API Reference

biokb_coconut.db.models

This module contains the SQLAlchemy ORM models for the biokb_coconut database.

Each class in this module represents a table in the database, with attributes corresponding to the columns of the table. Relationships between tables are defined using SQLAlchemy's relationship function.

CAS

Bases: Base

Class definition for table cas.

Attributes:

Name	Type	Description
id	int	Primary key.
number	str	Unique CAS number.
compounds	list[Compound]	List of compounds associated with this CAS number.

Source code in src/biokb_coconut/db/models.py

class CAS(Base):
    """Class definition for table cas.

    Attributes:
        id (int): Primary key.
        number (str): Unique CAS number.
        compounds (list[Compound]): List of compounds associated with this CAS number.
    """

    __tablename__ = Base.table_prefix + "cas"

    id = Column(Integer, primary_key=True)
    number = Column(
        String(255).with_variant(String(255, collation="utf8mb4_bin"), "mysql"),
        unique=True,
    )
    compounds: Mapped[list["Compound"]] = relationship(
        secondary=CompoundCAS.__table__, back_populates="cas_numbers"
    )

    def __repr__(self) -> str:
        return f"<CAS(id={self.id}, number={self.number})>"

ChemicalClass

Bases: Base, OnlyName

Chemical Class model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the chemical class.
compounds	list[Compound]	List of compounds associated with this class.

Source code in src/biokb_coconut/db/models.py

class ChemicalClass(Base, OnlyName):
    """Chemical Class model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the chemical class.
        compounds (list[Compound]): List of compounds associated with this class.
    """

    __tablename__ = Base.table_prefix + "chemical_class"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(back_populates="chemical_class")

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<ChemicalClass(id={self.id}, name={self.name})>"

ChemicalSubClass

Bases: Base, OnlyName

Chemical Sub-Class model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the chemical sub-class.
compounds	list[Compound]	List of compounds associated with this sub-class.

Source code in src/biokb_coconut/db/models.py

class ChemicalSubClass(Base, OnlyName):
    """Chemical Sub-Class model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the chemical sub-class.
        compounds (list[Compound]): List of compounds associated with this sub-class.
    """

    __tablename__ = Base.table_prefix + "chemical_sub_class"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(
        back_populates="chemical_sub_class"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<ChemicalSubClass(id={self.id}, name={self.name})>"

ChemicalSuperClass

Bases: Base, OnlyName

Chemical Super-Class model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the chemical super-class.
compounds	list[Compound]	List of compounds associated with this super-class.

Source code in src/biokb_coconut/db/models.py

class ChemicalSuperClass(Base, OnlyName):
    """Chemical Super-Class model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the chemical super-class.
        compounds (list[Compound]): List of compounds associated with this super-class.
    """

    __tablename__ = Base.table_prefix + "chemical_super_class"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(
        back_populates="chemical_super_class"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<ChemicalSuperClass(id={self.id}, name={self.name})>"

Collection

Bases: Base

Class definition for table collection.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the collection.
compounds	list[Compound]	List of compounds associated with this collection.

Source code in src/biokb_coconut/db/models.py

class Collection(Base):
    """Class definition for table collection.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the collection.
        compounds (list[Compound]): List of compounds associated with this collection.
    """

    __tablename__ = Base.table_prefix + "collection"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(
        String(255).with_variant(String(255, collation="utf8mb4_bin"), "mysql"),
        unique=True,
    )
    compounds: Mapped[list["Compound"]] = relationship(
        secondary=CompoundCollection.__table__, back_populates="collections"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<Collection(id={self.id}, name={self.name})>"

Compound

Bases: Base

Class definition for table compound.

Attributes:

Name	Type	Description
id	int	Primary key.
identifier	str	Unique identifier for the compound.
canonical_smiles	str	Canonical SMILES representation of the compound.
standard_inchi	str	Standard InChI representation of the compound.
standard_inchi_key	str	Standard InChI Key of the compound.
name	Optional[str]	Name of the compound.
iupac_name	Optional[str]	IUPAC name of the compound.
annotation_level	int	Annotation level of the compound.
total_atom_count	int	Total atom count of the compound.
heavy_atom_count	int	Heavy atom count of the compound.
molecular_weight	float	Molecular weight of the compound.
exact_molecular_weight	float	Exact molecular weight of the compound.
molecular_formula	str	Molecular formula of the compound.
alogp	float	ALogP value of the compound.
topological_polar_surface_area	float	Topological polar surface area of the compound.
rotatable_bond_count	int	Rotatable bond count of the compound.
hydrogen_bond_acceptors	int	Number of hydrogen bond acceptors.
hydrogen_bond_donors	int	Number of hydrogen bond donors.
hydrogen_bond_acceptors_lipinski	int	Number of hydrogen bond acceptors according to Lipinski's rule.
hydrogen_bond_donors_lipinski	int	Number of hydrogen bond donors according to Lipinski's rule.
lipinski_rule_of_five_violations	int	Number of Lipinski's rule of five violations.
aromatic_rings_count	int	Aromatic rings count of the compound.
qed_drug_likeliness	float	QED drug-likeliness score of the compound.
formal_charge	int	Formal charge of the compound.
fractioncsp3	float	Fraction of sp3 hybridized carbons in the compound.
number_of_minimal_rings	int	Number of minimal rings in the compound.
van_der_walls_volume	Optional[float]	Van der Waals volume of the compound.
contains_sugar	Optional[bool]	Indicates if the compound contains sugar.
contains_ring_sugars	bool	Indicates if the compound contains ring sugars.
contains_linear_sugars	bool	Indicates if the compound contains linear sugars.
murcko_framework	Optional[str]	Murcko framework of the compound.
np_likeness	float	Natural product-likeness score of the compound.
np_classifier_is_glycoside	Optional[bool]	Indicates if the compound is classified as a glycoside by the NP classifier.
chemical_class_id	Optional[int]	Foreign key to the chemical class table.
chemical_sub_class_id	Optional[int]	Foreign key to the chemical sub-class table.
direct_parent_classification_id	Optional[int]	Foreign key to the direct parent classification table.
chemical_super_class_id	Optional[int]	Foreign key to the chemical super-class table.
np_classifier_pathway_id	Optional[int]	Foreign key to the NP classifier pathway table.
np_classifier_superclass_id	Optional[int]	Foreign key to the NP classifier superclass table.
np_classifier_class_id	Optional[int]	Foreign key to the NP classifier class table.
chemical_class	Optional[ChemicalClass]	Relationship to the chemical class.
chemical_sub_class	Optional[ChemicalSubClass]	Relationship to the chemical sub-class.
direct_parent_classification	Optional[DirectParentClassification]	Relationship to the direct parent classification.
chemical_super_class	Optional[ChemicalSuperClass]	Relationship to the chemical super-class.
np_classifier_pathway	Optional[NpClassifierPathway]	Relationship to the NP classifier pathway.
np_classifier_superclass	Optional[NpClassifierSuperclass]	Relationship to the NP classifier superclass.
np_classifier_class	Optional[NpClassifierClass]	Relationship to the NP classifier class.
organisms	list[Organism]	List of organisms associated with the compound.
collections	list[Collection]	List of collections associated with the compound.
dois	list[DOI]	List of DOIs associated with the compound.
synonyms	list[Synonym]	List of synonyms associated with the compound.
cas_numbers	list[CAS]	List of CAS numbers associated with the compound.

Source code in src/biokb_coconut/db/models.py

class Compound(Base):
    """Class definition for table compound.

    Attributes:
        id (int): Primary key.
        identifier (str): Unique identifier for the compound.
        canonical_smiles (str): Canonical SMILES representation of the compound.
        standard_inchi (str): Standard InChI representation of the compound.
        standard_inchi_key (str): Standard InChI Key of the compound.
        name (Optional[str]): Name of the compound.
        iupac_name (Optional[str]): IUPAC name of the compound.
        annotation_level (int): Annotation level of the compound.
        total_atom_count (int): Total atom count of the compound.
        heavy_atom_count (int): Heavy atom count of the compound.
        molecular_weight (float): Molecular weight of the compound.
        exact_molecular_weight (float): Exact molecular weight of the compound.
        molecular_formula (str): Molecular formula of the compound.
        alogp (float): ALogP value of the compound.
        topological_polar_surface_area (float): Topological polar surface area of the compound.
        rotatable_bond_count (int): Rotatable bond count of the compound.
        hydrogen_bond_acceptors (int): Number of hydrogen bond acceptors.
        hydrogen_bond_donors (int): Number of hydrogen bond donors.
        hydrogen_bond_acceptors_lipinski (int): Number of hydrogen bond acceptors according to Lipinski's rule.
        hydrogen_bond_donors_lipinski (int): Number of hydrogen bond donors according to Lipinski's rule.
        lipinski_rule_of_five_violations (int): Number of Lipinski's rule of five violations.
        aromatic_rings_count (int): Aromatic rings count of the compound.
        qed_drug_likeliness (float): QED drug-likeliness score of the compound.
        formal_charge (int): Formal charge of the compound.
        fractioncsp3 (float): Fraction of sp3 hybridized carbons in the compound.
        number_of_minimal_rings (int): Number of minimal rings in the compound.
        van_der_walls_volume (Optional[float]): Van der Waals volume of the compound.
        contains_sugar (Optional[bool]): Indicates if the compound contains sugar.
        contains_ring_sugars (bool): Indicates if the compound contains ring sugars.
        contains_linear_sugars (bool): Indicates if the compound contains linear sugars.
        murcko_framework (Optional[str]): Murcko framework of the compound.
        np_likeness (float): Natural product-likeness score of the compound.
        np_classifier_is_glycoside (Optional[bool]): Indicates if the compound is classified as a glycoside by the NP classifier.
        chemical_class_id (Optional[int]): Foreign key to the chemical class table.
        chemical_sub_class_id (Optional[int]): Foreign key to the chemical sub-class table.
        direct_parent_classification_id (Optional[int]): Foreign key to the direct parent classification table.
        chemical_super_class_id (Optional[int]): Foreign key to the chemical super-class table.
        np_classifier_pathway_id (Optional[int]): Foreign key to the NP classifier pathway table.
        np_classifier_superclass_id (Optional[int]): Foreign key to the NP classifier superclass table.
        np_classifier_class_id (Optional[int]): Foreign key to the NP classifier class table.
        chemical_class (Optional[ChemicalClass]): Relationship to the chemical class.
        chemical_sub_class (Optional[ChemicalSubClass]): Relationship to the chemical sub-class.
        direct_parent_classification (Optional[DirectParentClassification]): Relationship to the direct parent classification.
        chemical_super_class (Optional[ChemicalSuperClass]): Relationship to the chemical super-class.
        np_classifier_pathway (Optional[NpClassifierPathway]): Relationship to the NP classifier pathway.
        np_classifier_superclass (Optional[NpClassifierSuperclass]): Relationship to the NP classifier superclass.
        np_classifier_class (Optional[NpClassifierClass]): Relationship to the NP classifier class.
        organisms (list[Organism]): List of organisms associated with the compound.
        collections (list[Collection]): List of collections associated with the compound.
        dois (list[DOI]): List of DOIs associated with the compound.
        synonyms (list[Synonym]): List of synonyms associated with the compound.
        cas_numbers (list[CAS]): List of CAS numbers associated with the compound.
    """

    __tablename__ = Base.table_prefix + "compound"

    id: Mapped[int] = mapped_column(primary_key=True, autoincrement=True)
    identifier: Mapped[str] = mapped_column(String(255), unique=True, nullable=False)
    canonical_smiles: Mapped[str] = mapped_column(Text)
    standard_inchi: Mapped[str] = mapped_column(Text)
    standard_inchi_key: Mapped[str] = mapped_column(String(32))
    name: Mapped[Optional[str]] = mapped_column(String(10000), nullable=True)
    iupac_name: Mapped[Optional[str]] = mapped_column(Text)
    annotation_level: Mapped[int]
    total_atom_count: Mapped[int]
    heavy_atom_count: Mapped[int]
    molecular_weight: Mapped[Decimal] = mapped_column(Numeric(8, 2))
    exact_molecular_weight: Mapped[Decimal] = mapped_column(Numeric(11, 5))
    molecular_formula: Mapped[str] = mapped_column(String(255))
    alogp: Mapped[Decimal] = mapped_column(Numeric(6, 2))
    topological_polar_surface_area: Mapped[Decimal] = mapped_column(Numeric(8, 2))
    rotatable_bond_count: Mapped[int]
    hydrogen_bond_acceptors: Mapped[int]
    hydrogen_bond_donors: Mapped[int]
    hydrogen_bond_acceptors_lipinski: Mapped[int]
    hydrogen_bond_donors_lipinski: Mapped[int]
    lipinski_rule_of_five_violations: Mapped[int]
    aromatic_rings_count: Mapped[int]
    qed_drug_likeliness: Mapped[Decimal] = mapped_column(Numeric(5, 2))
    formal_charge: Mapped[int]
    fractioncsp3: Mapped[Decimal] = mapped_column(Numeric(5, 2))
    number_of_minimal_rings: Mapped[int]
    van_der_walls_volume: Mapped[Optional[Decimal]] = mapped_column(Numeric(8, 2))
    contains_sugar: Mapped[Optional[bool]]
    contains_ring_sugars: Mapped[bool]
    contains_linear_sugars: Mapped[bool]
    murcko_framework: Mapped[Optional[str]] = mapped_column(Text)
    np_likeness: Mapped[Decimal] = mapped_column(Numeric(5, 2))
    np_classifier_is_glycoside: Mapped[Optional[bool]]
    number_of_organisms: Mapped[Optional[int]] = mapped_column(
        Integer, default=0, server_default=text("0")
    )

    # foreign keys to classification tables
    chemical_class_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "chemical_class.id")
    )
    chemical_sub_class_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "chemical_sub_class.id")
    )
    direct_parent_classification_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "direct_parent_classification.id")
    )
    chemical_super_class_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "chemical_super_class.id")
    )
    np_classifier_pathway_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "np_classifier_pathway.id")
    )
    np_classifier_superclass_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "np_classifier_superclass.id")
    )
    np_classifier_class_id: Mapped[Optional[int]] = mapped_column(
        ForeignKey(Base.table_prefix + "np_classifier_class.id")
    )

    # relationships
    chemical_class: Mapped[Optional["ChemicalClass"]] = relationship(
        back_populates="compounds"
    )
    chemical_sub_class: Mapped[Optional["ChemicalSubClass"]] = relationship(
        back_populates="compounds"
    )
    direct_parent_classification: Mapped[Optional["DirectParentClassification"]] = (
        relationship(back_populates="compounds")
    )
    chemical_super_class: Mapped[Optional["ChemicalSuperClass"]] = relationship(
        back_populates="compounds"
    )
    np_classifier_pathway: Mapped[Optional["NpClassifierPathway"]] = relationship(
        back_populates="compounds"
    )
    np_classifier_superclass: Mapped[Optional["NpClassifierSuperclass"]] = relationship(
        back_populates="compounds"
    )
    np_classifier_class: Mapped[Optional["NpClassifierClass"]] = relationship(
        back_populates="compounds"
    )
    # many-to-many relationships
    organisms: Mapped[list["Organism"]] = relationship(
        secondary=CompoundOrganism.__table__, back_populates="compounds"
    )
    collections: Mapped[list["Collection"]] = relationship(
        secondary=CompoundCollection.__table__, back_populates="compounds"
    )
    dois: Mapped[list["DOI"]] = relationship(
        secondary=CompoundDOI.__table__, back_populates="compounds"
    )
    synonyms: Mapped[list["Synonym"]] = relationship(
        secondary=CompoundSynonym.__table__, back_populates="compounds"
    )
    cas_numbers: Mapped[list["CAS"]] = relationship(
        secondary=CompoundCAS.__table__, back_populates="compounds"
    )

    @property
    def organism_names(self) -> list[str]:
        return [organism.name for organism in self.organisms]

    def __repr__(self) -> str:
        return (
            f"<Compound(id={self.id}, name={self.name}, identifier={self.identifier})>"
        )

    __table_args__ = (
        Index(
            f"ix_{__tablename__}__name",
            "name",
            mysql_length=768,
        ),
    )

CompoundCAS

Bases: Base

Joining table for Compound and CAS many-to-many relationship.

Attributes:

Name	Type	Description
compound_id	int	Foreign key to the compound table.
cas_number_id	int	Foreign key to the cas table.

Source code in src/biokb_coconut/db/models.py

class CompoundCAS(Base):
    """Joining table for Compound and CAS many-to-many relationship.

    Attributes:
        compound_id (int): Foreign key to the compound table.
        cas_number_id (int): Foreign key to the cas table.
    """

    __tablename__ = Base.table_prefix + "compound_cas"

    compound_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "compound.id"), primary_key=True
    )
    cas_number_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "cas.id"), primary_key=True
    )

CompoundCollection

Bases: Base

Joining table for Compound and Collection many-to-many relationship.

Attributes:

Name	Type	Description
compound_id	int	Foreign key to the compound table.
collection_id	int	Foreign key to the collection table.

Source code in src/biokb_coconut/db/models.py

class CompoundCollection(Base):
    """Joining table for Compound and Collection many-to-many relationship.

    Attributes:
        compound_id (int): Foreign key to the compound table.
        collection_id (int): Foreign key to the collection table.
    """

    __tablename__ = Base.table_prefix + "compound__collection"

    compound_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "compound.id"), primary_key=True
    )
    collection_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "collection.id"), primary_key=True
    )

CompoundDOI

Bases: Base

Joining table for Compound and DOI many-to-many relationship.

Attributes:

Name	Type	Description
compound_id	int	Foreign key to the compound table.
doi_id	int	Foreign key to the doi table.

Source code in src/biokb_coconut/db/models.py

class CompoundDOI(Base):
    """Joining table for Compound and DOI many-to-many relationship.

    Attributes:
        compound_id (int): Foreign key to the compound table.
        doi_id (int): Foreign key to the doi table.
    """

    __tablename__ = Base.table_prefix + "compound_doi"

    compound_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "compound.id"), primary_key=True
    )
    doi_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "doi.id"), primary_key=True
    )

CompoundOrganism

Bases: Base

Joining table for Compound and Organism many-to-many relationship.

Attributes:

Name	Type	Description
compound_id	int	Foreign key to the compound table.
organism_id	int	Foreign key to the organism table.

Source code in src/biokb_coconut/db/models.py

class CompoundOrganism(Base):
    """Joining table for Compound and Organism many-to-many relationship.

    Attributes:
        compound_id (int): Foreign key to the compound table.
        organism_id (int): Foreign key to the organism table.
    """

    __tablename__ = Base.table_prefix + "compound__organism"

    compound_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "compound.id"), primary_key=True
    )
    organism_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "organism.id"), primary_key=True
    )

CompoundSynonym

Bases: Base

Joining table for Compound and Synonym many-to-many relationship.

Attributes:

Name	Type	Description
compound_id	int	Foreign key to the compound table.
synonym_id	int	Foreign key to the synonym table.

Source code in src/biokb_coconut/db/models.py

class CompoundSynonym(Base):
    """Joining table for Compound and Synonym many-to-many relationship.

    Attributes:
        compound_id (int): Foreign key to the compound table.
        synonym_id (int): Foreign key to the synonym table.
    """

    __tablename__ = Base.table_prefix + "compound__synonym"

    compound_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "compound.id"), primary_key=True
    )
    synonym_id: Mapped[int] = mapped_column(
        ForeignKey(Base.table_prefix + "synonym.id"), primary_key=True
    )

DOI

Bases: Base

Class definition for table doi.

Attributes:

Name	Type	Description
id	int	Primary key.
identifier	str	Unique identifier for the DOI.
compounds	list[Compound]	List of compounds associated with this DOI.

Source code in src/biokb_coconut/db/models.py

class DOI(Base):
    """Class definition for table doi.

    Attributes:
        id (int): Primary key.
        identifier (str): Unique identifier for the DOI.
        compounds (list[Compound]): List of compounds associated with this DOI.
    """

    __tablename__ = Base.table_prefix + "doi"

    id: Mapped[int] = mapped_column(primary_key=True)
    identifier: Mapped[str] = mapped_column(
        String(255).with_variant(String(255, collation="utf8mb4_bin"), "mysql"),
        unique=True,
    )
    compounds: Mapped[list["Compound"]] = relationship(
        secondary=CompoundDOI.__table__, back_populates="dois"
    )

    def __repr__(self) -> str:
        return f"<DOI(id={self.id}, identifier={self.identifier})>"

DirectParentClassification

Bases: Base, OnlyName

Direct Parent Classification model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the direct parent classification.
compounds	list[Compound]	List of compounds associated with this classification.

Source code in src/biokb_coconut/db/models.py

class DirectParentClassification(Base, OnlyName):
    """Direct Parent Classification model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the direct parent classification.
        compounds (list[Compound]): List of compounds associated with this classification.
    """

    __tablename__ = Base.table_prefix + "direct_parent_classification"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(
        back_populates="direct_parent_classification"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<DirectParentClassification(id={self.id}, name={self.name})>"

NpClassifierClass

Bases: Base, OnlyName

Natural Product Classifier Class model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the NP classifier class.
compounds	list[Compound]	List of compounds associated with this class.

Source code in src/biokb_coconut/db/models.py

class NpClassifierClass(Base, OnlyName):
    """Natural Product Classifier Class model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the NP classifier class.
        compounds (list[Compound]): List of compounds associated with this class.
    """

    __tablename__ = Base.table_prefix + "np_classifier_class"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(
        back_populates="np_classifier_class"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<NpClassifierClass(id={self.id}, name={self.name})>"

NpClassifierPathway

Bases: Base, OnlyName

Natural Product Classifier Pathway model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the NP classifier pathway.
compounds	list[Compound]	List of compounds associated with this pathway.

Source code in src/biokb_coconut/db/models.py

class NpClassifierPathway(Base, OnlyName):
    """Natural Product Classifier Pathway model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the NP classifier pathway.
        compounds (list[Compound]): List of compounds associated with this pathway.
    """

    __tablename__ = Base.table_prefix + "np_classifier_pathway"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(
        back_populates="np_classifier_pathway"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<NpClassifierPathway(id={self.id}, name={self.name})>"

NpClassifierSuperclass

Bases: Base, OnlyName

Natural Product Classifier Superclass model.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the NP classifier superclass.
compounds	list[Compound]	List of compounds associated with this superclass.

Source code in src/biokb_coconut/db/models.py

class NpClassifierSuperclass(Base, OnlyName):
    """Natural Product Classifier Superclass model.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the NP classifier superclass.
        compounds (list[Compound]): List of compounds associated with this superclass.
    """

    __tablename__ = Base.table_prefix + "np_classifier_superclass"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(255), unique=True)

    compounds: Mapped[list["Compound"]] = relationship(
        back_populates="np_classifier_superclass"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    def __repr__(self) -> str:
        return f"<NpClassifierSuperclass(id={self.id}, name={self.name})>"

Organism

Bases: Base

Class definition for table organism.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Name of the organism.
tax_id	Optional[int]	NCBI taxonomy identifier.
wcvp_id	Optional[int]	WCVP identifier.
powo_id	Optional[str]	POWO identifier.
compounds	list[Compound]	List of compounds associated with this organism.

Source code in src/biokb_coconut/db/models.py

class Organism(Base):
    """Class definition for table organism.

    Attributes:
        id (int): Primary key.
        name (str): Name of the organism.
        tax_id (Optional[int]): NCBI taxonomy identifier.
        wcvp_id (Optional[int]): WCVP identifier.
        powo_id (Optional[str]): POWO identifier.
        compounds (list[Compound]): List of compounds associated with this organism.
    """

    __tablename__ = Base.table_prefix + "organism"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(String(1000))
    tax_id: Mapped[Optional[int]] = mapped_column(index=True)
    wcvp_id: Mapped[Optional[int]]
    powo_id: Mapped[Optional[str]] = mapped_column(String(255))
    compounds: Mapped[list["Compound"]] = relationship(
        secondary=CompoundOrganism.__table__, back_populates="organisms"
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    __table_args__ = (
        Index(
            f"ix_{__tablename__}__name",
            "name",
            mysql_length=768,
        ),
    )

    def __repr__(self) -> str:
        return f"<Organism(id={self.id}, name={self.name}, tax_id={self.tax_id})>"

Synonym

Bases: Base

Class definition for table synonym.

Attributes:

Name	Type	Description
id	int	Primary key.
name	str	Unique name of the synonym.
compounds	list[Compound]	List of compounds associated with this synonym.

Source code in src/biokb_coconut/db/models.py

class Synonym(Base):
    """Class definition for table synonym.

    Attributes:
        id (int): Primary key.
        name (str): Unique name of the synonym.
        compounds (list[Compound]): List of compounds associated with this synonym.
    """

    __tablename__ = Base.table_prefix + "synonym"

    id: Mapped[int] = mapped_column(primary_key=True)
    name: Mapped[str] = mapped_column(
        String(1000).with_variant(String(1000, collation="utf8mb4_bin"), "mysql")
    )

    @property
    def compound_identifiers(self) -> list[str]:
        return [compound.identifier for compound in self.compounds]

    # m2m relationship
    compounds: Mapped[list["Compound"]] = relationship(
        secondary=CompoundSynonym.__table__, back_populates="synonyms"
    )
    __table_args__ = (Index("uq_my_model_name", "name", unique=True, mysql_length=768),)

    def __repr__(self) -> str:
        return f"<Synonym(id={self.id}, name={self.name})>"

TaxonomyName

Bases: Base

Class definition for table taxonomy_name. Name from NCBI taxonomy https://www.ncbi.nlm.nih.gov/taxonomys.

Attributes:

Name	Type	Description
id	int	Primary key.
tax_id	int	NCBI taxonomy Identifier.
name	str	Name associated with the tax_id.
name_type	str	Type of the name (e.g., scientific name, common name, synonym).

Source code in src/biokb_coconut/db/models.py

class TaxonomyName(Base):
    """Class definition for table taxonomy_name. Name from
    NCBI taxonomy https://www.ncbi.nlm.nih.gov/taxonomys.

    Attributes:
        id (int): Primary key.
        tax_id (int): NCBI taxonomy Identifier.
        name (str): Name associated with the tax_id.
        name_type (str): Type of the name (e.g., scientific name, common name, synonym).
    """

    __tablename__ = Base.table_prefix + "taxonomy_name"
    id: Mapped[int] = mapped_column(primary_key=True)
    tax_id: Mapped[int] = mapped_column(index=True, comment="NCBI taxonomy Identifier")
    name: Mapped[str] = mapped_column(Text)
    name_type: Mapped[str] = mapped_column(String(255), index=True)

    __table_args__ = (
        Index(
            f"ix_{__tablename__}__name",
            name,
            mysql_length=255,
        ),
    )

    def __repr__(self) -> str:
        return f"<TaxonomyName(id={self.id}, tax_id={self.tax_id}, name={self.name}, name_type={self.name_type})>"

WCVPPlant

Bases: Base

Class definition for table wcvp_plant. Plant names from World Checklist of Vascular Plants (WCVP).

Attributes:

Name	Type	Description
plant_name_id	int	Primary key.
taxon_name	Optional[str]	Taxon name of the plant.
accepted_plant_name_id	Optional[int]	Accepted plant name identifier.
powo_id	Optional[str]	POWO identifier.

Source code in src/biokb_coconut/db/models.py

class WCVPPlant(Base):
    """Class definition for table wcvp_plant. Plant names from
    World Checklist of Vascular Plants (WCVP).

    Attributes:
        plant_name_id (int): Primary key.
        taxon_name (Optional[str]): Taxon name of the plant.
        accepted_plant_name_id (Optional[int]): Accepted plant name identifier.
        powo_id (Optional[str]): POWO identifier.
    """

    __tablename__ = Base.table_prefix + "wcvp_plant"
    plant_name_id: Mapped[int] = mapped_column(primary_key=True)
    taxon_name: Mapped[Optional[str]] = mapped_column(String(1000))
    accepted_plant_name_id: Mapped[Optional[int]] = mapped_column(index=True)
    powo_id: Mapped[Optional[str]] = mapped_column(String(255))

    __table_args__ = (
        Index(
            f"ix_{__tablename__}__taxon_name",
            "taxon_name",
            mysql_length=768,
        ),
    )

    def __repr__(self) -> str:
        return f"<WCVPPlant(plant_name_id={self.plant_name_id}, taxon_name={self.taxon_name})>"