ovo.core.logic.design_logic

Module Contents

Functions

get_design_jobs_table	Get pandas DataFrame with job and pool metadata and workflow parameter information.
get_pools_table
format_pool_status
get_workflows_table	Get pandas DataFrame with workflow parameter information for each pool.
submit_design_workflow	Submit a design workflow to the scheduler and create a Pool and DesignJob in the DB.
get_log	Get the log of a design job from the scheduler.
get_tasks	Get design job tasks table from the scheduler.
process_results	Process the results of a design job and return the pool object.
update_acceptance_thresholds	Update the accepted designs in a pool based on the given acceptance thresholds.
update_accepted_design_ids
set_designs_accepted	Update the accepted field of designs based on the given thresholds (does not save to DB)
collect_storage_paths	Collect storage paths from designs based on fields returned by DesignWorkflow.get_download_fields().
create_designs_from_dataframe	Create Design objects from a DataFrame.
create_designs_from_structure_files
get_common_chain_ids	Get chain IDs that exist across all provided designs’ specs

API

ovo.core.logic.design_logic.get_design_jobs_table(project_id: str = None, round_ids: list[str] = None, update=True, **pool_filters) → pandas.DataFrame

Get pandas DataFrame with job and pool metadata and workflow parameter information.

ovo.core.logic.design_logic.get_pools_table(project_id: str = None, round_ids: list[str] = None)

ovo.core.logic.design_logic.format_pool_status(job: ovo.core.database.models.DesignJob, processed: bool, update_status: bool = True)

ovo.core.logic.design_logic.get_workflows_table(jobs: list[ovo.core.database.models.DesignJob])

Get pandas DataFrame with workflow parameter information for each pool.

ovo.core.logic.design_logic.submit_design_workflow(workflow: ovo.core.database.models.Workflow, scheduler_key: str, round_id: str, pool_name: str, pool_description: str, return_existing: bool = True, pipeline_name: str = None, resume_failed: bool = False, submission_args: dict = None) → tuple[ovo.core.database.models.DesignJob, ovo.core.database.models.Pool]

Submit a design workflow to the scheduler and create a Pool and DesignJob in the DB.

Parameters:

• workflow – Workflow object to submit

• scheduler_key – Key of the scheduler to use

• round_id – ID of the Round to associate the Pool with

• pool_name – Name of the Pool to create

• pool_description – Description of the Pool to create

• return_existing – If a Pool with the same name and parameters already exists in this round, return it instead of raising an error

• pipeline_name – Override the pipeline name to submit, e.g. ovo.rfdiffusion-end-to-end or a github url with @version

• resume_failed – If a Pool with the same name already exists in this round but its job has failed, submit the job again.

• submission_args – Extra submission arguments to override in the scheduler, e.g. {“profile”: “conda”} or {“stub”: True}

Returns:

Tuple of (DesignJob, Pool)

ovo.core.logic.design_logic.get_log(design_job: ovo.core.database.models.DesignJob, task_id: str = None, preview: bool = False, tail: int = None) → str

Get the log of a design job from the scheduler.

ovo.core.logic.design_logic.get_tasks(design_job: ovo.core.database.models.DesignJob) → pandas.DataFrame

Get design job tasks table from the scheduler.

ovo.core.logic.design_logic.process_results(design_job: ovo.core.database.models.DesignJob, callback: Callable = None, wait=True) → ovo.core.database.models.Pool

Process the results of a design job and return the pool object.

This downloads/copies the workflow results into Storage and saves the Design and DescriptorValue objects to the database.

ovo.core.logic.design_logic.update_acceptance_thresholds(pools: list[ovo.core.database.models.Pool], acceptance_thresholds: dict[str, ovo.core.database.models.Threshold])

Update the accepted designs in a pool based on the given acceptance thresholds.

Save the Design objects and the DesignJob.workflow.acceptance_thresholds to the DB.

ovo.core.logic.design_logic.update_accepted_design_ids(pool_ids: list[str], accepted_design_ids: list[str])

ovo.core.logic.design_logic.set_designs_accepted(designs: list[ovo.core.database.models.Design], descriptor_values: list[ovo.core.database.models.DescriptorValue], job: ovo.core.database.models.DesignJob, no_warning_for_missing_prefix: str | tuple = None)

Update the accepted field of designs based on the given thresholds (does not save to DB)

Makes the following modifications IN PLACE:

• If a threshold is enabled but its descriptor values are missing:

  • set threshold.enabled to False

  • add a warning in the DesignJob job.warnings

• Update the accepted field of each design based on whether it passes the thresholds or not.

Parameters:

• designs – List of Design objects to update

• descriptor_values – List of DescriptorValue objects to use for checking thresholds

• job – DesignJob object

• no_warning_for_missing_prefix – Do not add a warning for missing descriptor keys that start with this prefix/prefixes

ovo.core.logic.design_logic.collect_storage_paths(download_fields: dict[str, tuple[ovo.core.database.models.Base, str]], design_ids: list) → list[str]

Collect storage paths from designs based on fields returned by DesignWorkflow.get_download_fields().

ovo.core.logic.design_logic.create_designs_from_dataframe(df: pandas.DataFrame, id_column: str, column_chains: dict[str, str], pool_id: str) → list[ovo.core.database.models.Design]

Create Design objects from a DataFrame.

Args: df: pandas DataFrame with design data id_column: column name to use as design ID column_chains: mapping of column names to chain IDs (e.g., {“seq_A”: “A”, “seq_B”: “B”}) pool_id: pool ID for the designs

Returns: list of Design objects

ovo.core.logic.design_logic.create_designs_from_structure_files(structure_files: list, chains: list[str], pool: ovo.core.database.models.Pool, project_id: str) → tuple[list[ovo.core.database.models.Design], list[str]]

ovo.core.logic.design_logic.get_common_chain_ids(design_ids: list[str]) → tuple[list[str], list[str]]

Get chain IDs that exist across all provided designs’ specs