Source code for openprotein.align.schemas
"""Schemas for OpenProtein align system."""
from enum import Enum
from typing import Literal
from pydantic import BaseModel, Field
from openprotein.jobs import Job, JobType
class AlignType(str, Enum):
"""
Enumeration of alignment types.
Attributes
----------
INPUT : str
Raw input alignment.
MSA : str
Generated multiple sequence alignment.
PROMPT : str
Prompt-based alignment.
"""
INPUT = "RAW"
MSA = "GENERATED"
PROMPT = "PROMPT"
class MSASamplingMethod(str, Enum):
"""
Enumeration of MSA sampling methods.
Attributes
----------
RANDOM : str
Random sampling.
NEIGHBORS : str
Sampling based on neighbors.
NEIGHBORS_NO_LIMIT : str
Neighbor sampling without limit.
NEIGHBORS_NONGAP_NORM_NO_LIMIT : str
Neighbor sampling without gap normalization and without limit.
TOP : str
Top scoring sampling.
"""
RANDOM = "RANDOM"
NEIGHBORS = "NEIGHBORS"
NEIGHBORS_NO_LIMIT = "NEIGHBORS_NO_LIMIT"
NEIGHBORS_NONGAP_NORM_NO_LIMIT = "NEIGHBORS_NONGAP_NORM_NO_LIMIT"
TOP = "TOP"
class PromptPostParams(BaseModel):
"""
Parameters for posting a prompt to generate an MSA.
Attributes
----------
msa_id : str
Identifier for the MSA.
num_sequences : int or None, optional
Number of sequences to sample (default is None, must be >=0 and <100).
num_residues : int or None, optional
Number of residues to sample (default is None, must be >=0 and <24577).
method : MSASamplingMethod, optional
Sampling method to use (default is NEIGHBORS_NONGAP_NORM_NO_LIMIT).
homology_level : float, optional
Homology level threshold (default is 0.8, must be between 0 and 1).
max_similarity : float, optional
Maximum similarity threshold (default is 1.0, must be between 0 and 1).
min_similarity : float, optional
Minimum similarity threshold (default is 0.0, must be between 0 and 1).
always_include_seed_sequence : bool, optional
Whether to always include the seed sequence (default is False).
num_ensemble_prompts : int, optional
Number of ensemble prompts to generate (default is 1).
random_seed : int or None, optional
Random seed for reproducibility (default is None).
"""
msa_id: str
num_sequences: int | None = Field(None, ge=0, lt=100)
num_residues: int | None = Field(None, ge=0, lt=24577)
method: MSASamplingMethod = MSASamplingMethod.NEIGHBORS_NONGAP_NORM_NO_LIMIT
homology_level: float = Field(0.8, ge=0, le=1)
max_similarity: float = Field(1.0, ge=0, le=1)
min_similarity: float = Field(0.0, ge=0, le=1)
always_include_seed_sequence: bool = False
num_ensemble_prompts: int = 1
random_seed: int | None = None
class MSAJob(Job):
"""
Base class for MSA-related jobs.
Attributes
----------
job_type : Literal[JobType.align_align]
The type of job (must be JobType.align_align).
"""
job_type: Literal[JobType.align_align]
@property
def msa_id(self):
"""
Returns the MSA identifier for this job.
Returns
-------
str
The MSA identifier.
"""
return self.msa_id
class MafftJob(MSAJob, Job):
"""
Job for running MAFFT alignment.
Attributes
----------
job_type : Literal[JobType.mafft]
The type of job (must be JobType.mafft).
"""
job_type: Literal[JobType.mafft]
class ClustalOJob(MSAJob, Job):
"""
Job for running Clustal Omega alignment.
Attributes
----------
job_type : Literal[JobType.clustalo]
The type of job (must be JobType.clustalo).
"""
job_type: Literal[JobType.clustalo]
class AbNumberJob(MSAJob, Job):
"""
Job for running AbNumber alignment.
Attributes
----------
job_type : Literal[JobType.abnumber]
The type of job (must be JobType.abnumber).
"""
job_type: Literal[JobType.abnumber]
[docs]
class AbNumberScheme(str, Enum):
"""Antibody numbering scheme."""
IMGT = "imgt"
CHOTHIA = "chothia"
KABAT = "kabat"
AHO = "aho"
