workflow

`list_lcc_files(session_dir)`

List all lcc.mrc files in the PowerFit runs in the session directory.

Parameters:

Name	Type	Description	Default
`session_dir`	`Path`	Directory containing the session data.	required

Yields:

Type	Description
`Generator[tuple[str, str, Path]]`	Tuples containing the run ID, structure name, and path to the lcc.mrc

`powerfit_commands(target, resolution, session_dir, /, *, options, powerfit_run_id=None)`

Generate PowerFit commands for structure files in the session directory.

Parameters:

Name	Type	Description	Default
`target`	`Path`	Target density map to fit the model in. Data should either be in CCP4 or MRC format	required
`resolution`	`float`	Resolution of map in Angstrom	required
`session_dir`	`Path`	Session directory for input and output	required
`options`	`PowerfitOptions`	Powerfit options.	required
`powerfit_run_id`	`str \| None`	ID of the PowerFit run to use. If not provided, will autoincrement based on existing runs.	`None`

Raises:

Type	Description
`FileNotFoundError`	If no structure files are found in the session directory.
`FileExistsError`	If the PowerFit run directory already exists.

Returns:

Type	Description
`tuple[list[str], str]`	A tuple containing a list of PowerFit commands and the PowerFit run ID.

`powerfit_filtered_report(session_dir, powerfit_run_id=None, top=1, group_by_structure=True)`

Return PowerFit solutions filtered by rank and grouping mode.

Parameters:

Name	Type	Description	Default
`session_dir`	`Path`	Directory containing the session data.	required
`powerfit_run_id`	`str \| None`	Optional ID of the PowerFit run to report. If None, reports over all runs.	`None`
`top`	`int`	Number of top solutions to return.	`1`
`group_by_structure`	`bool`	Whether to group solutions by structure before selecting top solutions.	`True`

Raises:

Type	Description
`FileNotFoundError`	If no structure files are found in the session directory.

Returns:

Type	Description
`DataFrame`	A DataFrame containing the filtered PowerFit solutions.

`powerfit_fit_models(session_dir, powerfit_run_id=None, top=1, group_by_structure=True)`

Fit models using PowerFit solutions.

Parameters:

Name	Type	Description	Default
`session_dir`	`Path`	Directory containing the session data.	required
`powerfit_run_id`	`str \| None`	Optional ID of the PowerFit run to report. If None, reports over all runs.	`None`
`top`	`int`	Number of top solutions to fit.	`1`
`group_by_structure`	`bool`	Whether to group solutions by structure before selecting top solutions.	`True`

Raises:

Type	Description
`FileNotFoundError`	If no structure files are found in the session directory.

Returns:

Type	Description
`DataFrame`	A DataFrame containing following columns: powerfit_run_id: ID of the PowerFit run structure: Name of the structure file rank: Rank of the solution fitted_model_file: Path to the fitted model file unfitted_model_file: Path to the unfitted model file Dataframe is written to `<session_dir>/powerfit/fitted_models.csv` with paths relative to session dir.

`powerfit_list_runs(session_dir)`

List all PowerFit runs in the session directory.

Parameters:

Name	Type	Description	Default
`session_dir`	`Path`	Directory containing the session data.	required

Raises:

Type	Description
`FileNotFoundError`	If no density map is found in any run directory.

Returns:

Type	Description
`list[RunInfo]`	A list of RunInfo dictionaries for each PowerFit run.

`powerfit_report(session_dir, powerfit_run_id=None)`

Return a DataFrame containing the PowerFit solutions.

Parameters:

Name	Type	Description	Default
`session_dir`	`Path`	Directory containing the session data.	required
`powerfit_run_id`	`str \| None`	Optional ID of the PowerFit run to report. If None,	`None`

Raises:

Type	Description
`FileNotFoundError`	If no structure files are found in the session directory.

Returns:

Type Description

DataFrame

A DataFrame containing the PowerFit solutions. With following columns:

powerfit_run_id: ID of the PowerFit run
structure: Name of the structure file
rank: Rank of the solution
cc: Cross-correlation coefficient of the solution
fishz: FishZ score of the solution
relz: Relative Z-score of the solution
translation: Translation vector of the solution
rotation: Rotation matrix of the solution
template_file: Path to the template structure file, relative to the session directory
uniprot_accessions: Comma-separated list of UniProt accessions
structure_id: Structure ID of the template structure
is_alphafold: Whether the template structure comes from AlphaFoldDB

`powerfit_run_options_from_rocrate(session_dir)`

Extract PowerFit run options from the RO-Crate metadata.

Parameters:

Name	Type	Description	Default
`session_dir`	`Path`	Directory containing the session data.	required

Raises:

Type	Description
`FileNotFoundError`	If the RO-Crate file is missing from the session directory.

Returns:

Type	Description
`dict[str, str]`	A dictionary mapping PowerFit run IDs to their corresponding options.

`powerfit_runs(target, resolution, session_dir, /, *, options, powerfit_run_id=None, scheduler_address=None)`

Run PowerFit on PDB files in the session directory and store results.

Parameters:

Name	Type	Description	Default
`target`	`Path`	Target density map to fit the model in. Data should either be in CCP4 or MRC format	required
`resolution`	`float`	Resolution of map in Angstrom	required
`session_dir`	`Path`	Session directory for input and output	required
`options`	`PowerfitOptions`	Powerfit options.	required
`powerfit_run_id`	`str \| None`	ID of the PowerFit run to use. If not provided, will autoincrement based on existing runs.	`None`
`scheduler_address`	`str \| Cluster \| None`	Address of the Dask scheduler to use. If not provided, will create a local Dask cluster. If set to "sequential", will run PowerFit sequentially without using Dask.	`None`

Raises:

Type	Description
`FileNotFoundError`	If no structure files are found in the session directory.
`FileExistsError`	If the PowerFit run directory already exists.

Returns:

Type	Description
`str`	The PowerFit run ID.

`powerfit_solutions_query(join)`

Generate SQL query that reads PowerFit solutions files and joins them with fittable structures.

Parameters:

Name	Type	Description	Default
`join`	`str`	JOIN clause that combines the solutions subquery with the fittable structures, for example `JOIN read_csv($fittable_structures_csv) AS fittable_structures USING (structure)` or `JOIN fittable_structures USING (structure)` when the table already exists.	required

Returns:

Type	Description
`str`	SQL query string with named parameter `$solutions_pattern`
`str`	and any parameters referenced by `join`.