schrodinger.livedesign.entity_registration.classification module

schrodinger.livedesign.entity_registration.classification.ANTIBODY_MONOMER_CLASSES = {'ANTIBODY_HEAVY_FAB', 'ANTIBODY_HEAVY_FAB_PRIME', 'ANTIBODY_HEAVY_FULL', 'ANTIBODY_HEAVY_FV', 'ANTIBODY_LIGHT_FAB', 'ANTIBODY_LIGHT_FV'}

The polymer graph is used to represent the graph of polymers and how they are connected to each other so that the classification logic can make decisions based on connectivity (such as light-heavy-heavy-light for antibodies). The FROM_ANNOTATION key may be present to indicate that the polymer graph was constructured from extended annotations, meaning full connectivity information may be missing.

class schrodinger.livedesign.entity_registration.classification.EntityTree(mol, children, entity_class='UNKNOWN_BIOLOGIC', simple_polymer_id=None, monomer_string=None, polymer_label=None)

Bases: object

__init__(mol, children, entity_class='UNKNOWN_BIOLOGIC', simple_polymer_id=None, monomer_string=None, polymer_label=None)

schrodinger.livedesign.entity_registration.classification.classify_antibody(antibody_type: str, region_names: list[str]) → EntityClass

schrodinger.livedesign.entity_registration.classification.classify_protein(sequence) → str

schrodinger.livedesign.entity_registration.classification.light_heavy_heavy_light(lcs, hcs, polymer_graph) → bool

Check if the given light and heavy chains are connected in light - heavy - heavy - light order.

Parameters:

• lcs – list of light chain entity tree nodes

• hcs – list of heavy chain entity tree nodes

• polymer_graph – the graph of connected polymer chains

Returns:

True if the chains are connected in light - heavy - heavy - light order, False otherwise

schrodinger.livedesign.entity_registration.classification.classify_ab_parent(parent_node: EntityTree, polymer_graph: Dict[str, Set[str]] = None) → str

Given a parent entity tree node, classify its overall entity class based on its children’s entity classes.

Parameters:

parent_node – the parent entity tree node

Returns:

the overall entity class of the parent node

schrodinger.livedesign.entity_registration.classification.classify_na_parent(parent_node: EntityTree) → str

Given a parent entity tree node, classify its overall entity class based on its children’s entity classes.

Parameters:

parent_node – the parent entity tree node

Returns:

the overall entity class of the parent node