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 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) auto3d() (in module rush.auto3d) Auto3DResult (class in rush.auto3d) Auto3DStats (class in rush.auto3d) 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) boltz() (in module rush.boltz) Bond (class in rush.mol) BondOrder (class in rush.mol) C ccd (rush.boltz.Modification 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() (in module rush.exess) ClosestAtomBatching (class in rush.exess) collect_run() (in module rush.client) combine_small_children (rush.exess.Octree attribute) compress_ri_b (rush.exess.SCFKeywords attribute) concatenate_hdf5_files (rush.exess.ExportKeywords attribute) conformer (rush.auto3d.Auto3DResult 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.Auto3DStats 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.RushRun 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.RushRun attribute) delta_energy_threshold (rush.exess.OptimizationConvergenceCriteria attribute) density_basis_set_projection_fallback_enabled (rush.exess.SCFKeywords attribute) density_threshold (rush.exess.SCFKeywords attribute) description (rush.client.RunOpts attribute) (rush.client.RushRun attribute) descriptor_grid (rush.exess.ExportKeywords attribute) DescriptorGrid (class in rush.exess) dimer_cutoff (rush.exess.FragKeywords attribute) distance_between_atoms() (rush.mol.Topology method) distance_metric (rush.exess.FragKeywords attribute) distance_to_point() (rush.mol.Topology method) download_object() (in module rush.client) dp_threshold (rush.exess.KSDFTKeywords attribute) E e_rel_kcal_mol (rush.auto3d.Auto3DStats attribute) e_tot_hartrees (rush.auto3d.Auto3DStats 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) energy_mev (rush.nnxtb.NnxtbResults attribute) epsilon (rush.exess.LBFGSKeywords attribute) exchange_screening_threshold (rush.exess.SCFKeywords attribute) exess() (in module rush.exess) 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) extend() (rush.mol.Chains method) (rush.mol.Residues method) (rush.mol.Topology method) (rush.mol.TRC method) F f_max (rush.auto3d.Auto3DStats attribute) 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_build_type (rush.exess.SCFKeywords attribute) force_cartesian_basis_sets (rush.exess.Model attribute) forces_mev_per_angstrom (rush.nnxtb.NnxtbResults attribute) formal_charges (rush.mol.Topology attribute) FormalCharge (class in rush.mol) FragKeywords (class in rush.exess) Fragment (class in rush.mol) fragment_formal_charges (rush.mol.Topology attribute) fragment_partial_charges (rush.mol.Topology attribute) FragmentRef (class in rush.mol) fragments (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.NnxtbResults attribute) 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_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) 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 hessian_guess (rush.exess.OptimizationKeywords attribute) homo_lumo_guess_rotation_angle (rush.exess.SCFKeywords attribute) I id (rush.boltz.LigandSequence attribute) (rush.boltz.ProteinSequence attribute) (rush.client.RushRun 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) 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) LigandSequence (class in rush.boltz) light_json (rush.exess.ExportKeywords attribute) linesearch (rush.exess.LBFGSKeywords attribute) load_structure() (in module rush.convert) M 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_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.RunError attribute) method (rush.exess.KSDFTKeywords attribute) metric (rush.exess.OptimizationConvergenceCriteria attribute) min (rush.exess.RegularDescriptorGrid attribute) min_radius (rush.exess.TrustRegionKeywords attribute) mmseqs2() (in module rush.mmseqs2) Model (class in rush.exess) Modification (class in rush.boltz) modifications (rush.boltz.ProteinSequence attribute) module rush.auto3d rush.boltz rush.client rush.convert rush.exess rush.mmseqs2 rush.mol rush.nnxtb rush.pbsa rush.prepare_complex rush.prepare_protein msa (rush.boltz.ProteinSequence attribute) N n_corrections (rush.exess.LBFGSKeywords attribute) name (rush.client.RunOpts attribute) (rush.client.RushRun 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) nnxtb() (in module rush.nnxtb) NnxtbResults (class in rush.nnxtb) nodes (rush.client.RunSpec attribute) non_amino_acid_indices() (rush.mol.Residues method) nonpolar_solvation_energy (rush.pbsa.PBSAResults attribute) O 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) optimizer_reset_interval (rush.exess.OptimizationKeywords attribute) order (rush.exess.DescriptorGrid attribute) (rush.mol.Bond attribute) oversubscribe_gpus (rush.exess.System attribute) P partial_charges (rush.mol.Topology attribute) PartialCharge (class in rush.mol) pbsa() (in module rush.pbsa) PBSAResults (class in rush.pbsa) points_per_shell (rush.exess.DescriptorGrid attribute) polar_solvation_energy (rush.pbsa.PBSAResults attribute) position (rush.boltz.Modification attribute) prepare_complex() (in module rush.prepare_complex) prepare_protein() (in module rush.prepare_protein) ProteinSequence (class in rush.boltz) pruning_scheme (rush.exess.XCGridParameters attribute) Q qmmm() (in module rush.exess) R radial_quad (rush.exess.XCGridParameters attribute) radial_size (rush.exess.CustomGridResolution 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) Restraints (class in rush.exess) result (rush.client.RushRun attribute) RunError (class in rush.client) 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 module rush.mmseqs2 module rush.mol module rush.nnxtb module rush.pbsa module rush.prepare_complex module rush.prepare_protein module RushRun (class in rush.client) S save_energy_outputs() (in module rush.exess) save_json() (in module rush.client) save_object() (in module rush.client) save_outputs() (in module rush.auto3d) (in module rush.prepare_protein) save_structure() (in module rush.convert) scale (rush.exess.DescriptorGrid attribute) SCFKeywords (class in rush.exess) SchemaVersion (class in rush.mol) 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) smiles (rush.boltz.LigandSequence attribute) solvation_energy (rush.pbsa.PBSAResults attribute) 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 (rush.auto3d.Auto3DResult attribute) status (rush.client.RushRun attribute) stdout (rush.client.RushRun attribute) step_component_threshold (rush.exess.OptimizationConvergenceCriteria 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) symbols (rush.mol.Topology attribute) System (class in rush.exess) T tags (rush.client.RunOpts attribute) (rush.client.RushRun 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_json() (in module rush.convert) (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) trace (rush.client.RunError attribute) (rush.client.RushRun attribute) training_db (rush.exess.ExportKeywords attribute) Trajectory (class in rush.exess) 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.RushRun 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) X XCGridParameters (class in rush.exess)
