API Physical and Chemical Properties

get_area_buried(molecular_system[, element, ...])	Average area buried per residue group upon protein folding.
assess_chemical_template(molecular_system, ...)	Assessing chemical compatibility through an exhaustive declared atom map.
apply_chemical_template(molecular_system, ...)	Applying compatible declared template assignments to an independent system.
get_autodock_atom_types(molecular_system, ...)	Getting full-graph chemical AutoDock labels before filtering source atoms.
get_aromaticity(molecular_system[, ...])	Perceiving aromatic flags on a complete graph before filtering source indices.
get_atomic_radius(molecular_system[, ...])	Atomic radius for each selected atom.
get_buried_fraction(molecular_system[, ...])	Fraction of residues observed in a buried environment.
get_cip_stereochemistry(molecular_system[, ...])	Getting accurate CIP labels from declared stereo or one selected 3D structure.
get_charge(molecular_system[, element, ...])	Electric charge for the selected elements.
get_charge_centers(molecular_system[, ...])	Identifying formal-charge centers in a selected chemical state.
get_chemical_readiness(molecular_system[, ...])	Assessing stored chemical fields without repairing or completing chemistry.
get_electronegativity(molecular_system[, ...])	Electronegativity for each selected atom.
get_hbond_sites(molecular_system[, ...])	Recognizing donor-hydrogen pairs and acceptors with an attributed rule.
get_hydrogen_inventory(molecular_system[, ...])	Getting indexed and stored hydrogen counts for selected parent atoms.
get_halogen_bond_sites(molecular_system[, ...])	Recognizing ordered donor-halogen and acceptor-reference atom pairs.
get_hydrophobicity(molecular_system[, ...])	Hydrophobicity index per residue group from a reference scale.
get_hydrophobic_sites(molecular_system[, ...])	Recognizing hydrophobic atom sites from complete declared chemical graphs.
get_metal_coordination_sites(molecular_system)	Recognizing metal and candidate ligand atoms from declared chemical graphs.
get_water_sites(molecular_system[, ...])	Recognizing neutral water molecules with three explicitly indexed atoms.
get_mass(molecular_system[, element, ...])	Total mass of the selected elements.
get_partial_charges(molecular_system, method)	Calculating partial charges on a complete graph before selecting atoms.
get_peptide_chemical_template(residue_names, ...)	Constructing a heavy-atom peptide template with explicit chemical states.
normalize_aromatic_bond_orders(molecular_system)	Normalizing declared aromatic bonds to fractional order 1.5 on a copy.
get_polarity(molecular_system[, element, ...])	Polarity index per residue group from a reference scale.
get_protor_atom_type(molecular_system[, ...])	Determining the ProtOr atom type for selected atoms.
get_protor_vdw_radius(molecular_system[, ...])	Calculating the ProtOr atomic van der Waals radius for selected atoms.
get_sasa(molecular_system[, element, ...])	Solvent-accessible surface area (SASA) per atom or residue group.
get_surface_area(molecular_system[, ...])	Getting standard surface area values for elements in a molecular system.
get_transmembrane_tendency(molecular_system)	Transmembrane tendency index per residue group.
get_volume(molecular_system[, selection, ...])	Side-chain volume per residue group from a reference scale.