Using list(Path('files').rglob('*.pdb')) will get all the pdb files of subfolders. Here we define a function that can limit the depth of search.
rglob (path, pattern, max_depth)
Get a file list given folder depths
[PosixPath('/teamspace/studios/this_studio/kdock/nbs/core/files/7OFF_receptor.pdb'),
PosixPath('/teamspace/studios/this_studio/kdock/nbs/core/files/7OFF_lig.pdb'),
PosixPath('/teamspace/studios/this_studio/kdock/nbs/core/files/7OFF.pdb')]copy_files (file_list, dest_dir)
Copy a list of files to the destination directory, or zip them if dest_dir ends with .zip.
get_rec_lig (pdb_id:str, lig_id:str, out_dir='.')
Download pdb and extract receptor and ligand from a PDB ID.
| Type | Default | Details | |
|---|---|---|---|
| pdb_id | str | pdb id for download | |
| lig_id | str | ligand id shown on the protein page | |
| out_dir | str | . | directory path to save pdb files |
get_box (sdf_file, autobox_add=4.0, tolist=False)
Get the box coordinates of ligand.sdf; mimic GNINA’s –autobox_ligand behavior.
{'center_x': 38.848,
'center_y': -26.77,
'center_z': 10.419,
'size_x': 14.652,
'size_y': 8.942,
'size_z': 12.509}view_mol (file)
Visualize pdb or sdf file
| Details | |
|---|---|
| file | sdf or pdb file |
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view_complex (receptor, ligand, ori_ligand=None, box=None)
Visualize the receptor, ligand, optional original ligand, and optional box via py3Dmol.
| Type | Default | Details | |
|---|---|---|---|
| receptor | protein file | ||
| ligand | ligand (green), or docked ligand | ||
| ori_ligand | NoneType | None | original ligand (yellow) |
| box | NoneType | None | optional box: [x, y, z, sizeX, sizeY, sizeZ] |
[38.848, -26.77, 10.419, 14.652, 8.942, 12.509]