Query Database Schema

This page lists every field of the Query Database that can be referenced in a query step’s filter expression (see Query Examples for example syntax). This table is generated directly from the chemreporter.query_database_tools.table_schemas module.

Core Fields

  • key (String): Unique identifier for each structure

  • entry_key (String): Unique identifier for each structure

  • database_name (String): Name of the source database (set when processing)

  • split_name (String): Split name (set when processing)

  • basis_set (String): Basis set used for the DFT calculation

  • functional (String): Functional used for the DFT calculation

  • correction_term (String): Dispersion or post-DFT correction term

  • subset (String): Dataset subset name (for example spice, anix, biomolecules)

  • composition (String): Brutto formula of the structure

  • net_charge (Int64, e): Net molecular charge

  • spin_multiplicity (Float64, unitless): Spin multiplicity

  • num_atoms (Int64): Number of atoms

  • atomic_numbers (List(Int64)): Atomic numbers by atom

  • energy (Float64, eV): Raw DFT total energy (not cohesive/atomization energy)

Computed Properties

  • dipole_moment_magnitude (Float64, Debye): Magnitude of dipole moment

  • net_force_norm (Float64, eV/Å): Norm of net force vector

  • max_force_norm (Float64, eV/Å): Maximum force magnitude on any atom

  • atomic_symbols (String): Unique element symbols in alphabetical order

  • molecular_weight (Float64, g/mol): Molecular weight

  • is_molecular_structure_valid (Boolean): Historic structure check (hydrogen coordination)

  • num_water_molecules (Int64): Number of water molecules

  • graph_properties_candidate (Boolean): Whether the structure is suitable for graph-based analysis

  • error_graph_properties (Boolean): Whether graph property calculation failed

  • logp (Float64, unitless): Partition coefficient (lipophilicity)

  • tpsa (Float64, Ų): Topological polar surface area

  • smiles (String): SMILES representation

Molecular Fingerprints

  • fingerprint_0 to fingerprint_1023 (Int64, 0 or 1): 1024-bit Morgan fingerprint for similarity searches.

Bio motif counts

  • num_ala, num_arg, num_asn, num_asp, num_cys, num_gln, num_glu, num_gly, num_his, num_ile, num_leu, num_lys, num_met, num_phe, num_pro, num_ser, num_thr, num_trp, num_tyr, num_val (Int64): RDKit substructure counts per motif code.

  • is_protein (Boolean): True when the sum of amino-acid motif counts exceeds 3

  • num_ade, num_cyt, num_gua, num_thy, num_ura (Int64): RDKit substructure counts per motif code.

  • is_nucleobase (Boolean): True when the sum of nucleobase motif counts exceeds 3

Reaction Properties

Present when extracted from OMOL25 source metadata for reactive subsets.

  • reaction_id (String): Reaction identifier

  • reaction_pathway_id (Int64): Pathway identifier (if applicable)

  • is_reactant (Boolean): Whether the structure is a reactant

  • is_product (Boolean): Whether the structure is a product

  • is_transition_state (Boolean): Whether the structure is a transition state

  • reaction_step_idx (Int64): Index of the reaction step

Catalysis Properties

Present when extracted from OC20 supplementary metadata.

  • catalyst_bulk_id (String): Catalyst bulk identifier

  • catalyst_adsorbate_id (String): Catalyst adsorbate identifier

  • catalyst_bulk_symbols (String): Element symbols in the bulk

  • catalyst_adsorbate_symbols (String): Element symbols in the adsorbate

  • catalyst_adsorbate_smiles (String): SMILES of the adsorbate

  • catalyst_num_adsorbate_atoms (Int64): Number of atoms in the adsorbate

  • catalyst_num_bulk_atoms (Int64): Number of atoms in the bulk

  • catalyst_reference_energy (Float64, eV): Reference energy of the catalyst system

  • catalyst_class (String): Catalyst class label

  • catalyst_anomaly (String): Catalyst anomaly label

  • catalyst_substrate_height (Float64, Å): Substrate height

  • catalyst_miller_index (List(Int64)): Miller indices (h, k, l) of the surface

  • catalyst_relaxation_frame_idx (Int64): Relaxation frame index

  • catalyst_xyz_adsorbate_is_valid (Boolean): Whether adsorbate coordinates pass the OC20 xyz validity check

For more detailed information about the units used for each field, see Units and Physical Quantities.

Known caveats

num_water_molecules might be slightly overestimated: compounds containing an R-OHH group are counted as containing one water molecule. Such cases are assumed to be sufficiently rare, so this approximation is not currently corrected for.