kinoml.core.systems

System objects define a collection of related MolecularComponent instances. They are normally attached to a Measurement, and, in the context of a machine learning exercise, will be featurized with different classes found under kinoml.features. Featurization turns a System into a tensor-like object, like Numpy arrays.

Module Contents

class kinoml.core.systems.System(components: Iterable[kinoml.core.components.MolecularComponent], strict: bool = True, *args, **kwargs)

System objects host one or more MolecularComponent.

Parameters:

• components (list of MolecularComponent) – Molecular entities defining this system

• strict (bool, optional=True) – Whether to perform sanity checks (default) or not.

featurizations

This dictionary will store the different featurization steps a System is submitted to. The keys for this dictionary are usually the name of the featurizer class. Additionally, a Pipeline might define a last key, indicating that particular object was the final result of a chain of featurizers.

Type:

dict

components

featurizations

_components_by_type(type_)

Yield MolecularComponent objects of a given type only

check()

property name: str

Generates a readable name out of the components names

property weight: float

Calculate the molecular weight of the system

Note: This is just an example on how/why this level of abstraction can be useful.

__repr__() → str

class kinoml.core.systems.ProteinSystem(components: Iterable[kinoml.core.components.MolecularComponent], strict: bool = True, *args, **kwargs)

Bases: System

A System that contains Protein objects. It defines two properties:

• protein: get the first Protein found in the components

• proteins: get all Protein objects found in the components

property protein

property proteins

check()

class kinoml.core.systems.LigandSystem(components: Iterable[kinoml.core.components.MolecularComponent], strict: bool = True, *args, **kwargs)

Bases: System

A System that contains Ligand objects. It defines two properties:

• ligand: get the first Ligand found in the components

• ligands: get all Ligand objects found in the components

property ligand

property ligands

check()

class kinoml.core.systems.ProteinLigandComplex(components: Iterable[kinoml.core.components.MolecularComponent], strict: bool = True, *args, **kwargs)

Bases: ProteinSystem, LigandSystem

A system with at least one protein and one ligand

check()