3.1.1.2. obj_tables.chem package¶

3.1.1.2.1. Submodules¶

3.1.1.2.2. obj_tables.chem.core module¶

Chemistry attributes

Author: Jonathan Karr <karr@mssm.edu>
Date: 2017-05-10
Copyright: 2017, Karr Lab
License: MIT

class obj_tables.chem.core.ChemicalFormulaAttribute(default=None, none_value=None, verbose_name='', description="A chemical formula (e.g. 'H2O', 'CO2', or 'NaCl')", primary=False, unique=False)[source]¶

Bases: obj_tables.core.LiteralAttribute

Chemical formula attribute

Parameters

default (chem.EmpiricalFormula, dict, str, or None, optional) – default value
none_value (object, optional) – none value
verbose_name (str, optional) – verbose name
description (str, optional) – description
primary (bool, optional) – indicate if attribute is primary attribute
unique (bool, optional) – indicate if attribute value must be unique

deserialize(value)[source]¶

Deserialize value

Parameters

value (str) – semantically equivalent representation

Returns

chem.EmpiricalFormula: cleaned value
core.InvalidAttribute: cleaning error

Return type

tuple

from_builtin(json)[source]¶

Decode a simple Python representation (dict, list, str, float, bool, None) of a value of the attribute that is compatible with JSON and YAML

Parameters: json (dict) – simple Python representation of a value of the attribute
Returns: decoded value of the attribute
Return type: chem.EmpiricalFormula

get_xlsx_validation(sheet_models=None, doc_metadata_model=None)[source]¶

Get XLSX validation

Parameters

sheet_models (list of Model, optional) – models encoded as separate sheets
doc_metadata_model (type) – model whose worksheet contains the document metadata

Returns

validation

Return type

wc_utils.workbook.io.FieldValidation

serialize(value)[source]¶

Serialize string

Parameters: value (chem.EmpiricalFormula) – Python representation
Returns: simple Python representation
Return type: str

to_builtin(value)[source]¶

Encode a value of the attribute using a simple Python representation (dict, list, str, float, bool, None) that is compatible with JSON and YAML

Parameters: value (chem.EmpiricalFormula) – value of the attribute
Returns: simple Python representation of a value of the attribute
Return type: dict

validate(obj, value)[source]¶

Determine if value is a valid value

Parameters

obj (Model) – class being validated
value (chem.EmpiricalFormula) – value of attribute to validate

Returns

None if attribute is valid, other return: list of errors as an instance of core.InvalidAttribute

Return type

core.InvalidAttribute or None

validate_unique(objects, values)[source]¶

Determine if the attribute values are unique

Parameters

objects (list of Model) – list of Model objects
values (list of chem.EmpiricalFormula) – list of values

Returns

None if values are unique, otherwise return a: list of errors as an instance of core.InvalidAttribute

Return type

core.InvalidAttribute or None

class obj_tables.chem.core.ChemicalStructure(value=None, serialized_format=None)[source]¶

Bases: object

A chemical structure

Attributes

value (openbabel.OBMol, bpforms.BpForm, bcforms.BcForm): value serialized_value (str): serialized value serialized_format (ChemicalStructureFormat): serialized format

_value (openbabel.OBMol, bpforms.BpForm, bcforms.BcForm): value _serialized_value (str): serialized value _serialized_format (ChemicalStructureFormat): serialized format

Parameters

value (str, openbabel.OBMol, bpforms.BpForm, bcforms.BcForm, optional) – value
serialized_format (ChemicalStructureFormat, openbabel) – serialized format

deserialize(serialized_value)[source]¶

Set value from a string representation

Parameters: serialized_value (str) – string representation
Returns: self
Return type: ChemicalStructure

from_dict(dict_value)[source]¶

Set value from a dictionary representation

Parameters: dict_value (dict) – dictionary representation
Returns: self
Return type: ChemicalStructure

serialize()[source]¶

Generate a string representation

Returns: string representation
Return type: str

property serialized_format[source]¶

property serialized_value[source]¶

to_dict()[source]¶

Get a dictionary representation

Returns: dictionary representation
Return type: dict

property value[source]¶

class obj_tables.chem.core.ChemicalStructureFormat[source]¶

Bases: int, wc_utils.util.enumerate.CaseInsensitiveEnum

Format of a chemical structure

bcforms = 4[source]¶

bpforms = 3[source]¶

inchi = 1[source]¶

smiles = 2[source]¶

class obj_tables.chem.core.ChemicalStructureAttribute(verbose_name='', description='The InChI, SMILES-, BpForms, BcForms-encoded structure of a compound.nnExamples:n Small molecules (SMILES): C([N+])C([O-])=On DNA (BpForms/dna): A{m2C}GTn RNA (BpForms/rna): AC{02G}Un Protein (BpForms/protein): RNC{AA0037}En Complex (BcForms): 2 * subunit-A + subunit-B', primary=False, unique=False)[source]¶

Bases: obj_tables.core.LiteralAttribute

Attribute for the structures of chemical compounds

Parameters

verbose_name (str, optional) – verbose name
description (str, optional) – description
primary (bool, optional) – indicate if attribute is primary attribute
unique (bool, optional) – indicate if attribute value must be unique

deserialize(value)[source]¶

Deserialize value

Parameters

value (str) – string representation of structure

Returns

str: cleaned value
core.InvalidAttribute: cleaning error

Return type

tuple

from_builtin(json)[source]¶

Decode a simple Python representation (dict, list, str, float, bool, None) of a value of the attribute that is compatible with JSON and YAML

Parameters: json (dict) – simple Python representation of a value of the attribute
Returns: chemical structure
Return type: ChemicalStructure

get_xlsx_validation(sheet_models=None, doc_metadata_model=None)[source]¶

Get XLSX validation

Parameters

sheet_models (list of Model, optional) – models encoded as separate sheets
doc_metadata_model (type) – model whose worksheet contains the document metadata

Returns

validation

Return type

wc_utils.workbook.io.FieldValidation

serialize(value)[source]¶

Serialize chemical structure

Parameters: value (ChemicalStructure) – structure
Returns: string representation
Return type: str

to_builtin(value)[source]¶

Encode a value of the attribute using a simple Python representation (dict, list, str, float, bool, None) that is compatible with JSON and YAML

Parameters: value (ChemicalStructure) – chemical structure
Returns: simple Python representation of a value of the attribute
Return type: dict

validate(obj, value)[source]¶

Determine if value is a valid value

Parameters

obj (Model) – class being validated
value (ChemicalStructure) – value of attribute to validate

Returns

None if attribute is valid, other return list of: errors as an instance of core.InvalidAttribute

Return type

core.InvalidAttribute or None

validate_unique(objects, values)[source]¶

Determine if the attribute values are unique

Parameters

objects (list of Model) – list of Model objects
values (list of ChemicalStructure) – list of values

Returns

None if values are unique, otherwise return a: list of errors as an instance of core.InvalidAttribute

Return type

core.InvalidAttribute or None

class obj_tables.chem.core.ReactionEquation[source]¶

Bases: list

Reaction equation

class ParseTreeTransformer(species=None, compartments=None)[source]¶

Bases: lark.visitors.Transformer

Transforms parse trees into an instance of ReactionEquation

species[source]¶

dictionary that maps species ids to instances

Type: dict

compartments[source]¶

dictionary that maps compartment ids to instances

Type: dict

Parameters

species (dict, optional) – dictionary that maps species ids to instances
compartments (dict, optional) – dictionary that maps compartment ids to instances

gbl(*args)[source]¶

gbl_part(*args)[source]¶

gbl_parts(*args)[source]¶

lcl(*args)[source]¶

lcl_part(*args)[source]¶

lcl_parts(*args)[source]¶

start(parts)[source]¶

deserialize(value, species=None, compartments=None)[source]¶

Set the participants from a string representation

Parameters

value (str) – string representation
species (dict, optional) – dictionary that maps species ids to instances
compartments (dict, optional) – dictionary that maps compartment ids to instances

file = <_io.TextIOWrapper name='/root/project/obj_tables/chem/reaction_equation.lark' mode='r' encoding='UTF-8'>[source]¶

is_equal(other)[source]¶

Determine if two reaction equations are semantically equivalent

Parameters: other (ReactionEquation) – other reaction equation
Returns: True if the objects are semantically equivalent
Return type: bool

parser = Lark(open('<string>'), parser='earley', lexer='dynamic', ...)[source]¶

serialize()[source]¶

Generate a string representation

Returns: string representation
Return type: str

to_dict()[source]¶

Get a simple Python representation compatible with JSON

Returns: simple Python representation
Return type: list

class obj_tables.chem.core.ReactionParticipant(species=None, compartment=None, stoichiometry=None)[source]¶

Bases: object

Participant in a reaction

species[source]¶

species

Type: str or core.Model

compartment[source]¶

compartment

Type: str or core.Model

stoichiometry[source]¶

stoichiometry

Type: float

Parameters

species (str or core.Model, optional) – species
compartment (str or core.Model, optional) – compartment
stoichiometry (float, optional) – stoichiometry

is_equal(other)[source]¶

Determine if two reaction participants are semantically equivalent

Parameters: other (ReactionParticipant) – other reaction equation
Returns: True if the objects are semantically equivalent
Return type: bool

serialize(include_compartment=True)[source]¶

Generate a string representation

Parameters: include_compartment (bool, optional) – if True, include compartment in string representation
Returns: string representation
Return type: str

to_dict()[source]¶

Get a simple Python representation compatible with JSON

Returns: simple Python representation
Return type: dict

class obj_tables.chem.core.ReactionEquationAttribute(verbose_name='', description="A reaction equation (e.g. 'A[c] <=> B[e]', '[c]: A <=> B')", none=True, unique=False, species_cls=None, compartment_cls=None)[source]¶

Bases: obj_tables.core.BaseRelatedAttribute, obj_tables.core.LiteralAttribute

Reaction equation attribute

none[source]¶

if False, the attribute is invalid if its value is None

Type: bool

species_cls[source]¶

class which represents species compartment_cls (type or str): class which represents compartments

Type: type or str

Parameters

verbose_name (str, optional) – verbose name
description (str, optional) – description
none (bool, optional) – if False, the attribute is invalid if its value is None
unique (bool, optional) – indicate if attribute value must be unique
species_cls (type or str, optional) – class which represents species
compartment_cls (type or str, optional) – class which represents compartments

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

Deserialize value

Parameters

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

Returns

ReactionEquation: cleaned value
core.InvalidAttribute: cleaning error

Return type

tuple

from_builtin(json)[source]¶

Decode a simple Python representation (dict, list, str, float, bool, None) of a value of the attribute that is compatible with JSON and YAML

Parameters: json (dict) – simple Python representation of a value of the attribute
Returns: decoded value of the attribute
Return type: ReactionEquation

get_xlsx_validation(sheet_models=None, doc_metadata_model=None)[source]¶

Get XLSX validation

Parameters

sheet_models (list of Model, optional) – models encoded as separate sheets
doc_metadata_model (type) – model whose worksheet contains the document metadata

Returns

validation

Return type

wc_utils.workbook.io.FieldValidation

serialize(value)[source]¶

Serialize string

Parameters: value (ReactionEquation) – Python representation
Returns: simple Python representation
Return type: str

to_builtin(value)[source]¶

Encode a value of the attribute using a simple Python representation (dict, list, str, float, bool, None) that is compatible with JSON and YAML

Parameters: value (ReactionEquation) – value of the attribute
Returns: simple Python representation of a value of the attribute
Return type: dict

validate(obj, value)[source]¶

Determine if value is a valid value

Parameters

obj (Model) – class being validated
value (ReactionEquation) – value of attribute to validate

Returns

None if attribute is valid, other return: list of errors as an instance of core.InvalidAttribute

Return type

core.InvalidAttribute or None

validate_unique(objects, values)[source]¶

Determine if the attribute values are unique

Parameters

objects (list of Model) – list of Model objects
values (list of ReactionEquation) – list of values

Returns

None if values are unique, otherwise return a: list of errors as an instance of core.InvalidAttribute

Return type

core.InvalidAttribute or None

3.1.1.2. obj_tables.chem package¶

3.1.1.2.1. Submodules¶

3.1.1.2.2. obj_tables.chem.core module¶

3.1.1.2.3. Module contents¶