cli
commands(target, resolution, session_dir, /, *, options=None, powerfit_run_id=None, output=None, _=None)
Generate PowerFit commands for structure files in the session directory.
See powerfit --help for more information on the available options.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
target
|
Annotated[Path, Parameter(validator=Path(file_okay=True, dir_okay=False, exists=True))]
|
Target density map to fit the model in. Data should either be in CCP4 or MRC format |
required |
resolution
|
PositiveFloat
|
Resolution of map in Angstrom |
required |
session_dir
|
Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=True, exists=True))]
|
Session directory for input and output |
required |
options
|
PowerfitOptions | None
|
Powerfit specific options. |
None
|
powerfit_run_id
|
str | None
|
ID of the PowerFit run to use. If not provided, will autoincrement based on existing runs. |
None
|
output
|
StdioPath | None
|
Output file path. If not specified, defaults to standard output. |
None
|
fit_models(session_dir, /, *, powerfit_run_id=None, top=1, no_group_by_structure=False, output=None)
Fit models to the best PowerFit solutions.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
session_dir
|
Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=True, exists=True))]
|
Session directory containing PowerFit results |
required |
powerfit_run_id
|
str | None
|
ID of the PowerFit run to report on |
None
|
top
|
int
|
Number of top solutions to fit per structure. |
1
|
no_group_by_structure
|
Annotated[bool, Parameter(negative='')]
|
If absent, group solutions by structure. If present, top will be overall instead of per structure. |
False
|
output
|
StdioPath | None
|
Output file for fitted models table. If set to '-' (default) will print to stdout. |
None
|
list_runs(session_dir, /, *, output=None)
List all PowerFit runs in the session directory.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
session_dir
|
Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=True, exists=True))]
|
Directory containing the session data. |
required |
output
|
StdioPath | None
|
Comma separated output file for listing runs. If set to '-' (default) will print to stdout. |
None
|
report(session_dir, /, *, powerfit_run_id=None, top=1, no_group_by_structure=False, output=None)
Generate a report of the best PowerFit solutions.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
session_dir
|
Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=True, exists=True))]
|
Session directory containing PowerFit results |
required |
powerfit_run_id
|
str | None
|
ID of the PowerFit run to report on |
None
|
top
|
int
|
Number of top solutions to report per structure. |
1
|
no_group_by_structure
|
Annotated[bool, Parameter(negative='')]
|
If absent, group solutions by structure. If present, top will be overall instead of per structure. |
False
|
output
|
StdioPath | None
|
Output file for solutions table. If set to '-' (default) will print to stdout. |
None
|
run(target, resolution, session_dir, /, *, options=None, powerfit_run_id=None, scheduler_address=None)
Run PowerFit on PDB files in the session directory and store results.
See powerfit --help for more information on the available options.
Unlike powerfit command, no cross-correlation map (lcc.mrc file) is generated.
If you need the lcc.mrc file, use powerfit commands to generate the commands and run them manually.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
target
|
Annotated[Path, Parameter(validator=Path(file_okay=True, dir_okay=False, exists=True))]
|
Target density map to fit the model in. Data should either be in CCP4 or MRC format |
required |
resolution
|
PositiveFloat
|
Resolution of map in Angstrom |
required |
session_dir
|
Annotated[Path, Parameter(validator=Path(file_okay=False, dir_okay=True, exists=True))]
|
Session directory for input and output |
required |
options
|
PowerfitOptions | None
|
Powerfit specific options. |
None
|
powerfit_run_id
|
str | None
|
ID of the PowerFit run to use. If not provided, will autoincrement based on existing runs. |
None
|
scheduler_address
|
Annotated[str | None, Parameter(group=process_group)]
|
Address of the Dask scheduler to use.
Use |
None
|