options
PowerfitOptions
dataclass
Options for the Powerfit command.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
target
|
Path
|
Path to the density map file. |
required |
resolution
|
float
|
Resolution of the density map. |
required |
angle
|
float
|
Angle for the fitting. |
10
|
laplace
|
bool
|
Whether to use Laplace smoothing. |
False
|
core_weighted
|
bool
|
Whether to use core weighted fitting. |
False
|
no_resampling
|
bool
|
Whether to disable resampling. |
False
|
resampling_rate
|
float
|
Rate of resampling. |
2
|
no_trimming
|
bool
|
Whether to disable trimming . |
False
|
trimming_cutoff
|
float | None
|
Cutoff for trimming. |
None
|
gpu
|
int
|
Number of workers per GPU. If > 0 then Powerfit will use GPU acceleration otherwise CPU. |
0
|
nproc
|
int
|
Number of processes to use. Ignored if GPU is used. |
1
|
from_args(parsed_args)
staticmethod
Create PowerfitOptions from parsed command line arguments.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
parsed_args
|
Namespace
|
Parsed command line arguments. |
required |
Returns:
| Name | Type | Description |
|---|---|---|
PowerfitOptions |
PowerfitOptions
|
An instance of PowerfitOptions populated with the parsed arguments. |
to_command(density_map, 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 |
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. |