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, aPipeline
might define alast
key, indicating that particular object was the final result of a chain of featurizers.- Type
dict
- 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.
- _components_by_type(type_)¶
Yield MolecularComponent objects of a given type only
- check()¶
- __repr__() str ¶
Return repr(self).
- 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 componentsproteins
: 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 componentsligands
: 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()¶