Provides an Intake interface to synthetic cryoEM images from Parakeet.
pip install git+https://github.com/rosalind-franklin-institute/scivision-parakeet.git
NOTE: Because the package needs to be built locally from source and has some external dependencies you may need to ensure your environment is ready before running this command. You need to set the location of the CUDA compiler and possibly G++ and FFTW libraries. For full instructions please see the installation documentation here.
import intake
config = {
"sample": {"molecules": {"pdb": [{"id": "4v1w", "instances": 1}]}},
"scan": {
"mode": "tilt_series",
"num_images": 10,
"start_angle": -10,
"step_angle": 2,
},
}
ds = intake.open_scivision_parakeet(
config=config, directory="parakeet_data"
)
data = ds.read()