RDiffusion/src/utils/inference_types.py at main · A4Bio/RDiffusion · GitHub

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from dataclasses import dataclass
from typing import List, Optional, Sequence, Union

import torch


TargetType = Union[int, Sequence[int], None]
TaskType = str


@dataclass
class RfamCondition:
    label: Optional[int] = None
    func_cond: Optional[Union[str, List[str]]] = None


@dataclass
class ProteinCondition:
    targets: Optional[List[int]] = None
    func_cond: Optional[Union[str, List[str]]] = None
    seq_cond: Optional[torch.Tensor] = None


@dataclass
class DiseaseCondition:
    label: Optional[int] = None
    func_cond: Optional[Union[str, List[str]]] = None


@dataclass
class TextCondition:
    func_cond: Optional[Union[str, List[str]]] = None


@dataclass
class SSCondition:
    secondary_structure: Optional[str] = None
    icshape: Optional[str] = None
    seq_cond: Optional[torch.Tensor] = None


@dataclass
class TSCondition:
    seq_cond: Optional[torch.Tensor] = None
    reference_sequence: Optional[str] = None
    pdb_path: Optional[str] = None


@dataclass
class CAS13Condition:
    target_before: Optional[str] = None
    target_at_guide: Optional[str] = None
    target_after: Optional[str] = None
    guide_seq: Optional[str] = None


@dataclass
class ConditionBundle:
    rfam: RfamCondition
    proteins: ProteinCondition
    disease: DiseaseCondition
    text: TextCondition
    ss: SSCondition
    ts: TSCondition
    cas13: CAS13Condition


@dataclass
class GuidanceConfig:
    guidance_scale: float = 1.0
    update_all: bool = True
    use_gumbel: bool = False
    update_by_guide: bool = False
    argmax: bool = False
    use_best: bool = True
    constrain_logits: bool = False


GUIDE_LENGTH = 28
TARGET_CONTEXT_LENGTH = 20
TARGET_WINDOW_LENGTH = 28
GUIDE_PADDING_LENGTH = 20
TARGET_SEQUENCE_LENGTH = TARGET_CONTEXT_LENGTH + TARGET_WINDOW_LENGTH + TARGET_CONTEXT_LENGTH
GUIDE_EXTENDED_LENGTH = GUIDE_PADDING_LENGTH + GUIDE_LENGTH + GUIDE_PADDING_LENGTH
MODEL_SEQUENCE_LENGTH = TARGET_SEQUENCE_LENGTH + GUIDE_EXTENDED_LENGTH