graph_toolbox

utilities for graph-like data processing and neural network related

submodules

IO

save_json(data: Union[dict, list], file: str)
load_gpickle(file: str)
save_gpickle(obj, file: str)
unpack_gzip_to_pdb_atomium_obj(gzip_file_path: str)

parse

read XYZ coordinates, sequence and optionally secondary structure

parse_xyz(path: str, chain: str, get_pdb_ss:bool=False)-> th.FloatTensor, List[str]

select residues from structure

atomium_select(structure: atomium.structures.Model, chain: str, pdb_list: list) -> List[atomium.structures.Residue]

plot

tensor_to_3d_position(tensor: th.FloatTensor) -> Dict[int, list]

pymol

PyMolColor

feature

read_struct(pdb_loc: Union[str,atomium.structures.Model], chain: Union[str, None], t: int)