Attributes

MolSysMT attributes describe non-exclusive layers of a molecular system. Stable topological attributes identify atoms and semantic hierarchy. Structural attributes describe geometry and trajectories. atom_index and n_atoms belong to both layers: they define the stable atom inventory and the atom axis shared by structural arrays. Mechanical attributes contain force-field data. Chemical-state attributes describe chemistry that may differ between states, including bonds, formal charge, aromaticity, radicals, implicit hydrogens, stereochemistry, and covalent components.

A molecular form does not need to contain every attribute. Use molsysmt.basic.has_attribute() to distinguish information stored in a particular object from information supported by its form. By default it reports instance presence, so an optional temperature, occupancy, component label, or chemical-state ID that is absent returns False; include_none=True asks only whether the form supports the attribute. For MolSys, this check composes its topology, structures, and molecular-mechanics form contracts rather than adding methods to the native component classes. Native objects resolve chemical-state attributes through chemical_state='reference', chemical_state='structure', or an explicit 0-based state index. The explicit index is execution-local: it does not mutate the stored reference. The 'structure' resolver uses the nullable structure_chemical_state_index association owned by MolSys and requires the selected structures to share one known state. State IDs are labels and are not selectors because duplicates are valid.

Attributes you can get

The following table shows the list of attribute arguments you can use in molsysmt.basic.get(), together with their meaning and the list of elements they can be used with.

Property	Category	Elements
allows_implicit_hydrogens	Chemical State	atom
alternate_location	Structural	atom, system
atom_ff_type	Mechanical	atom, system
atom_id	Topological	atom, group, component, molecule, chain, entity
atom_index	Topological, Structural	atom, group, component, molecule, chain, entity
atom_is_aromatic	Chemical State	atom
atom_name	Topological	atom, group, component, molecule, chain, entity
atom_stereochemistry	Chemical State	atom
atom_type	Topological	atom, group, component, molecule, chain, entity
b_factor	Structural	atom, system
bioassembly	Structural	system
bond_acceptor_atom_index	Chemical State	bond
bond_donor_atom_index	Chemical State	bond
bond_evidence	Chemical State	bond
bond_id	Topological, Chemical State	bond
bond_index	Topological, Chemical State	atom, bond, system
bond_is_aromatic	Chemical State	bond
bond_is_conjugated	Chemical State	bond
bond_joins_components	Chemical State	bond
bond_order	Topological, Chemical State	bond
bond_stereo_atom_indices	Chemical State	bond
bond_stereochemistry	Chemical State	bond
bond_type	Topological, Chemical State	bond
bonded_atom_pairs	Topological	atom, bond, system
bonded_atoms	Topological	atom, bond, system
box	Structural	system
box_angles	Structural	system
box_lengths	Structural	system
box_shape	Structural	system
box_volume	Structural	system
chain_id	Topological	atom, group, component, molecule, chain, entity
chain_index	Topological	atom, group, component, molecule, chain, entity
chain_name	Topological	atom, group, component, molecule, chain, entity
chain_type	Topological	atom, group, component, molecule, chain, entity
chemical_state_id	Chemical State	system
chemical_state_index	Chemical State	system
component_completeness	Chemical State	system
component_evidence	Chemical State	system
component_id	Topological, Chemical State	atom, group, component, molecule, chain, entity
component_index	Topological, Chemical State	atom, group, component, molecule, chain, entity
component_name	Topological, Chemical State	atom, group, component, molecule, chain, entity
component_type	Topological, Chemical State	atom, group, component, molecule, chain, entity
connectivity_completeness	Chemical State	system
constraints	Mechanical	system
coordinates	Structural	atom, system
cutoff_distance	Mechanical	system
dispersion_correction	Mechanical	system
entity_id	Topological	atom, group, component, molecule, chain, entity
entity_index	Topological	atom, group, component, molecule, chain, entity
entity_name	Topological	atom, group, component, molecule, chain, entity
entity_type	Topological	atom, group, component, molecule, chain, entity
ewald_error_tolerance	Mechanical	system
flexible_constraints	Mechanical	system
forcefield	Mechanical	system
formal_charge	Chemical State	atom, system
fractional_bond_order	Chemical State	bond
friction	General	system
group_id	Topological	atom, group, component, molecule, chain, entity
group_index	Topological	atom, group, component, molecule, chain, entity
group_name	Topological	atom, group, component, molecule, chain, entity
group_type	Topological	atom, group, component, molecule, chain, entity
hydrogen_mass	Mechanical	system
implicit_solvent	Mechanical	system
inner_bond_index	Topological	atom, system
inner_bonded_atom_pairs	Topological	atom, system
inner_bonded_atoms	Topological	atom, system
integrator	General	system
isotope	Topological	atom
kappa	Mechanical	system
kinetic_energy	Structural	system
molecule_id	Topological	atom, group, component, molecule, chain, entity
molecule_index	Topological	atom, group, component, molecule, chain, entity
molecule_name	Topological	atom, group, component, molecule, chain, entity
molecule_type	Topological	atom, group, component, molecule, chain, entity
n_amino_acids	Topological	atom, group, component, molecule, chain, entity, system
n_atoms	Topological, Structural	atom, group, component, molecule, chain, entity, system
n_bioassemblies	Structural	system
n_bonds	Topological	atom, group, component, molecule, chain, entity, system
n_chains	Topological	atom, group, component, molecule, chain, entity, system
n_chemical_states	Chemical State	system
n_components	Topological	atom, group, component, molecule, chain, entity, system
n_dnas	Topological	atom, group, component, molecule, chain, entity, system
n_entities	Topological	atom, group, component, molecule, chain, entity, system
n_groups	Topological	atom, group, component, molecule, chain, entity, system
n_implicit_hydrogens	Chemical State	atom
n_inner_bonds	Topological	atom, group, component, molecule, chain, entity, system
n_ions	Topological	atom, group, component, molecule, chain, entity, system
n_lipids	Topological	atom, group, component, molecule, chain, entity, system
n_molecules	Topological	atom, group, component, molecule, chain, entity, system
n_nucleotides	Topological	atom, group, component, molecule, chain, entity, system
n_peptides	Topological	atom, group, component, molecule, chain, entity, system
n_polysaccharides	Topological	atom, group, component, molecule, chain, entity, system
n_proteins	Topological	atom, group, component, molecule, chain, entity, system
n_rnas	Topological	atom, group, component, molecule, chain, entity, system
n_saccharides	Topological	atom, group, component, molecule, chain, entity, system
n_small_molecules	Topological	atom, group, component, molecule, chain, entity, system
n_structures	Structural	system
n_unpaired_electrons	Chemical State	atom
n_waters	Topological	atom, group, component, molecule, chain, entity, system
non_bonded_method	Mechanical	system
occupancy	Structural	atom
partial_charge	Mechanical	atom, system
potential_energy	Structural	system
reference_chemical_state_index	Chemical State	system
rigid_water	Mechanical	system
salt_concentration	Mechanical	system
solute_dielectric	Mechanical	system
solvent_dielectric	Mechanical	system
structure_chemical_state_index	Structural, Chemical State	system
structure_id	Structural	system
structure_index	Structural
switch_distance	Mechanical	system
temperature	Structural	system
time	Structural	system
time_step	General	system
total_energy	Structural	system
velocities	Structural	atom, system
water_model	Mechanical	system