ovo.core.database.models_clustering

Module Contents

Classes

ProteinClusteringWorkflow	Class that provides abstraction for protein clustering workflows and defines necessary variables for all clustering methods.
ProteinClusteringTool
FoldseekParams
FoldseekClusteringWorkflow

Data

FOLDSEEK_UMAP_PIPELINE
PROTEIN_CLUSTERING_TOOLS
PROTEIN_CLUSTERING_TOOLS_BY_KEY
CLUSTERING_WORKFLOWS_BY_TOOL_KEY

API

class ovo.core.database.models_clustering.ProteinClusteringWorkflow

Bases: ovo.core.database.models.DescriptorWorkflow

Class that provides abstraction for protein clustering workflows and defines necessary variables for all clustering methods.

n_neighbors: List[int]

‘field(…)’

tool_key: str | None

None

params: ovo.core.database.models.WorkflowParams

‘field(…)’

classmethod get_registered_workflow_names() → list[str]

Get all registered workflow names that are ProteinClusteringWorkflow subclasses

validate()

class ovo.core.database.models_clustering.ProteinClusteringTool

name: str

None

tool_key: str

None

supports_conda: bool

False

ovo.core.database.models_clustering.FOLDSEEK_UMAP_PIPELINE

‘ProteinClusteringTool(…)’

class ovo.core.database.models_clustering.FoldseekParams

Bases: ovo.core.database.models.WorkflowParams

e: float

10.0

alignment_type: int

2

c: float

0.0

tmscore_threshold: float

0.0

exhaustive_search: bool

False

embedding_metric: str

‘qtmscore’

min_seq_id: float

0.0

s: float

9.5

class ovo.core.database.models_clustering.FoldseekClusteringWorkflow

Bases: ovo.core.database.models_clustering.ProteinClusteringWorkflow

tool_key: str

None

designs_target: List[ovo.core.database.models.Design]

‘field(…)’

params: ovo.core.database.models_clustering.FoldseekParams

‘field(…)’

get_pipeline_name() → str

prepare_params(workdir: str) → dict

process_results(job: ovo.core.database.DescriptorJob, callback: Callable = None)

validate()

ovo.core.database.models_clustering.PROTEIN_CLUSTERING_TOOLS

None

ovo.core.database.models_clustering.PROTEIN_CLUSTERING_TOOLS_BY_KEY

None

ovo.core.database.models_clustering.CLUSTERING_WORKFLOWS_BY_TOOL_KEY

None