genome_entropy.encode3di.types

Data types for 3Di encoding.

Classes

IndexedSeq(idx, seq)	A sequence paired with its original position in the input list.
ThreeDiRecord(protein, three_di, method, ...)	Represents a 3Di structural encoding of a protein.

class genome_entropy.encode3di.types.ThreeDiRecord(protein, three_di, method, model_name, inference_device)

Represents a 3Di structural encoding of a protein.

Parameters:

• protein (ProteinRecord)

• three_di (str)

• method (Literal['prostt5_aa2fold'])

• model_name (str)

• inference_device (str)

protein

The ProteinRecord that was encoded

Type:

genome_entropy.translate.translator.ProteinRecord

three_di

The 3Di token sequence

Type:

str

method

Method used for encoding (always “prostt5_aa2fold”)

Type:

Literal[‘prostt5_aa2fold’]

model_name

Name of the ProstT5 model used

Type:

str

inference_device

Device used for inference (“cuda”, “mps”, or “cpu”)

Type:

str

protein: ProteinRecord

three_di: str

method: Literal['prostt5_aa2fold']

model_name: str

inference_device: str

__init__(protein, three_di, method, model_name, inference_device)

Parameters:

• protein (ProteinRecord)

• three_di (str)

• method (Literal['prostt5_aa2fold'])

• model_name (str)

• inference_device (str)

Return type:

None

class genome_entropy.encode3di.types.IndexedSeq(idx, seq)

A sequence paired with its original position in the input list.

Parameters:

• idx (int)

• seq (str)

idx: int

seq: str

__init__(idx, seq)

Parameters:

• idx (int)

• seq (str)

Return type:

None