynamic concentrations are used in the rate law

Type:: list of Species

observables[source]¶

observables whose values are used in the rate law

Type:: list of Observable

Related attributes:: rate_law (RateLaw): the RateLaw which uses this RateLawExpression

class Meta[source]¶

Bases: obj_tables.Model.Meta, obj_tables.math.expression.Expression.Meta

attribute_order = ('expression', 'parameters', 'species', 'observables')[source]¶

table_format[source]¶

ordering = ('expression',)[source]¶

expression_term_models = ('Parameter', 'Species', 'Observable')[source]¶

expression_unit_registry[source]¶

expression[source]¶

parameters[source]¶

species[source]¶

observables[source]¶

serialize()[source]¶: Generate string representation :returns: value of primary attribute :rtype: str

classmethod deserialize(value, objects)[source]¶

Deserialize value :param value: String representation :type value: str :param objects: dictionary of objects, grouped by model :type objects: dict

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of RateLawExpression, InvalidAttribute or None

class wc_kb.core.RateLaw[source]¶

Bases: KnowledgeBaseObject

Rate law

reaction[source]¶

reaction

Type:: Reaction

direction[source]¶

direction

Type:: RateLawDirection

expression[source]¶

expression

Type:: RateLawExpression

units[source]¶

units

Type:: unit_registry.Unit

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

class Meta[source]¶

Bases: obj_tables.Model.Meta, obj_tables.math.expression.ExpressionExpressionTermMeta

attribute_order = ('id', 'reaction', 'direction', 'expression', 'units', 'identifiers', 'references', 'comments')[source]¶

expression_term_model[source]¶

expression_term_units = 'units'[source]¶

reaction[source]¶

expression[source]¶

units[source]¶

references[source]¶

identifiers[source]¶

direction[source]¶

gen_id()[source]¶: Generate identifier :returns: identifier :rtype: str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value

Parameters:

value (str) – String representation
objects (dict) – dictionary of objects, grouped by model
decoded (dict, optional) – dictionary of objects that have already been decoded

Returns: