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) alpha_helices (rush.mol.Chains attribute) amino_acid_indices() (rush.mol.Residues method) AminoAcidSeq (class in rush.mol) angular_size (rush.exess.CustomGridResolution attribute) atom1 (rush.mol.Bond attribute) atom2 (rush.mol.Bond attribute) AtomRef (class in rush.mol) B batch_size (rush.exess.GauXCBatching attribute) (rush.exess.SCFKeywords attribute) batches_per_batch (rush.exess.KSDFTKeywords attribute) batching (rush.exess.XCGridParameters attribute) beta_sheets (rush.mol.Chains attribute) bf_cutoff_threshold (rush.exess.SCFKeywords attribute) Bond (class in rush.mol) bond_orders (rush.exess.Nmer attribute) BondOrder (class in rush.mol) 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) Chain (class in rush.mol) chain_id (rush.mol.ResidueId attribute) ChainRef (class in rush.mol) Chains (class in rush.mol) chains (rush.mol.Chains attribute) (rush.mol.TRC attribute) charge (rush.mol.FormalCharge attribute) (rush.mol.PartialCharge attribute) check() (rush.mol.Chains method) (rush.mol.Residues method) (rush.mol.Topology method) (rush.mol.TRC method) 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_run() (in module rush.client) 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) conformer (rush.auto3d.Result attribute) (rush.auto3d.ResultPaths attribute) connectivity (rush.mol.Topology attribute) consider_weight_zero (rush.exess.XCGridParameters attribute) constraints (rush.exess.OptimizationKeywords attribute) constrict_factor (rush.exess.TrustRegionKeywords attribute) contains() (rush.mol.Chain method) (rush.mol.Residue method) converged (rush.auto3d.Stats attribute) convergence_criteria (rush.exess.OptimizationKeywords attribute) convergence_metric (rush.exess.SCFKeywords attribute) convergence_threshold (rush.exess.SCFKeywords attribute) coordinate_system (rush.exess.OptimizationKeywords attribute) cpus (rush.client.RunSpec attribute) created_at (rush.client.RushRunInfo attribute) CustomDescriptorGrid (class in rush.exess) CustomGridResolution (class in rush.exess) cutoff_type (rush.exess.FragKeywords attribute) 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.client) deleted_at (rush.client.RushRunInfo 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.client.RunOpts attribute) (rush.client.RushRunInfo 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_between_atoms() (rush.mol.Topology method) distance_method (rush.exess.ManyBodyExpansion attribute) distance_metric (rush.exess.FragKeywords attribute) (rush.exess.ManyBodyExpansion attribute) distance_to_point() (rush.mol.Topology method) dp_threshold (rush.exess.KSDFTKeywords attribute) E e_rel_kcal_mol (rush.auto3d.Stats attribute) e_tot_hartrees (rush.auto3d.Stats attribute) Element (class in rush.mol) email (rush.client.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) extend() (rush.mol.Chains method) (rush.mol.Residues method) (rush.mol.Topology method) (rush.mol.TRC method) 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.pbsa.ResultRef method) (rush.prepare.ResultRef method) fetch_object() (in module rush.client) fetch_run_info() (in module rush.client) fetch_runs() (in module rush.client) 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) fold() (in module rush.boltz) force_cartesian_basis_sets (rush.exess.Model attribute) forces_mev_per_angstrom (rush.nnxtb.Result attribute) formal_charges (rush.mol.Topology attribute) FormalCharge (class in rush.mol) format (rush.client.RushObject attribute) FragKeywords (class in rush.exess) Fragment (class in rush.mol) fragment_distance (rush.exess.Nmer attribute) fragment_formal_charges (rush.mol.Topology attribute) fragment_partial_charges (rush.mol.Topology attribute) FragmentRef (class in rush.mol) fragments (rush.exess.Nmer attribute) (rush.mol.Topology 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.client.RushObject class method) (rush.exess.Calculation class method) (rush.exess.ManyBodyExpansion class method) (rush.exess.Nmer class method) from_json() (in module rush.convert) (rush.mol.Chains static method) (rush.mol.Residues static method) (rush.mol.Topology static method) 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) from_str() (rush.mol.Element class method) 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) geometry (rush.mol.Topology attribute) get_atoms_near_point() (rush.mol.Topology method) get_fragments_near_fragment() (rush.mol.Topology method) gpus (rush.client.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) 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.client.RushRunInfo 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) insertion_code (rush.mol.ResidueId attribute) insertion_codes (rush.mol.Residues attribute) interaction_energy() (in module rush.exess) interval (rush.exess.Trajectory attribute) iptm (rush.boltz.Metrics attribute) is_amino_acid() (rush.mol.AminoAcidSeq class method) (rush.mol.Residues method) K k (rush.exess.Restraints attribute) KSDFTKeywords (class in rush.exess) L labeled (rush.mol.Chains attribute) (rush.mol.Residues attribute) labels (rush.mol.Chains attribute) (rush.mol.Residues attribute) (rush.mol.Topology attribute) lbfgs_keywords (rush.exess.OptimizationKeywords attribute) LBFGSKeywords (class in 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.client.RushRunError attribute) method (rush.exess.KSDFTKeywords attribute) (rush.exess.ManyBodyExpansion attribute) 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.client rush.convert rush.exess._energy rush.exess._optimization rush.exess._qmmm rush.mmseqs2 rush.mol rush.nnxtb rush.pbsa rush.prepare 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.client.RunOpts attribute) (rush.client.RushRunInfo attribute) new_chains_from_residue_subset() (rush.mol.Chains method) new_residues_from_subset() (rush.mol.Residues method) new_topology_from_residue_subset() (rush.mol.Topology method) new_trc_from_residue_subset() (rush.mol.TRC method) Nmer (class in rush.exess) nmers (rush.exess.ManyBodyExpansion attribute) nodes (rush.client.RunSpec attribute) non_amino_acid_indices() (rush.mol.Residues method) 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 (class in rush.client) Octree (class in rush.exess) octree (rush.exess.SpaceFillingBatching attribute) OctreeBatching (class in rush.exess) optimization() (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) (rush.mol.Bond 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) partial_charges (rush.mol.Topology attribute) PartialCharge (class in rush.mol) path (rush.client.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) 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) reference_fragment (rush.exess.FragKeywords attribute) (rush.exess.ManyBodyExpansion attribute) RegularDescriptorGrid (class in rush.exess) rejection_threshold (rush.exess.TrustRegionKeywords attribute) Residue (class in rush.mol) residue_name (rush.mol.ResidueId attribute) ResidueId (class in rush.mol) ResidueRef (class in rush.mol) Residues (class in rush.mol) residues (rush.mol.Residues attribute) (rush.mol.TRC 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.client.RushRunInfo 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) RunOpts (class in rush.client) RunSpec (class in rush.client) RunStatus (in module rush.client) rush.auto3d module rush.boltz module rush.client 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 RushObject (class in rush.client) RushRunError RushRunInfo (class in rush.client) S s_squared_eigenvalue (rush.exess.Nmer attribute) save() (rush.auto3d.ResultRef method) (rush.boltz.ResultRef method) (rush.client.RushObject method) (rush.exess.OptimizationResultRef method) (rush.exess.QMMMResultRef method) (rush.exess.ResultRef method) (rush.mmseqs2.ResultRef method) (rush.nnxtb.ResultRef method) (rush.pbsa.ResultRef method) (rush.prepare.ResultRef method) save_json() (in module rush.client) save_object() (in module rush.client) save_structure() (in module rush.convert) scale (rush.exess.DescriptorGrid attribute) SCFKeywords (class in rush.exess) SchemaVersion (class in rush.mol) search() (in module rush.mmseqs2) seq_ns (rush.mol.Residues attribute) seqs (rush.mol.Residues attribute) sequence (rush.boltz.ProteinSequence attribute) sequence_number (rush.mol.ResidueId attribute) set_opts() (in module rush.client) size (rush.client.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) start (rush.exess.Trajectory attribute) Stats (class in rush.auto3d) stats (rush.auto3d.Result attribute) (rush.auto3d.ResultPaths attribute) status (rush.client.RushRunInfo attribute) stdout (rush.client.RushRunInfo attribute) step_component_threshold (rush.exess.OptimizationConvergenceCriteria attribute) steps (rush.exess.OptimizationResult attribute) (rush.exess.OptimizationResultPaths attribute) (rush.exess.OptimizationResultRef attribute) storage (rush.client.RunSpec attribute) storage_units (rush.client.RunSpec attribute) StorageUnit (in module rush.client) store_ri_b_on_host (rush.exess.SCFKeywords attribute) sus (rush.client.RushRunInfo attribute) symbols (rush.mol.Topology attribute) System (class in rush.exess) T tags (rush.client.RunOpts attribute) (rush.client.RushRunInfo attribute) Target (in module rush.client) target (rush.client.RunSpec attribute) target_batch_size (rush.exess.SpaceFillingBatching attribute) teams_per_node (rush.exess.System attribute) tetramer_cutoff (rush.exess.FragKeywords attribute) to_dict() (in module rush.convert) (rush.client.RushObject method) (rush.mol.Chains method) (rush.mol.Residues method) (rush.mol.Topology method) to_pdb() (in module rush.convert) to_single_letter() (rush.mol.AminoAcidSeq method) Topology (class in rush.mol) topology (rush.mol.TRC attribute) total_energy (rush.exess.OptimizationStep attribute) trace (rush.client.RushRunError attribute) (rush.client.RushRunInfo 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) TRC (class in rush.mol) trimer_cutoff (rush.exess.FragKeywords attribute) trust_region_keywords (rush.exess.OptimizationKeywords attribute) TrustRegionKeywords (class in rush.exess) U updated_at (rush.client.RushRunInfo attribute) upload_object() (in module rush.client) use_c_opt (rush.exess.KSDFTKeywords attribute) use_ri (rush.exess.SCFKeywords attribute) V value (rush.exess.CustomDescriptorGrid attribute) (rush.exess.StandardDescriptorGrid attribute) velocities (rush.mol.Topology attribute) W walltime (rush.client.RunSpec attribute) (rush.client.RushRunInfo attribute) X XCGridParameters (class in rush.exess)
