Molecule

class specatalog.models.molecules.Molecule(**kwargs)[source]

Base clase representing a molecule.

This class represents a chemical molecule, including both basic descriptive metadata (name, molecular formula) and a structural representation. It serves as the base class for a polymorphic hierarchy of molecule types, enabling specialised subclasses to extend the core attributes defined here.

The measurements relationship links each molecule to all associated spectroscopic measurements, with deletions cascading automatically to dependent measurement entries.

id

Primary key of the molecule entry.

Type:: int

name

Human-readable molecular name. Must be unique.

Type:: str

molecular_formula

Standard chemical formula such as C20H14O.

Type:: str

structural_formula

Path to a file with the structural formula (e.g. .cdx and .pdf format). The file should be saved at /molecules/MOLxy. Must be unique.

Type:: str

measurements

All spectroscopic measurements associated with this molecule.

Type:: list[Measurement]

additional_info

Optional free-text field containing supplementary information about the molecule.

Type:: str or None

group

Polymorphic discriminator used by SQLAlchemy to select the correct molecule subclass upon loading.

Type:: str

Notes

The tablename is molecules.
This class forms the base of a polymorphic SQLAlchemy hierarchy.
Subclasses define their own polymorphic_identity values.
The measurements relationship uses passive_deletes=True so that deleting a molecule cascades to related measurement entries automatically.
Timestamp fields created_at and updated_at are inherited from TimeStampedModel.

Examples

Creating a molecule:

>>> from models import Molecule
>>> mol = Molecule(
...     name="Perylene",
...     molecular_formula="C20H12",
...     structural_formula="/molecule/MOL5",
...     group="base",
... )
>>> session.add(mol)
>>> session.commit()

Accessing linked measurements:

>>> mol = session.get(Molecule, 5)
>>> mol.measurements
[Measurement(...), TREPR(...), PulseEPR(...)]