List of all items

Structs

• ConformerConfig
• ConformerResult
• alignment::kabsch::AlignmentResult
• charges::gasteiger::ChargeResult
• charges::gasteiger::GasteigerParams
• dipole::dipole::DipoleResult
• distgeom::embedding::MinstdRand
• distgeom::embedding::Mt19937
• distgeom::validation::TetrahedralCenter
• dos::dos::DosResult
• eht::basis::AtomicOrbital
• eht::basis::GaussianPrimitive
• eht::basis::SlaterOrbital
• eht::marching_cubes::IsosurfaceMesh
• eht::params::EhtParams
• 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
• materials::assembly::CrystalAtom
• materials::assembly::CrystalStructure
• materials::assembly::Topology
• materials::cell::CellParameters
• materials::cell::UnitCell
• materials::sbu::ConnectionPoint
• materials::sbu::Sbu
• optimization::bfgs::RustBfgsEngine
• population::population::PopulationResult
• smarts::SmartsAtom
• smarts::SmartsBond
• smarts::SmartsPattern
• smiles::SmilesParser
• surface::sasa::SasaResult
• 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

Enums

• forcefield::mmff94::Mmff94AtomType
• graph::BondOrder
• graph::BondStereo
• graph::ChiralType
• graph::Hybridization
• materials::sbu::CoordinationGeometry
• smarts::AtomQuery
• smarts::BondQuery
• 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
• assemble_framework
• charges::gasteiger::gasteiger_marsili_charges
• charges::gasteiger::get_gasteiger_params
• compute_charges
• compute_dipole
• compute_dos
• compute_esp
• compute_population
• compute_rmsd
• compute_sasa
• compute_uff_energy
• 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
• eht::basis::build_basis
• eht::basis::gaussian_p_value
• eht::basis::gaussian_s_value
• eht::basis::sto3g_expansion
• eht::hamiltonian::build_hamiltonian
• eht::marching_cubes::marching_cubes
• eht::overlap::build_overlap_matrix
• eht::params::get_params
• eht::params::num_basis_functions
• 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::snap_torsions_to_preferred
• 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
• materials::assembly::assemble_framework
• parse
• population::population::compute_population
• population::population::lowdin_charges
• population::population::mulliken_charges
• smarts::parse_smarts
• smarts::substruct_match
• smarts::torsion_matcher::match_experimental_torsions
• surface::sasa::compute_sasa
• surface::sasa::compute_sasa_parallel
• surface::sasa::vdw_radius
• 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

Constants

• distgeom::validation::MAX_MINIMIZED_E_PER_ATOM
• eht::params::DEFAULT_K
• 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