schrodinger.livedesign.custom_entity.registration module¶

This file contains the registration logic for custom entities.

General Description:

This module retrieves the RegistrationData objects for custom entities.

Common Registration Examples:

You can use this module to register:

Example 1: Monospecific Antibody An antibody with one unique heavy chain, one unique light chain, one unique antibody arm and a full antibody (containing two duplicate arms)
Example 2: Bispecific Antibody An antibody with one or two unqiue heavy chains, one or two unique light chains, two unique antibody arms and a full antibody (containing two unique arms)
Example 3: ADC An antibody-drug conjugate with a small molecule, a link and a full antibody (either monospecific or bispecific described above)
Example 4: OLED An OLED with layer(s) that contain formulation(s).

A general example can be formulated using the following template:

general_entity = {

‘entity_type’: <A known entity from the EntityClass>, ‘input_property_data’: <A dictionary describing any/all additional input data>, ‘chemical_information’: <A representation of the chemical information (SMILES string, Helm string, etc)> ‘children’: [(child_entity, <Number of repeating child entities>)]

}

The child_entity can be described using the general entity example. When there are no children, an empty list can be provided or the key/value pair omitted.

Unsupported Features:

Currently, this module does not support entities that do not have a corresponding EntityClass. However, custom entities can be constructed and designed using ‘Unknown’ EntityClass types.

class schrodinger.livedesign.custom_entity.registration.EntityComponent¶

Bases: StrEnum

ENTITY_TYPE = 'entity_type'¶

INPUT_PROPERTY_DATA = 'input_property_data'¶

CHEMICAL_INFORMATION = 'chemical_information'¶

CHILDREN = 'children'¶

COUNT = 'self_count'¶

class schrodinger.livedesign.custom_entity.registration.ChildDataComponent¶

Bases: StrEnum

COUNT = 'count'¶

class schrodinger.livedesign.custom_entity.registration.InputPropertyDataComponent¶

Bases: StrEnum

THICKNESS = 'thickness'¶

ID = 'ID'¶

schrodinger.livedesign.custom_entity.registration.get_registration_data(data: str, input_format: Format, options: Optional[RegistrationOptions] = None) → Iterator[RegistrationData]¶

schrodinger.livedesign.custom_entity.registration.extract_registration_data(entity: dict) → Iterator[RegistrationData]¶

Given a stack of dictionaries, yield RegistrationData objects.

Parameters:: entity – The dictionary stack.
Returns:: An iterator of RegistrationData objects.

schrodinger.livedesign.custom_entity.registration.get_rdmol(chemical_information: str) → str¶

Given a chemical information string, return the corresponding RDKit molecule in binary base64 format.

Parameters:: chemical_information – The chemical information string.
Returns:: The corresponding RDKit molecule in binary base64 format.

schrodinger.livedesign.custom_entity.registration.get_chemical_model(rdmol_binary: str) → Mol¶

Given a rdmol_binary string, return the corresponding chemical model.

Parameters:: rdmol_binary – The rdmol_binary string.
Returns:: The corresponding chemical model.

schrodinger.livedesign.custom_entity.registration.get_deduplication_hash(entity: dict) → str¶

Given a dictionary that describes an entity, return the corresponding deduplication hash.

Parameters:: entity – The entity dictionary.
Returns:: The corresponding deduplication hash.

schrodinger.livedesign.custom_entity.registration.get_canonical_entity(entity: dict) → dict¶

Given an entity dictionary, return the corresponding canonical entity dictionary.

Parameters:: entity – The entity dictionary.
Returns:: The corresponding canonical entity dictionary.

schrodinger.livedesign.custom_entity.registration.remove_non_deduplication_keys(entity: dict, deduplication_hash_keys: set) → None¶

Given an entity dictionary, remove all keys that are not used for deduplication.

Parameters:: entity – The entity dictionary.

schrodinger.livedesign.custom_entity.registration.get_display_string(chemical_model: Mol) → str¶

Given a chemical model, return the corresponding display string.

Parameters:: chemical_model – The chemical model.
Returns:: The corresponding display string.

schrodinger.livedesign.custom_entity.registration.get_entity_class(entity_type: str) → EntityClass¶

Given a string entity type, return the corresponding EntityClass enum.

Parameters:: entity_type – The string entity type.
Returns:: The corresponding EntityClass enum.

schrodinger.livedesign.custom_entity.registration.validate_registration_data(registration_data: RegistrationData) → None¶

Validate the registration data.

Parameters:: registration_data – The registration data.