# The MIT License (MIT)
#
# Copyright (c) 2019, Moritz E. Beber.
# Copyright (c) 2018 Institute for Molecular Systems Biology, ETH Zurich.
# Copyright (c) 2018 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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# THE SOFTWARE.
"""Provide a compound ORM model."""
from typing import List, Optional
from sqlalchemy import Column, Float, String
from sqlalchemy.orm import relationship
from . import CompoundAnnotation, CompoundName
from .base import Base
[docs]class Compound(Base):
"""
Define a compound ORM model.
Attributes
----------
inchi : str, optional
inchi_key : str, optional
smiles : str, optional
chemical_formula : str, optional
charge : float, optional
mass : float, optional
notes : str, optional
names : list of cobra_component_models.orm.CompoundName, optional
annotation : list of cobra_component_models.orm.CompoundAnnotation, optional
"""
__tablename__ = "compounds"
inchi: Optional[str] = Column(String, nullable=True, index=True, unique=True)
inchi_key: Optional[str] = Column(
String(27), nullable=True, index=True, unique=True
)
smiles: Optional[str] = Column(String, nullable=True, index=True)
chemical_formula: Optional[str] = Column(String, nullable=True, index=True)
charge: Optional[float] = Column(Float, nullable=True)
mass: Optional[float] = Column(Float, nullable=True)
notes: Optional[str] = Column(String, nullable=True)
names: List[CompoundName] = relationship("CompoundName")
annotation: List[CompoundAnnotation] = relationship("CompoundAnnotation")
[docs] def __repr__(self):
"""Return a string representation of the object."""
return f"{type(self).__name__}(id={self.id}, inchi_key={self.inchi_key})"