options
PowerfitOptions
dataclass
PowerFit specific options.
Attributes:
| Name | Type | Description |
|---|---|---|
angle |
PositiveFloat
|
Rotational sampling density in degree. Increasing this number by a factor of 2 results in approximately 8 times more rotations sampled. |
no_laplace |
Annotated[bool, Parameter(negative='')]
|
Do not use the Laplace pre-filter density data. |
no_core_weighted |
Annotated[bool, Parameter(negative='')]
|
Do not use core-weighted local cross-correlation score. |
no_resampling |
Annotated[bool, Parameter(negative='')]
|
Do not resample the density map. |
resampling_rate |
PositiveFloat
|
Resampling rate compared to Nyquist. |
no_trimming |
Annotated[bool, Parameter(negative='')]
|
Do not trim the density map. |
trimming_cutoff |
PositiveFloat | None
|
Intensity cutoff to which the map will be trimmed. Default is 10 percent of maximum intensity. |
cpu |
Annotated[bool, Parameter(group=process_group, negative='')]
|
Use CPU for the intensive calculations. Otherwise off-loads to GPU. |
workers_per_gpu |
Annotated[PositiveInt, Parameter(group=process_group)]
|
Number of workers to run per GPU. |
gpu_backend |
Annotated[GpuBackend, Parameter(group=process_group)]
|
Backend to use for GPU processing. |
nproc |
Annotated[PositiveInt, Parameter(group=process_group)]
|
Number of processors used during search. The number will be capped at the total number of available processors on your machine. |
batch_size |
Annotated[NonNegativeInt, Parameter(group=process_group)]
|
GPU batch size to use. Use 0 to disable batching entirely, or a positive integer to force a specific batch size. Applies to GPU backends (CUDA/OpenCL). If set too high will cause out-of-memory errors. |
gpu
property
Whether to use GPU for the intensive calculations.
to_command(density_map, resolution, template, out_dir, powerfit_cmd='powerfit', gpu_cycler=None)
Generate command from options and given arguments.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
density_map
|
Path
|
Path to the density map file. |
required |
resolution
|
float
|
Resolution of the density map in Angstroms. |
required |
template
|
Path
|
Path to the template PDB file. |
required |
out_dir
|
Path
|
Directory to save the output files. |
required |
powerfit_cmd
|
str
|
Command to run Powerfit (default is "powerfit"). |
'powerfit'
|
gpu_cycler
|
Generator[int] | None
|
Generator to cycle through GPU indices. |
None
|
Returns:
| Type | Description |
|---|---|
str
|
A string representing the command to run Powerfit. |