List of all items

Structs

• AromaticityAnalysis
• ConformerClusterSummary
• ConformerConfig
• ConformerEnsembleMember
• ConformerResult
• ConformerSearchResult
• GraphFeatureAnalysis
• MethodCapability
• MethodComparisonEntry
• MethodComparisonResult
• MethodMetadata
• PropertyMethodPlan
• StereocenterAnalysis
• SystemCapabilities
• SystemMethodPlan
• alignment::kabsch::AlignmentResult
• ani::aev_params::AevParams
• ani::api::AniConfig
• ani::api::AniResult
• ani::neighbor::CellList
• ani::neighbor::NeighborPair
• ani::nn::DenseLayer
• ani::nn::FeedForwardNet
• charges::gasteiger::ChargeResult
• charges::gasteiger::GasteigerConfig
• charges::gasteiger::GasteigerParams
• clustering::ClusterResult
• dipole::dipole::DipoleResult
• distgeom::embedding::MinstdRand
• distgeom::embedding::Mt19937
• distgeom::validation::TetrahedralCenter
• dos::dos::DosResult
• dynamics::MdFrame
• dynamics::MdTrajectory
• dynamics::NebImage
• dynamics::NebPathResult
• eht::basis::AtomicOrbital
• eht::basis::GaussianPrimitive
• eht::basis::SlaterOrbital
• eht::marching_cubes::IsosurfaceMesh
• eht::params::EhtParams
• eht::params::EhtSupport
• eht::params::OrbitalDef
• eht::solver::EhtResult
• eht::volume::VolumeSlab
• eht::volume::VolumetricGrid
• esp::esp::CubeFile
• esp::esp::EspGrid
• forcefield::bounds_ff::ChiralSet
• forcefield::bounds_ff::EmbedTorsion
• forcefield::dg_terms::ChiralViolation
• forcefield::dg_terms::DistanceViolation
• forcefield::energy::FFParams
• forcefield::etkdg_3d::AngleConstraint
• forcefield::etkdg_3d::DistConstraint
• forcefield::etkdg_3d::Etkdg3DFF
• forcefield::etkdg_3d::M6TorsionContrib
• forcefield::etkdg_3d::UFFInversionContrib
• forcefield::etkdg_lite::M6Params
• forcefield::mmff94::Mmff94AngleBend
• forcefield::mmff94::Mmff94BondStretch
• forcefield::mmff94::Mmff94BufferedVanDerWaals
• forcefield::mmff94::Mmff94Builder
• forcefield::mmff94::Mmff94Torsion
• forcefield::params::UffAtomParams
• forcefield::traits::MolecularForceField
• forcefield::uff::UffAngleBend
• forcefield::uff::UffHarmonicBondStretch
• forcefield::uff::UffInversion
• forcefield::uff::UffLennardJones
• forcefield::uff::UffTorsion
• graph::Atom
• graph::Bond
• graph::Molecule
• graph::NodeIndex
• hf::api::Hf3cResult
• hf::api::HfConfig
• hf::basis::BasisSet
• hf::basis::Shell
• hf::cis::CisResult
• hf::cis::Excitation
• hf::d3::D3Result
• hf::scf::ScfConfig
• hf::scf::ScfResult
• ir::vibrations::IrPeak
• ir::vibrations::IrSpectrum
• ir::vibrations::Thermochemistry
• ir::vibrations::VibrationalAnalysis
• ir::vibrations::VibrationalMode
• materials::assembly::CrystalAtom
• materials::assembly::CrystalStructure
• materials::assembly::Topology
• materials::cell::CellParameters
• materials::cell::UnitCell
• materials::sbu::ConnectionPoint
• materials::sbu::Sbu
• mesh::OrbitalMeshResult
• ml::descriptors::MolecularDescriptors
• ml::models::LipinskiResult
• ml::models::MlPropertyResult
• nmr::coupling::JCoupling
• nmr::coupling::KarplusParams
• nmr::hose::HoseCode
• nmr::hose::HoseShiftLookup
• nmr::shifts::ChemicalShift
• nmr::shifts::NmrShiftResult
• nmr::spectrum::NmrPeak
• nmr::spectrum::NmrSpectrum
• nmr::spectrum::PeakIntegration
• optimization::bfgs::RustBfgsEngine
• pm3::params::Pm3Params
• pm3::solver::Pm3Result
• population::population::BondOrderEntry
• population::population::BondOrderResult
• population::population::PopulationResult
• reactivity::CondensedFukuiAtom
• reactivity::EmpiricalPkaResult
• reactivity::EmpiricalPkaSite
• reactivity::FrontierDescriptors
• reactivity::FukuiDescriptors
• reactivity::ReactivityRanking
• reactivity::ReactivitySiteScore
• reactivity::StdaExcitation
• reactivity::StdaUvVisSpectrum
• reactivity::UffHeuristicEnergy
• reactivity::UvVisPeak
• reactivity::UvVisSpectrum
• rings::ecfp::ECFPFingerprint
• rings::sssr::RingInfo
• rings::sssr::SssrResult
• smarts::SmartsAtom
• smarts::SmartsBond
• smarts::SmartsPattern
• smiles::SmilesParser
• solvation::GbSolvation
• solvation::NonPolarSolvation
• stereo::DoubleBondStereo
• stereo::StereoAnalysis
• stereo::Stereocenter
• surface::sasa::SasaResult
• topology::MetalCoordinationCenter
• topology::TopologyAnalysisResult
• transport::arrow::ColumnSchema
• transport::arrow::Float64Column
• transport::arrow::Int32Column
• transport::arrow::RecordBatch
• transport::arrow::Uint8Column
• transport::chunked::ChunkedIterator
• transport::chunked::DataChunk
• transport::worker::WorkerResult
• transport::worker::WorkerTask
• xtb::params::XtbParams
• xtb::solver::XtbResult

Enums

• ElectronicWorkflowResult
• MethodComparisonPayload
• MethodComparisonStatus
• PropertyRequest
• ScientificMethod
• ani::nn::Activation
• eht::params::SupportLevel
• forcefield::mmff94::Mmff94AtomType
• graph::BondOrder
• graph::BondStereo
• graph::ChiralType
• graph::Hybridization
• hf::basis::ShellType
• ir::hessian::HessianMethod
• ir::vibrations::BroadeningType
• materials::sbu::CoordinationGeometry
• mesh::MeshMethod
• nmr::spectrum::NmrNucleus
• reactivity::BroadeningType
• smarts::AtomQuery
• smarts::BondQuery
• topology::CoordinationGeometryGuess
• transport::arrow::DataType
• transport::chunked::ChunkKind
• transport::worker::TaskKind

Traits

• distgeom::embedding::DistGeomRng
• forcefield::traits::ForceFieldContribution

Functions

• alignment::kabsch::align_coordinates
• alignment::kabsch::align_quaternion
• alignment::kabsch::compute_rmsd
• analyze_graph_features
• analyze_stereo
• ani::aev::compute_aevs
• ani::aev_params::default_ani2x_params
• ani::aev_params::species_index
• ani::api::compute_ani
• ani::api::compute_ani_batch
• ani::api::compute_ani_test
• ani::cutoff::cosine_cutoff
• ani::cutoff::cosine_cutoff_deriv
• ani::gradients::compute_forces
• ani::weights::load_weights
• ani::weights::make_test_model
• ani::weights::save_weights
• assemble_framework
• butina_cluster
• charges::gasteiger::gasteiger_marsili_charges
• charges::gasteiger::gasteiger_marsili_charges_configured
• charges::gasteiger::get_gasteiger_params
• clustering::butina_cluster
• clustering::compute_rmsd_matrix
• clustering::filter_diverse_conformers
• compare_methods
• compute_ani
• compute_ani_with_models
• compute_bond_orders
• compute_charges
• compute_charges_configured
• compute_dipole
• compute_dos
• compute_ecfp
• compute_eht_or_uff_fallback
• compute_empirical_pka
• compute_ensemble_j_couplings
• compute_esp
• compute_esp_grid
• compute_frontier_descriptors
• compute_fukui_descriptors
• compute_gb_solvation
• compute_hf3c
• compute_hose_codes
• compute_ir_spectrum
• compute_ir_spectrum_broadened
• compute_md_trajectory
• compute_md_trajectory_nvt
• compute_ml_descriptors
• compute_mmff94_energy
• compute_nmr_spectrum
• compute_nonpolar_solvation
• compute_orbital_mesh
• compute_pm3
• compute_population
• compute_reactivity_ranking
• compute_rmsd
• compute_rmsd_matrix
• compute_sasa
• compute_simplified_neb_path
• compute_sssr
• compute_stda_uvvis
• compute_tanimoto
• compute_topology
• compute_uff_energy
• compute_uff_energy_with_aromatic_heuristics
• compute_uv_vis_spectrum
• compute_vibrational_analysis
• compute_xtb
• conformer::compute_total_bounds_energy_f64
• conformer::generate_3d_conformer
• conformer::generate_3d_conformer_best_of_k
• conformer::generate_3d_conformer_from_smiles
• conformer::generate_3d_conformer_with_torsions
• create_unit_cell
• dipole::dipole::compute_dipole
• dipole::dipole::compute_dipole_from_eht
• distgeom::bounds::calculate_bounds_matrix
• distgeom::bounds::calculate_bounds_matrix_opts
• distgeom::bounds::get_bond_length
• distgeom::bounds::smooth_bounds_matrix
• distgeom::bounds::triangle_smooth
• distgeom::bounds::triangle_smooth_tol
• distgeom::chirality::calc_chiral_volume
• distgeom::chirality::calc_chiral_volume_f64
• distgeom::chirality::identify_chiral_sets
• distgeom::embedding::compute_initial_coords_nalgebra
• distgeom::embedding::compute_initial_coords_nalgebra_f64
• distgeom::embedding::compute_initial_coords_rdkit
• distgeom::embedding::compute_metric_matrix
• distgeom::embedding::generate_3d_coordinates
• distgeom::embedding::generate_nd_coordinates
• distgeom::embedding::generate_smart_coordinates
• distgeom::embedding::pick_etkdg_distances
• distgeom::embedding::pick_random_distances
• distgeom::embedding::pick_rdkit_distances
• distgeom::embedding::power_eigen_solver
• distgeom::validation::check_chiral_centers
• distgeom::validation::check_double_bond_geometry
• distgeom::validation::check_planarity
• distgeom::validation::check_tetrahedral_centers
• distgeom::validation::find_sssr_pub
• distgeom::validation::identify_tetrahedral_centers
• dos::dos::compute_dos
• dos::dos::compute_dos_parallel
• dos::dos::compute_pdos
• dos::dos::compute_pdos_parallel
• dos::dos::dos_mse
• dos::dos::export_dos_json
• dynamics::compute_simplified_neb_path
• dynamics::simulate_velocity_verlet_uff
• eht::basis::build_basis
• eht::basis::gaussian_cartesian_norm
• eht::basis::gaussian_cartesian_value
• eht::basis::gaussian_p_value
• eht::basis::gaussian_s_value
• eht::basis::orbital_cartesian_terms
• eht::basis::sto3g_expansion
• eht::hamiltonian::build_hamiltonian
• eht::marching_cubes::marching_cubes
• eht::overlap::build_overlap_matrix
• eht::params::analyze_eht_support
• eht::params::get_params
• eht::params::is_transition_metal
• eht::params::num_basis_functions
• eht::params::support_level_for_element
• eht::solver::solve_eht
• eht::solver::solve_generalized_eigenproblem
• eht::volume::compute_grid_extents
• eht::volume::evaluate_density_on_grid
• eht::volume::evaluate_orbital_on_grid
• eht::volume::evaluate_orbital_on_grid_chunked
• eht::volume::evaluate_orbital_on_grid_parallel
• embed
• embed_batch
• esp::esp::compute_esp_grid
• esp::esp::compute_esp_grid_parallel
• esp::esp::esp_color_map
• esp::esp::esp_grid_to_colors
• esp::esp::export_cube
• esp::esp::read_cube
• etkdg::calculate_dihedral_angle
• etkdg::calculate_torsion_penalty
• forcefield::atom_typer::assign_uff_type
• forcefield::atom_typer::is_atom_aromatic
• forcefield::bounds_ff::bfgs::minimize_bfgs_rdkit
• forcefield::bounds_ff::energy::bounds_violation_energy
• forcefield::bounds_ff::energy::bounds_violation_energy_basin
• forcefield::bounds_ff::energy::bounds_violation_gradient
• forcefield::bounds_ff::energy::bounds_violation_gradient_basin
• forcefield::bounds_ff::energy::chiral_violation_energy
• forcefield::bounds_ff::energy::chiral_violation_energy_f64
• forcefield::bounds_ff::energy::chiral_violation_gradient
• forcefield::bounds_ff::energy::chiral_violation_gradient_f64
• forcefield::bounds_ff::energy::collect_embed_torsions
• forcefield::bounds_ff::lbfgs::minimize_bounds_lbfgs
• forcefield::bounds_ff::lbfgs::minimize_bounds_lbfgs_ex
• forcefield::bounds_ff::lbfgs::minimize_bounds_lbfgs_full
• forcefield::bounds_ff::lbfgs::minimize_bounds_with_torsions
• forcefield::bounds_ff::lbfgs::minimize_embedding_lbfgs
• forcefield::builder::build_uff_force_field
• forcefield::energy::angle_bend_energy
• forcefield::energy::bond_stretch_energy
• forcefield::energy::bounds_energy
• forcefield::energy::calculate_total_energy
• forcefield::energy::chirality_energy
• forcefield::energy::distance_constraint_energy
• forcefield::energy::oop_energy
• forcefield::energy::torsion_params
• forcefield::energy::torsional_energy
• forcefield::energy::uff_vdw_params
• forcefield::energy::vdw_energy
• forcefield::etkdg_3d::builder::build_etkdg_3d_ff
• forcefield::etkdg_3d::builder::build_etkdg_3d_ff_with_torsions
• forcefield::etkdg_3d::energy::etkdg_3d_energy
• forcefield::etkdg_3d::energy::etkdg_3d_energy_f64
• forcefield::etkdg_3d::energy::planarity_check_energy
• forcefield::etkdg_3d::energy::planarity_check_energy_f64
• forcefield::etkdg_3d::energy::uff_inversion_energy_only
• forcefield::etkdg_3d::gradient::etkdg_3d_gradient
• forcefield::etkdg_3d::gradient::etkdg_3d_gradient_f64
• forcefield::etkdg_3d::optimizer::correct_torsion_angles
• forcefield::etkdg_3d::optimizer::minimize_etkdg_3d
• forcefield::etkdg_3d::optimizer::minimize_etkdg_3d_bfgs
• forcefield::etkdg_3d::optimizer::minimize_etkdg_3d_with_ff
• forcefield::etkdg_lite::calc_torsion_energy_m6
• forcefield::etkdg_lite::calc_torsion_grad_m6
• forcefield::etkdg_lite::infer_etkdg_parameters
• forcefield::gradients::analytical_grad_angle
• forcefield::gradients::analytical_grad_bond
• forcefield::gradients::analytical_grad_bounds
• forcefield::gradients::analytical_grad_distance_constraint
• forcefield::gradients::analytical_grad_oop
• forcefield::gradients::analytical_grad_torsion
• forcefield::gradients::compute_analytical_gradient
• forcefield::minimizer::calculate_rmsd_kabsch
• forcefield::minimizer::minimize_energy_lbfgs
• forcefield::mmff94::assign_mmff94_type
• forcefield::mmff94::validate_gradients
• forcefield::params::get_uff_angle_force_constant
• forcefield::params::get_uff_bond_force_constant
• forcefield::params::get_uff_bond_length
• forcefield::params::get_uff_params
• forcefield::params::get_uff_torsion_params
• forcefield::torsion_scan::optimize_torsions_bounds
• forcefield::torsion_scan::optimize_torsions_greedy
• forcefield::torsion_scan::optimize_torsions_monte_carlo_bounds
• forcefield::torsion_scan::snap_torsions_to_preferred
• get_eht_support
• get_system_capabilities
• get_system_method_plan
• graph::atom_in_ring
• graph::bond_in_ring_of_size
• graph::get_corrected_ideal_angle
• graph::get_covalent_radius
• graph::get_ideal_angle
• graph::get_vdw_radius
• graph::min_path_excluding
• graph::min_path_excluding2
• hf::api::solve_hf3c
• hf::api::solve_hf3c_batch
• hf::basis::build_sto3g_basis
• hf::cis::compute_cis
• hf::d3::compute_d3_energy
• hf::fock::build_fock
• hf::fock::electronic_energy
• hf::fock::nuclear_repulsion
• hf::gcp::compute_gcp
• hf::integrals::compute_eris
• hf::integrals::eri_index
• hf::integrals::get_eri
• hf::nuclear::boys_function
• hf::nuclear::compute_nuclear_matrix
• hf::overlap_kin::compute_kinetic_matrix
• hf::overlap_kin::compute_overlap_matrix
• hf::scf::solve_scf
• hf::srb::compute_srb
• ir::hessian::compute_numerical_hessian
• ir::vibrations::compute_ir_spectrum
• ir::vibrations::compute_ir_spectrum_with_broadening
• ir::vibrations::compute_vibrational_analysis
• materials::assembly::assemble_framework
• mesh::compute_orbital_mesh
• ml::descriptors::compute_descriptors
• ml::models::predict_properties
• nmr::coupling::ensemble_averaged_j_couplings
• nmr::coupling::predict_j_couplings
• nmr::hose::generate_hose_codes
• nmr::hose::predict_shift_from_hose
• nmr::shifts::predict_chemical_shifts
• nmr::spectrum::compute_nmr_spectrum
• parse
• pm3::params::count_pm3_electrons
• pm3::params::get_pm3_params
• pm3::params::is_pm3_supported
• pm3::params::num_pm3_basis_functions
• pm3::solver::solve_pm3
• population::population::compute_bond_orders
• population::population::compute_population
• population::population::lowdin_charges
• population::population::mulliken_charges
• predict_ml_properties
• predict_nmr_couplings
• predict_nmr_shifts
• reactivity::apply_aromatic_uff_correction
• reactivity::compute_frontier_descriptors
• reactivity::compute_fukui_descriptors
• reactivity::compute_stda_uvvis_spectrum
• reactivity::compute_uv_vis_like_spectrum
• reactivity::estimate_empirical_pka
• reactivity::rank_reactivity_sites
• rings::ecfp::compute_ecfp
• rings::ecfp::compute_tanimoto
• rings::sssr::compute_sssr
• search_conformers_with_uff
• smarts::parse_smarts
• smarts::substruct_match
• smarts::torsion_matcher::match_experimental_torsions
• solvation::compute_born_radii
• solvation::compute_gb_solvation
• solvation::compute_nonpolar_solvation
• stereo::analyze_stereo
• surface::sasa::compute_sasa
• surface::sasa::compute_sasa_parallel
• surface::sasa::vdw_radius
• topology::analyze_topology
• transport::arrow::pack_conformers
• transport::arrow::pack_dos
• transport::arrow::pack_esp_grid
• transport::chunked::chunk_coordinates
• transport::chunked::chunk_dos
• transport::chunked::chunk_esp_grid
• transport::worker::estimate_workers
• transport::worker::merge_results
• transport::worker::split_batch
• version
• xtb::params::count_xtb_electrons
• xtb::params::get_xtb_params
• xtb::params::is_xtb_supported
• xtb::params::num_xtb_basis_functions
• xtb::solver::solve_xtb

Constants

• ani::aev_params::ANI_ELEMENTS
• ani::aev_params::N_SPECIES
• distgeom::validation::MAX_MINIMIZED_E_PER_ATOM
• eht::params::DEFAULT_K
• hf::basis::ANG_TO_BOHR
• smarts::torsion_data::TORSION_PREFS_MACROCYCLES
• smarts::torsion_data::TORSION_PREFS_SMALL_RINGS
• smarts::torsion_data::TORSION_PREFS_V2
• surface::sasa::DEFAULT_NUM_POINTS
• surface::sasa::DEFAULT_PROBE_RADIUS