mllf.cb.aev_processor

Functions

detect_minimized_pdb(prep_dir)	Detect the minimized system structure in a prep directory.
extract_charges_from_pdb(pdb_path)	Extract partial charges from PDB file.
extract_charges_from_rtf_metadata(rtf_entry)	Extract atomic charges from RTF metadata parsed by parse_rtf_dir.
extract_environment_atoms_from_minimized(...)	Extract environment atoms (protein or solvent) from minimized.pdb.
get_atom_features(pdb_path[, rtf_entry, ...])	Compute complete atom-level features for DeepSet input.
get_atom_features_with_context(...[, ...])	Compute atom-level features with full molecular context.
get_bond_edge_index_from_pdb(pdb_path[, ...])	Build bidirectional bond edge index and bond-type edge attributes.
get_substituent_aevs(pdb_path[, ...])	Compute AEVs for all atoms in a substituent PDB file.
map_element_to_species_id(element[, warn_rare])	Map element symbol to species ID with appropriate warnings.
parse_pdb_coordinates_and_elements(pdb_path)	Parse PDB file to extract coordinates and elements.