Command Line Interface

Spheronizator now includes a command line interface contributed by Dr. Raquel Dias and José Cediel-Becerra.

The command line interface allows generation of static data files from provided PDB files. It requires that Open Babel is installed. You may wish to install Spheronizator into a Conda environment to facilitate the installation of Open Babel.

Usage

The command line interface can be invoked by running the following command:

voxelize -h

usage: voxelize [-h] [--voxel_spacing VOXEL_SPACING] [--use_float_voxels USE_FLOAT_VOXELS] [--box_size BOX_SIZE] [--use_spheres USE_SPHERES]
                [--data_type DATA_TYPE] [--overwrite] [--atom_out_dir ATOM_OUT_DIR] [--bond_out_dir BOND_OUT_DIR] [--meta_out_dir META_OUT_DIR]
                pdb_file

Extract voxel boxes/spheres from a protein PDB file

positional arguments:
  pdb_file              Protein PDB file to process

options:
  -h, --help            show this help message and exit
  --voxel_spacing VOXEL_SPACING
                        Voxel spacing (default: 0.5)
  --use_float_voxels USE_FLOAT_VOXELS
                        Use float voxels (default: True)
  --box_size BOX_SIZE   Box size (default: 20)
  --use_spheres USE_SPHERES
                        Use spheres (default: True)
  --data_type DATA_TYPE
                        Data type (default: float16)
  --overwrite           Overwrite existing outputs if present
  --atom_out_dir ATOM_OUT_DIR
                        Directory for atom voxel outputs (default: ./output_vox_atoms)
  --bond_out_dir BOND_OUT_DIR
                        Directory for bond voxel outputs (default: ./output_vox_bonds)
  --meta_out_dir META_OUT_DIR
                        Directory for metadata outputs (default: ./metadata)

Examples

To run Spheronizator on a protein file:

voxelize tests/sampledata/1YU6_A.pdb

Outputs

The utility produces three main directories:

• metadata/
  Contains a .tsv file summarizing the metadata for each residue, including:

  • Box index
  • Residue index
  • Residue label

• output_vox_atoms/
  Contain a NumPy .npy file representing the atom-level voxelized features for each residue.

• output_vox_bonds/
  Contains a NumPy .npy file representing the bond-level voxelized features for each residue.