Convert Directory of PDBs to PNS Files
Run this script
uv run https://atrium.kyleharrington.com/bioinformatics/pdb-to-pns/0.0.1.py
Command Line Arguments
--input_dir
(str)
Directory containing PDB files
Default: Ellipsis
--output_dir
(str)
Base directory for output files
Default: output
--box_size
(int)
Size of density grid in pixels
Default: 128
--voxel_size
(float)
Voxel size in Angstroms
Default: 1.0
--sigma
(float)
Gaussian smoothing sigma
Default: 1.0
--iso_value
(float)
Isosurface threshold value
Default: 0.1
Dependencies
- numpy
- gemmi
- scipy
- typer
- scikit-image