Functional Tags for Monomers in QSPy

In QSPy, functional tags annotate monomers with biologically or computationally meaningful labels. These tags express a class/function relationship—such as marking a species as a receptor, adding additional expressiveness to model species while also supporting another way to filter monomers.

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Tagging Semantics

• Tags indicate class and function/subclass roles.
• Each monomer can have a single tag.
• Tags improve:
• Model expressiveness
• Filtering by biological function

Functional tags are in all caps and have the following pattern in model definitions:

CLASS.FUNCTION

Python Example

    with monomers():
        drug = (['b'], None, DRUG.INHIBITOR)

Functional tags are accesible by a monomer's functional_tag attribute:

>>> print(drug.functional_tag)

FunctionalTag(class_='drug', function='inhibitor')

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Recognized Classes and Functions

The table below lists standardized tags currently used in QSPy.

Class Tag	Function/Subclass	Description
DRUG	SMALL_MOLECULE, BIOLOGIC, ANTIBODY, MAB, INHIBITOR, AGONIST, ANTAGONIST, INVERSE_AGONIST, MODULATOR, ADC, RLT, PROTAC, IMMUNOTHERAPY, CHEMOTHERAPY	Therapeutic agents
PROTEIN	LIGAND, RECEPTOR, RECEPTOR_DECOY, KINASE, PHOSPHATASE, ADAPTOR, TRANSCRIPTION_FACTOR, ENZYME, ANTIBODY	Biologically active protein-based macromolecules
RNA	MESSENGER, MICRO, SMALL_INTERFERING, LONG_NONCODING	Transcribed nucleic acids involved in gene expression, regulation, or signal propagation
METABOLITE	SUBSTRATE, PRODUCT, COFACTOR	Small molecules involved in biochemical reactions, such as intermediates, reactants, and regulatory modulators
LIPID	EICOSANOID, PHOSPHOLIPID, GLYCOLIPID, STEROL	Hydrophobic or amphipathic molecules involved in signaling or other biological functions
ION	CALCIUM, CHLORIDE, MAGNESIUM, SODIUM, POTASSIUM	Charged atoms or small molecules involved in electrochemical signaling, osmotic balance, and catalysis
NANOPARTICLE	DRUG_DELIVERY, IMAGING, SENSING, THERMAL, THERANOSTIC	Engineered nanoscale particles designed for targeted delivery, imaging enhancement, or localized therapeutic functions

Custom tags

Users can define custom tags. For consistency, follow the schema above when possible.

Functional tags are subclasses of the enum.Enum object and can be defined as below:

from enum import Enum
from qspy.functionaltags import prefixer

MY_TAG_PREFIX = "mytag"
class MY_TAG(Enum):
    FUNCTION = prefixer("function", MY_TAG_PREFIX)
    SUBCLASS = prefixer("subclass", MY_TAG_PREFIX)

Then, you can use the custom tag like any other:

with monomers():
    A = (None, None, MY_TAG.FUNCTION)

Monomer('B') @ MY_TAG.SUBCLASS

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