Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X A Affinities (class in rush.boltz) affinities (rush.boltz.DiffusionSampleRef attribute) (rush.boltz.Result attribute) (rush.boltz.ResultPaths attribute) affinity_pred_value (rush.boltz.Affinities attribute) affinity_pred_value1 (rush.boltz.Affinities attribute) affinity_pred_value2 (rush.boltz.Affinities attribute) affinity_probability_binary (rush.boltz.Affinities attribute) affinity_probability_binary1 (rush.boltz.Affinities attribute) affinity_probability_binary2 (rush.boltz.Affinities attribute) algorithm (rush.exess.OptimizationKeywords attribute) angular_size (rush.exess.CustomGridResolution attribute) AuxBasisT (in module rush.exess) B BasisT (in module rush.exess) batch_size (rush.exess.GauXCBatching attribute) (rush.exess.SCFKeywords attribute) batches_per_batch (rush.exess.KSDFTKeywords attribute) batching (rush.exess.XCGridParameters attribute) bf_cutoff_threshold (rush.exess.SCFKeywords attribute) bond_orders (rush.exess.Nmer attribute) C calc (rush.exess.Result attribute) (rush.exess.ResultPaths attribute) (rush.exess.ResultRef attribute) calculate() (in module rush.exess) Calculation (class in rush.exess) calculation_time (rush.exess.Calculation attribute) ccd (rush.boltz.Modification attribute) ccsd_correction (rush.exess.Nmer attribute) chains (rush.objects.TRCPaths attribute) (rush.objects.TRCRef attribute) chelpg_charges (rush.exess.Nmer attribute) classical_water_energy (rush.exess.ManyBodyExpansion attribute) ClosestAtomBatching (class in rush.exess) coeffs_final (rush.exess.Nmer attribute) coeffs_initial (rush.exess.Nmer attribute) collect() (rush.runs.Run method) collect_run() (in module rush.runs) combine_small_children (rush.exess.Octree attribute) complex_ipde (rush.boltz.Metrics attribute) complex_iplddt (rush.boltz.Metrics attribute) complex_pde (rush.boltz.Metrics attribute) complex_plddt (rush.boltz.Metrics attribute) compress_ri_b (rush.exess.SCFKeywords attribute) concatenate_hdf5_files (rush.exess.ExportKeywords attribute) confidence_score (rush.boltz.Metrics attribute) configure() (in module rush.session) conformer (rush.auto3d.Result attribute) (rush.auto3d.ResultPaths attribute) consider_weight_zero (rush.exess.XCGridParameters attribute) constraints (rush.exess.OptimizationKeywords attribute) constrict_factor (rush.exess.TrustRegionKeywords attribute) converged (rush.auto3d.Stats attribute) convergence_criteria (rush.exess.OptimizationKeywords attribute) convergence_metric (rush.exess.SCFKeywords attribute) convergence_threshold (rush.exess.SCFKeywords attribute) ConvergenceMetricT (in module rush.exess) coordinate_system (rush.exess.OptimizationKeywords attribute) CoordinateSystemT (in module rush.exess) cpus (rush.runs.RunSpec attribute) created_at (rush.runs.RunInfo attribute) CustomDescriptorGrid (class in rush.exess) CustomGridResolution (class in rush.exess) cutoff_type (rush.exess.FragKeywords attribute) CutoffTypeT (in module rush.exess) cyclic (rush.boltz.ProteinSequence attribute) D decrease_factor (rush.exess.TrustRegionKeywords attribute) decrease_threshold (rush.exess.TrustRegionKeywords attribute) default_grid (rush.exess.DefaultGridResolution attribute) DefaultGridResolution (class in rush.exess) delete_run() (in module rush.runs) deleted_at (rush.runs.RunInfo attribute) delta_energy_threshold (rush.exess.OptimizationConvergenceCriteria attribute) delta_hf_energy (rush.exess.Nmer attribute) delta_mp2_os_correction (rush.exess.Nmer attribute) delta_mp2_ss_correction (rush.exess.Nmer attribute) density (rush.exess.Nmer attribute) density_basis_set_projection_fallback_enabled (rush.exess.SCFKeywords attribute) density_threshold (rush.exess.SCFKeywords attribute) description (rush.runs.RunInfo attribute) (rush.runs.RunOpts attribute) descriptor_grid (rush.exess.ExportKeywords attribute) DescriptorGrid (class in rush.exess) diffusion_samples (rush.boltz.ResultRef attribute) DiffusionSampleRef (class in rush.boltz) dimer_cutoff (rush.exess.FragKeywords attribute) distance_method (rush.exess.ManyBodyExpansion attribute) distance_metric (rush.exess.FragKeywords attribute) (rush.exess.ManyBodyExpansion attribute) DistanceMetricT (in module rush.exess) dp_threshold (rush.exess.KSDFTKeywords attribute) E e_rel_kcal_mol (rush.auto3d.Stats attribute) e_tot_hartrees (rush.auto3d.Stats attribute) email (rush.runs.RunOpts attribute) enable_speed (rush.exess.FragKeywords attribute) end (rush.exess.Trajectory attribute) energy() (in module rush.exess) (in module rush.nnxtb) energy_mev (rush.nnxtb.Result attribute) epsilon (rush.exess.LBFGSKeywords attribute) exchange_screening_threshold (rush.exess.SCFKeywords attribute) expanded_ccsd_correction (rush.exess.ManyBodyExpansion attribute) expanded_density (rush.exess.ManyBodyExpansion attribute) expanded_hf_energy (rush.exess.ManyBodyExpansion attribute) expanded_hf_gradients (rush.exess.ManyBodyExpansion attribute) expanded_mp2_gradients (rush.exess.ManyBodyExpansion attribute) expanded_mp2_os_correction (rush.exess.ManyBodyExpansion attribute) expanded_mp2_ss_correction (rush.exess.ManyBodyExpansion attribute) export_basis_labels (rush.exess.ExportKeywords attribute) export_bond_orders (rush.exess.ExportKeywords attribute) export_chelpg_charges (rush.exess.ExportKeywords attribute) export_density (rush.exess.ExportKeywords attribute) export_density_descriptors (rush.exess.ExportKeywords attribute) export_esp_descriptors (rush.exess.ExportKeywords attribute) export_expanded_density (rush.exess.ExportKeywords attribute) export_expanded_esp_descriptors (rush.exess.ExportKeywords attribute) export_expanded_gradient (rush.exess.ExportKeywords attribute) export_external_charge_gradient (rush.exess.ExportKeywords attribute) export_fock (rush.exess.ExportKeywords attribute) export_gradient (rush.exess.ExportKeywords attribute) export_h_caps (rush.exess.ExportKeywords attribute) export_h_core (rush.exess.ExportKeywords attribute) export_hessian (rush.exess.ExportKeywords attribute) export_hessian_frequencies (rush.exess.ExportKeywords attribute) export_mass_weighted_hessian (rush.exess.ExportKeywords attribute) export_molecular_orbital_coeffs (rush.exess.ExportKeywords attribute) export_mulliken_charges (rush.exess.ExportKeywords attribute) export_overlap (rush.exess.ExportKeywords attribute) export_relaxed_mp2_density_correction (rush.exess.ExportKeywords attribute) ExportKeywords (class in rush.exess) exports (rush.exess.Result attribute) (rush.exess.ResultPaths attribute) (rush.exess.ResultRef attribute) F f_max (rush.auto3d.Stats attribute) fetch() (rush.auto3d.ResultRef method) (rush.boltz.ResultRef method) (rush.exess.OptimizationResultRef method) (rush.exess.QMMMResultRef method) (rush.exess.ResultRef method) (rush.mmseqs2.ResultRef method) (rush.nnxtb.ResultRef method) (rush.objects.RushObject method) (rush.objects.TRCRef method) (rush.pbsa.ResultRef method) (rush.prepare.ResultRef method) (rush.runs.Run method) fetch_bytes() (rush.objects.RushObject method) fetch_dict() (rush.objects.RushObject method) fetch_json() (rush.objects.RushObject method) fetch_list() (rush.objects.RushObject method) fetch_object() (in module rush.objects) fetch_run_info() (in module rush.runs) fetch_runs() (in module rush.runs) fix_heavy (rush.exess.OptimizationKeywords attribute) (rush.exess.Restraints attribute) fixed_atoms (rush.exess.OptimizationKeywords attribute) (rush.exess.Restraints attribute) fixed_fragments (rush.exess.OptimizationKeywords attribute) (rush.exess.Restraints attribute) flatten_symmetric (rush.exess.ExportKeywords attribute) fock (rush.exess.Nmer attribute) fock_build_type (rush.exess.SCFKeywords attribute) FockBuildTypeT (in module rush.exess) fold() (in module rush.boltz) force_cartesian_basis_sets (rush.exess.Model attribute) forces_mev_per_angstrom (rush.nnxtb.Result attribute) format (rush.objects.RushObject attribute) FragKeywords (class in rush.exess) fragment_distance (rush.exess.Nmer attribute) FragmentLevelT (in module rush.exess) fragments (rush.exess.Nmer attribute) free_atoms (rush.exess.OptimizationKeywords attribute) (rush.exess.Restraints attribute) free_fragments (rush.exess.OptimizationKeywords attribute) (rush.exess.Restraints attribute) frequencies_inv_cm (rush.nnxtb.Result attribute) from_dict() (rush.exess.Calculation class method) (rush.exess.ManyBodyExpansion class method) (rush.exess.Nmer class method) (rush.objects.RushObject class method) from_json() (in module rush.convert) from_mmcif() (in module rush.convert) from_pdb() (in module rush.convert) from_raw_output() (rush.auto3d.ResultRef class method) (rush.boltz.ResultRef class method) (rush.exess.OptimizationResultRef class method) (rush.exess.QMMMResultRef class method) (rush.exess.ResultRef class method) (rush.mmseqs2.ResultRef class method) (rush.nnxtb.ResultRef class method) (rush.pbsa.ResultRef class method) (rush.prepare.ResultRef class method) from_sdf() (in module rush.convert) frozen_angle_slippage_tolerance_degrees (rush.exess.OptimizationKeywords attribute) frozen_distance_slippage_tolerance_angstroms (rush.exess.OptimizationKeywords attribute) functional (rush.exess.KSDFTKeywords attribute) G GauXCBatching (class in rush.exess) generate() (in module rush.auto3d) geometries (rush.exess.QMMMResult attribute) gpus (rush.runs.RunSpec attribute) gpus_per_team (rush.exess.System attribute) gradient_screening_threshold (rush.exess.SCFKeywords attribute) gradient_threshold (rush.exess.OptimizationConvergenceCriteria attribute) grid (rush.exess.KSDFTKeywords attribute) group_shared_exponents (rush.exess.SCFKeywords attribute) gtol (rush.exess.LBFGSKeywords attribute) H h_caps (rush.exess.Nmer attribute) h_core (rush.exess.Nmer attribute) hessian_guess (rush.exess.OptimizationKeywords attribute) HessianGuessTypeT (in module rush.exess) hf_energy (rush.exess.Nmer attribute) hf_gradients (rush.exess.Nmer attribute) homo_lumo_guess_rotation_angle (rush.exess.SCFKeywords attribute) I id (rush.boltz.LigandSequence attribute) (rush.boltz.ProteinSequence attribute) (rush.runs.Run property) (rush.runs.RunInfo attribute) include_waters (rush.exess.Trajectory attribute) included_fragments (rush.exess.FragKeywords attribute) increase_factor (rush.exess.TrustRegionKeywords attribute) increase_threshold (rush.exess.TrustRegionKeywords attribute) initial_radius (rush.exess.TrustRegionKeywords attribute) interaction_energy() (in module rush.exess) interval (rush.exess.Trajectory attribute) iptm (rush.boltz.Metrics attribute) K k (rush.exess.Restraints attribute) KSDFTKeywords (class in rush.exess) KSDFTMethodT (in module rush.exess) L lbfgs_keywords (rush.exess.OptimizationKeywords attribute) LBFGSKeywords (class in rush.exess) LBFGSLinesearchT (in module rush.exess) level (rush.exess.FragKeywords attribute) ligand_iptm (rush.boltz.Metrics attribute) LigandSequence (class in rush.boltz) light_json (rush.exess.ExportKeywords attribute) linesearch (rush.exess.LBFGSKeywords attribute) load_structure() (in module rush.convert) M ManyBodyExpansion (class in rush.exess) max (rush.exess.RegularDescriptorGrid attribute) max_depth (rush.exess.Octree attribute) max_diis_history_length (rush.exess.SCFKeywords attribute) max_distance (rush.exess.Octree attribute) max_gpu_memory_mb (rush.exess.System attribute) max_gradient_component (rush.exess.OptimizationStep attribute) max_iters (rush.exess.SCFKeywords attribute) max_linesearch (rush.exess.LBFGSKeywords attribute) max_radius (rush.exess.TrustRegionKeywords attribute) max_size (rush.exess.Octree attribute) merge_trcs() (in module rush.convert) message (rush.runs.RunError attribute) method (rush.exess.KSDFTKeywords attribute) (rush.exess.ManyBodyExpansion attribute) MethodT (in module rush.exess) metric (rush.exess.OptimizationConvergenceCriteria attribute) Metrics (class in rush.boltz) metrics (rush.boltz.DiffusionSampleRef attribute) (rush.boltz.Result attribute) (rush.boltz.ResultPaths attribute) min (rush.exess.RegularDescriptorGrid attribute) min_radius (rush.exess.TrustRegionKeywords attribute) Model (class in rush.exess) model (rush.boltz.DiffusionSampleRef attribute) (rush.boltz.Result attribute) (rush.boltz.ResultPaths attribute) models (rush.prepare.ResultRef attribute) Modification (class in rush.boltz) modifications (rush.boltz.ProteinSequence attribute) module rush.auto3d rush.boltz rush.convert rush.exess._energy rush.exess._optimization rush.exess._qmmm rush.mmseqs2 rush.mol rush.nnxtb rush.pbsa rush.prepare rush.session molecular_orbital_energies (rush.exess.Nmer attribute) mp2_gradients (rush.exess.Nmer attribute) mp2_os_correction (rush.exess.Nmer attribute) mp2_ss_correction (rush.exess.Nmer attribute) msa (rush.boltz.ProteinSequence attribute) msas (rush.mmseqs2.ResultRef attribute) mulliken_charges (rush.exess.Nmer attribute) N n_corrections (rush.exess.LBFGSKeywords attribute) name (rush.runs.RunInfo attribute) (rush.runs.RunOpts attribute) Nmer (class in rush.exess) nmers (rush.exess.ManyBodyExpansion attribute) nodes (rush.runs.RunSpec attribute) nonpolar_solvation_energy (rush.pbsa.Result attribute) (rush.pbsa.ResultRef attribute) num_basis_fns (rush.exess.Nmer attribute) num_iters (rush.exess.ManyBodyExpansion attribute) (rush.exess.Nmer attribute) O ObjectID (in module rush.objects) Octree (class in rush.exess) octree (rush.exess.SpaceFillingBatching attribute) OctreeBatching (class in rush.exess) optimization() (in module rush.exess) OptimizationAlgorithmTypeT (in module rush.exess) OptimizationConvergenceCriteria (class in rush.exess) OptimizationKeywords (class in rush.exess) OptimizationResult (class in rush.exess) OptimizationResultPaths (class in rush.exess) OptimizationResultRef (class in rush.exess) OptimizationStep (class in rush.exess) optimizer_reset_interval (rush.exess.OptimizationKeywords attribute) order (rush.exess.DescriptorGrid attribute) output (rush.exess.QMMMResultPaths attribute) (rush.exess.QMMMResultRef attribute) (rush.nnxtb.ResultPaths attribute) (rush.nnxtb.ResultRef attribute) (rush.pbsa.ResultPaths attribute) overlap (rush.exess.Nmer attribute) oversubscribe_gpus (rush.exess.System attribute) P pae (rush.boltz.DiffusionSampleRef attribute) (rush.boltz.Result attribute) (rush.boltz.ResultPaths attribute) path (rush.objects.RushObject attribute) plddt (rush.boltz.DiffusionSampleRef attribute) (rush.boltz.Result attribute) (rush.boltz.ResultPaths attribute) points_per_shell (rush.exess.DescriptorGrid attribute) polar_solvation_energy (rush.pbsa.Result attribute) (rush.pbsa.ResultRef attribute) position (rush.boltz.Modification attribute) protein() (in module rush.prepare) protein_iptm (rush.boltz.Metrics attribute) protein_ligand() (in module rush.prepare) ProteinSequence (class in rush.boltz) pruning_scheme (rush.exess.XCGridParameters attribute) PruningSchemeT (in module rush.exess) ptm (rush.boltz.Metrics attribute) Q qmmbe (rush.exess.Calculation attribute) qmmm() (in module rush.exess) QMMMResult (class in rush.exess) QMMMResultPaths (class in rush.exess) QMMMResultRef (class in rush.exess) R radial_quad (rush.exess.XCGridParameters attribute) radial_size (rush.exess.CustomGridResolution attribute) RadialQuadT (in module rush.exess) reference_fragment (rush.exess.FragKeywords attribute) (rush.exess.ManyBodyExpansion attribute) RegularDescriptorGrid (class in rush.exess) rejection_threshold (rush.exess.TrustRegionKeywords attribute) residues (rush.objects.TRCPaths attribute) (rush.objects.TRCRef attribute) resolution (rush.exess.XCGridParameters attribute) resolve() (rush.exess.KSDFTKeywords static method) Restraints (class in rush.exess) Result (class in rush.auto3d) (class in rush.boltz) (class in rush.exess) (class in rush.mmseqs2) (class in rush.nnxtb) (class in rush.pbsa) result (rush.runs.RunInfo attribute) ResultPaths (class in rush.auto3d) (class in rush.boltz) (class in rush.exess) (class in rush.mmseqs2) (class in rush.nnxtb) (class in rush.pbsa) ResultRef (class in rush.auto3d) (class in rush.boltz) (class in rush.exess) (class in rush.mmseqs2) (class in rush.nnxtb) (class in rush.pbsa) (class in rush.prepare) Run (class in rush.runs) RunBackendError (class in rush.runs) RunError (class in rush.runs) RunID (in module rush.runs) RunInfo (class in rush.runs) RunModuleError (class in rush.runs) RunOpts (class in rush.runs) RunSpec (class in rush.runs) RunStatus (in module rush.runs) rush.auto3d module rush.boltz module rush.convert module rush.exess._energy module rush.exess._optimization module rush.exess._qmmm module rush.mmseqs2 module rush.mol module rush.nnxtb module rush.pbsa module rush.prepare module rush.session module RushObject (class in rush.objects) S s_squared_eigenvalue (rush.exess.Nmer attribute) save() (rush.auto3d.ResultRef method) (rush.boltz.ResultRef method) (rush.exess.OptimizationResultRef method) (rush.exess.QMMMResultRef method) (rush.exess.ResultRef method) (rush.mmseqs2.ResultRef method) (rush.nnxtb.ResultRef method) (rush.objects.RushObject method) (rush.objects.TRCRef method) (rush.pbsa.ResultRef method) (rush.prepare.ResultRef method) (rush.runs.Run method) save_json() (in module rush.objects) save_object() (in module rush.objects) save_structure() (in module rush.convert) scale (rush.exess.DescriptorGrid attribute) SCFKeywords (class in rush.exess) search() (in module rush.mmseqs2) sequence (rush.boltz.ProteinSequence attribute) size (rush.objects.RushObject attribute) smiles (rush.boltz.LigandSequence attribute) solvation_energy (rush.pbsa.Result attribute) (rush.pbsa.ResultRef attribute) solvation_energy() (in module rush.pbsa) sp_threshold (rush.exess.KSDFTKeywords attribute) SpaceFillingBatching (class in rush.exess) spacing (rush.exess.RegularDescriptorGrid attribute) standard_orientation (rush.exess.Model attribute) StandardDescriptorGrid (class in rush.exess) StandardOrientationT (in module rush.exess) start (rush.exess.Trajectory attribute) Stats (class in rush.auto3d) stats (rush.auto3d.Result attribute) (rush.auto3d.ResultPaths attribute) status (rush.runs.RunInfo attribute) stdout (rush.runs.RunInfo attribute) step_component_threshold (rush.exess.OptimizationConvergenceCriteria attribute) steps (rush.exess.OptimizationResult attribute) (rush.exess.OptimizationResultPaths attribute) (rush.exess.OptimizationResultRef attribute) storage (rush.runs.RunSpec attribute) storage_units (rush.runs.RunSpec attribute) StorageUnit (in module rush.runs) store_ri_b_on_host (rush.exess.SCFKeywords attribute) sus (rush.runs.RunInfo attribute) System (class in rush.exess) T tags (rush.runs.RunInfo attribute) (rush.runs.RunOpts attribute) Target (in module rush.runs) target (rush.runs.RunSpec attribute) target_batch_size (rush.exess.SpaceFillingBatching attribute) teams_per_node (rush.exess.System attribute) TensorLike (in module rush.exess) tetramer_cutoff (rush.exess.FragKeywords attribute) to_dict() (in module rush.convert) (rush.objects.RushObject method) to_pdb() (in module rush.convert) topology (rush.objects.TRCPaths attribute) (rush.objects.TRCRef attribute) total_energy (rush.exess.OptimizationStep attribute) trace (rush.runs.RunError attribute) (rush.runs.RunInfo attribute) training_db (rush.exess.ExportKeywords attribute) Trajectory (class in rush.exess) trajectory (rush.exess.OptimizationResult attribute) (rush.exess.OptimizationResultPaths attribute) (rush.exess.OptimizationResultRef attribute) TRCPaths (class in rush.objects) TRCRef (class in rush.objects) trimer_cutoff (rush.exess.FragKeywords attribute) trust_region_keywords (rush.exess.OptimizationKeywords attribute) TrustRegionKeywords (class in rush.exess) U updated_at (rush.runs.RunInfo attribute) upload() (rush.objects.TRCRef class method) upload_object() (in module rush.objects) use_c_opt (rush.exess.KSDFTKeywords attribute) use_ri (rush.exess.SCFKeywords attribute) V value (rush.exess.CustomDescriptorGrid attribute) (rush.exess.StandardDescriptorGrid attribute) W walltime (rush.runs.RunInfo attribute) (rush.runs.RunSpec attribute) X XCBatchingSchemeT (in module rush.exess) XCGridParameters (class in rush.exess) XCGridResolutionT (in module rush.exess)
