Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W A accept_best() (in module tmol.relax) AcceptorHybridization (class in tmol.score) add_conformer_sampler() (tmol.pack.PackerTask method) add_conformer_sampler_by_block_mask() (tmol.pack.PackerTask method) add_constraints() (tmol.pose.ConstraintSet method) add_constraints_to_all_poses() (tmol.pose.ConstraintSet method) add_metal_coordination() (in module tmol.io) all_score_types() (tmol.score.ScoreFunction method) all_terms() (tmol.score.ScoreFunction method) Angles (in module tmol.numeric) annotate_packed_block_types() (tmol.pack.rotamer.ChiSampler method) (tmol.pack.rotamer.ConformerSampler method) (tmol.pack.rotamer.dunbrack.DunbrackChiSampler method) (tmol.pack.rotamer.FallbackSampler method) (tmol.pack.rotamer.FixedAAChiSampler method) (tmol.pack.rotamer.IncludeCurrentSampler method) (tmol.pack.rotamer.NaChiRotamerSampler method) annotate_packed_block_types_w_dslf_conn_inds() (in module tmol.pose) annotate_packed_block_types_w_kinematic_conns() (in module tmol.pose) annotate_residue_type() (tmol.pack.rotamer.ChiSampler method) (tmol.pack.rotamer.ConformerSampler method) (tmol.pack.rotamer.dunbrack.DunbrackChiSampler method) (tmol.pack.rotamer.FallbackSampler method) (tmol.pack.rotamer.FixedAAChiSampler method) (tmol.pack.rotamer.IncludeCurrentSampler method) (tmol.pack.rotamer.NaChiRotamerSampler method) apply_fragment_connections() (in module tmol.ligand) as_dict() (tmol.io.CanonicalForm method) assemble_input() (in module tmol.io) assign_chi_dofs_from_samples() (in module tmol.pack.rotamer) atom37_slot_map_for_ordering() (in module tmol.io) Atom37MappingError atom_array_from_cif() (in module tmol.io) atom_array_from_file() (in module tmol.io) atom_array_from_mol2() (in module tmol.io) atom_name() (tmol.database.RawResidueType method) atom_records_from_coords() (in module tmol.io) atom_records_from_pose_stack() (in module tmol.io) AtomFingerprint (class in tmol.pack.rotamer) AtomType (class in tmol.database) AtomTypeParamResolver (class in tmol.score) AtomTypeParams (class in tmol.score) atomworks_from_pose_stack() (in module tmol.io) AttrMapping (class in tmol.utility) AttrMutableMapping (class in tmol.utility) AutoNumber (class in tmol.utility) B BackboneTorsionEnergyTerm (class in tmol.score.backbone_torsion) BackboneTorsionTermCreator (class in tmol.score.terms) beta2016_score_function() (in module tmol.score) bi_bii_weight() (in module tmol.score.na_torsion) bind_to_args() (in module tmol.utility) biotite_from_canonical_form() (in module tmol.io) biotite_from_pose_stack() (in module tmol.io) block_identity_map() (tmol.pose.PoseStack method) block_type() (tmol.pose.PoseStack method) block_type_indices() (tmol.score.AtomTypeParamResolver method) block_type_params() (in module tmol.score.na_torsion) block_types_from_original() (tmol.pack.PackerPalette method) BlockPairScoringModule (class in tmol.score) BondDOF (class in tmol.kinematics) BondDOFTypes (class in tmol.kinematics) bonds_and_bond_ranges() (in module tmol.chemical) BondType (class in tmol.chemical) BSplineInterpolation (class in tmol.numeric) build_context_from_biotite() (in module tmol.io) build_coord_mask_for_mask_and_interacting_atoms() (in module tmol.ops) build_coord_mask_for_mask_and_nearby_blocks() (in module tmol.ops) build_coords_from_icoors() (in module tmol.chemical) build_ideal_coords() (in module tmol.chemical) build_kinforest_network() (in module tmol.optimization) build_missing_sidechains() (in module tmol.pack) build_rotamers() (in module tmol.pack.rotamer) build_sidechain_coord_mask() (in module tmol.ops) build_split_block_mapping() (in module tmol.ligand) bump_check (tmol.pack.PackerTask property) C calculate_block_pair_ddg() (in module tmol.ops) calculate_fragment_interactions() (in module tmol.score) calculate_rotamer_coords() (in module tmol.pack.rotamer) canonical_form_from_atom37() (in module tmol.io) canonical_form_from_atomworks() (in module tmol.io) canonical_form_from_biotite() (in module tmol.io) canonical_form_from_pdb() (in module tmol.io) canonical_form_from_pose_stack() (in module tmol.io) canonical_ordering_for_atomworks() (in module tmol.io) canonical_ordering_for_biotite() (in module tmol.io) CanonicalForm (class in tmol.io) CanonicalOrdering (class in tmol.io) CartBondedEnergyTerm (class in tmol.score.cartbonded) CartBondedTermCreator (class in tmol.score.terms) CartesianMinimizer (class in tmol.optimization) CartesianMoveMap (class in tmol.kinematics) CartesianSfxnNetwork (class in tmol.optimization) Casting (class in tmol.types) cat() (in module tmol.types) cat_differently_sized_tensors() (in module tmol.utility.tensor) chem_comp_types_from_cif() (in module tmol.ligand) ChemicalDatabase (class in tmol.database) ChiSampler (class in tmol.pack.rotamer) cif_from_atom_array() (in module tmol.io) classlogger_for() (in module tmol.utility) clone() (tmol.pose.ConstraintSet method) (tmol.pose.PoseStack method) clone_sharing_topology() (tmol.pose.PoseStack method) component_chemistry_from_cif() (in module tmol.io) compute_block_adjacency() (in module tmol.ops) compute_block_centroids_and_furthest_dist() (in module tmol.ops) concatenate() (tmol.pose.ConstraintSet class method) (tmol.pose.InterBlockBondsep class method) ConformerSampler (class in tmol.pack.rotamer) ConjugatedSCSampler (class in tmol.pack.rotamer) constrain_all_ca() (in module tmol.score.constraint) ConstraintEnergyTerm (class in tmol.score.constraint) ConstraintSet (class in tmol.pose) ConstraintTermCreator (class in tmol.score.terms) construct_kin_module_data_for_pose() (in module tmol.kinematics) construct_single_residue_kinforest() (in module tmol.pack.rotamer) constructor_convert() (in module tmol.types) convert_args() (in module tmol.types) ConvertAttrs (class in tmol.types) Coord64Array (in module tmol.numeric) coord_dihedrals() (in module tmol.numeric) CoordArray (in module tmol.kinematics) count_unique_blocks() (tmol.pose.ConstraintSet static method) create_dunbrack_sampler_from_database() (in module tmol.pack.rotamer.dunbrack) create_empty() (tmol.pose.ConstraintSet class method) create_mainchain_coordinate_constraints() (in module tmol.score.constraint) create_pose_stack_from_sequences() (in module tmol.io) create_restrict_to_repacking_mask() (tmol.pack.PackerPalette method) create_samples_for_poses() (tmol.pack.rotamer.ChiSampler method) (tmol.pack.rotamer.ConformerSampler method) (tmol.pack.rotamer.FallbackSampler method) (tmol.pack.rotamer.IncludeCurrentSampler method) create_stable_subset() (tmol.database.ParameterDatabase method) D default_canonical_ordering() (in module tmol.io) default_conformer_samplers() (tmol.pack.PackerPalette method) default_packed_block_types() (in module tmol.io) defines_rotamers_for_rt() (tmol.pack.rotamer.ChiSampler method) (tmol.pack.rotamer.ConformerSampler method) (tmol.pack.rotamer.dunbrack.DunbrackChiSampler method) (tmol.pack.rotamer.FallbackSampler method) (tmol.pack.rotamer.FixedAAChiSampler method) (tmol.pack.rotamer.IncludeCurrentSampler method) (tmol.pack.rotamer.NaChiRotamerSampler method) detect_nonstandard_residues() (in module tmol.ligand) Dim (class in tmol.types) disable_packing_by_block_mask() (tmol.pack.PackerTask method) disable_sampler_by_block_mask() (tmol.pack.PackerTask method) DisulfideEnergyTerm (class in tmol.score.disulfide) DisulfideTermCreator (class in tmol.score.terms) DOFMetadata (class in tmol.kinematics) DOFTypes (class in tmol.kinematics) DunbrackChiSampler (class in tmol.pack.rotamer.dunbrack) DunbrackEnergyTerm (class in tmol.score.dunbrack) DunbrackTermCreator (class in tmol.score.terms) DunSamplerPBTCache (class in tmol.pack.rotamer.dunbrack) DunSamplerRTCache (class in tmol.pack.rotamer.dunbrack) E EdgeType (class in tmol.kinematics) ElecEnergyTerm (class in tmol.score.elec) ElecTermCreator (class in tmol.score.terms) empty() (tmol.pose.InterBlockBondsep class method) enable_cuda_graphs() (tmol.score.WholePoseScoringModule method) eval_na_torsion_for_pose() (in module tmol.score.na_torsion) exclusive_cumsum() (in module tmol.utility) exclusive_cumsum1d() (in module tmol.utility) (in module tmol.utility.tensor) exclusive_cumsum2d() (in module tmol.utility) (in module tmol.utility.tensor) exclusive_cumsum2d_and_totals() (in module tmol.utility.tensor) exclusive_cumsum2d_w_totals() (in module tmol.utility) expand_coords() (tmol.pose.PoseStack method) expand_fragmented_ligands() (in module tmol.ligand) expand_into_task() (tmol.pack.rotamer.ConjugatedSCSampler method) (tmol.pack.rotamer.SidechainSampler method) extended() (tmol.chemical.ResidueTypeSet method) extended_pose_stack_from_sequences() (in module tmol.io) F FallbackSampler (class in tmol.pack.rotamer) fast_relax() (in module tmol.relax) fetch_pdb() (in module tmol.io) fill_dofs_for_samples() (tmol.pack.rotamer.ChiSampler method) (tmol.pack.rotamer.ConformerSampler method) (tmol.pack.rotamer.FallbackSampler method) (tmol.pack.rotamer.IncludeCurrentSampler method) first_sc_atoms_for_rt() (tmol.pack.rotamer.ChiSampler method) (tmol.pack.rotamer.ConformerSampler method) (tmol.pack.rotamer.dunbrack.DunbrackChiSampler method) (tmol.pack.rotamer.FallbackSampler method) (tmol.pack.rotamer.FixedAAChiSampler method) (tmol.pack.rotamer.IncludeCurrentSampler method) (tmol.pack.rotamer.NaChiRotamerSampler method) FixedAAChiSampler (class in tmol.pack.rotamer) FoldForest (class in tmol.kinematics) for_kinforest() (tmol.kinematics.DOFMetadata class method) forward() (tmol.kinematics.PoseStackKinematicsModule method) (tmol.optimization.CartesianSfxnNetwork method) (tmol.optimization.KinForestSfxnNetwork method) forward_sparse_entries() (tmol.score.RotamerScoringModule method) fragment_ids_from_atom_array() (in module tmol.ligand) FragmentConnection (class in tmol.ligand) FragmentInteractionScores (class in tmol.score) frame_from_coords() (in module tmol.chemical) from_block_type_names() (tmol.pose.PoseStackBuilder class method) from_bonded_graph() (tmol.pose.InterBlockBondsep class method) from_coordinates() (tmol.numeric.BSplineInterpolation class method) from_database() (tmol.pack.rotamer.NaChiRotamerSampler class method) (tmol.pack.rotamer.SidechainSampler class method) (tmol.score.AtomTypeParamResolver class method) from_edges() (tmol.kinematics.FoldForest class method) from_file() (tmol.database.ChemicalDatabase class method) (tmol.database.ParameterDatabase class method) (tmol.database.ScoringDatabase class method) from_frame() (tmol.kinematics.DOFMetadata class method) from_pose_stack() (tmol.kinematics.MoveMap class method) from_poses() (tmol.pose.PoseStackBuilder class method) from_restype_list() (tmol.pose.PackedBlockTypes class method) from_sfxn_file() (tmol.score.ScoreFunction class method) G GenBondedEnergyTerm (class in tmol.score.genbonded) GenBondedTermCreator (class in tmol.score.terms) get_all_residue_positions() (in module tmol.utility) get_all_segment_positions() (in module tmol.utility) get_chem_comp_type() (in module tmol.ligand) get_constraint_set() (tmol.pose.PoseStack method) get_converter() (in module tmol.types) get_default() (tmol.chemical.ResidueTypeSet class method) (tmol.database.ChemicalDatabase class method) (tmol.database.ParameterDatabase class method) get_named_torsions() (in module tmol.pose) get_torsion_names() (in module tmol.pose) get_validator() (in module tmol.types) get_weight() (tmol.score.ScoreFunction method) H HBondEnergyTerm (class in tmol.score.hbond) HBondTermCreator (class in tmol.score.terms) I ignore_unused_kwargs() (in module tmol.utility) impose_top_rotamer_assignments() (in module tmol.pack) include_paths() (in module tmol) IncludeCurrentSampler (class in tmol.pack.rotamer) IndexedBonds (class in tmol.score) inject_ligand_preparations() (in module tmol.ligand) inject_params_file() (in module tmol.ligand) inject_params_files() (in module tmol.ligand) inject_residue_params() (in module tmol.database) InterBlockBondsep (class in tmol.pose) interpolate() (tmol.numeric.BSplineInterpolation method) inverseKin() (in module tmol.kinematics) invert_mapping() (in module tmol.utility.tensor) is_polymer_linking_component_type() (in module tmol.ligand) is_real_block() (tmol.pose.PoseStack method) J join_tensors_and_report_real_entries() (in module tmol.utility.tensor) JumpDOF (class in tmol.kinematics) JumpDOFTypes (class in tmol.kinematics) just_one() (in module tmol.utility) K KinDOF (class in tmol.kinematics) KinematicModuleData (class in tmol.kinematics) KinForest (class in tmol.kinematics) KinForestScanData (class in tmol.kinematics) KinForestSfxnNetwork (class in tmol.optimization) L ligand_smiles_from_atom_array() (in module tmol.ligand) LigandFragmentDefinition (class in tmol.ligand) LigandPreparation (class in tmol.ligand) LigandPreparationError like_kwargs() (in module tmol.types) LJLKEnergyTerm (class in tmol.score.ljlk) LJLKTermCreator (class in tmol.score.terms) LKBallEnergyTerm (class in tmol.score.lk_ball) LKBallTermCreator (class in tmol.score.terms) load_params_file() (in module tmol.ligand) logger_for_class() (in module tmol.utility) LoggerMixin (class in tmol.utility) M max_n_atoms (tmol.pose.PoseStack property) max_n_block_atoms (tmol.pose.PoseStack property) max_n_blocks (tmol.pose.PoseStack property) max_n_pose_atoms (tmol.pose.PoseStack property) MCAtomIndices (class in tmol.score.constraint) MCFingerprint (class in tmol.pack.rotamer) measure_pose_dofs() (in module tmol.pack.rotamer) merge_conformer_samples() (in module tmol.pack.rotamer) MetalCoordinationTermCreator (class in tmol.score.terms) MinimizerMap (class in tmol.kinematics) module tmol tmol.chemical tmol.database tmol.io tmol.kinematics tmol.ligand tmol.numeric tmol.ops tmol.optimization tmol.pack tmol.pack.rotamer tmol.pack.rotamer.dunbrack tmol.pose tmol.relax tmol.score tmol.score.constraint tmol.score.na_torsion tmol.score.terms tmol.types tmol.utility tmol.utility.tensor MoveMap (class in tmol.kinematics) multi_body_terms() (tmol.score.ScoreFunction method) N n_ats_per_block (tmol.pose.PoseStack property) n_poses (tmol.pose.PoseStack property) n_res_per_pose (tmol.pose.PoseStack property) na_torsion_subterms() (in module tmol.score.na_torsion) NaChiRotamerSampler (class in tmol.pack.rotamer) NaTorsionEnergyTerm (class in tmol.score.na_torsion) NaTorsionParams (class in tmol.score.na_torsion) NaTorsionTermCreator (class in tmol.score.terms) NDArray (class in tmol.types) node() (tmol.kinematics.KinForest class method) NodeType (class in tmol.kinematics) nonstandard_residue_info_from_mol2() (in module tmol.ligand) nonstandard_residue_info_from_mol2_block() (in module tmol.ligand) nonstandard_residue_info_from_smiles_via_mol2() (in module tmol.ligand) nplus1d_tensor_from_list() (in module tmol.utility.tensor) nvtx_range() (in module tmol.utility) O one2three() (in module tmol.chemical) one_body_terms() (tmol.score.ScoreFunction method) OpenBabelUnavailableError or_bump_check() (tmol.pack.PackerTask method) or_expand_chi() (tmol.pack.PackerTask method) or_expand_chi_to() (tmol.pack.PackerTask method) P pack_rotamers() (in module tmol.pack) packed_block_types_for_atomworks() (in module tmol.io) packed_block_types_for_biotite() (in module tmol.io) PackedBlockTypes (class in tmol.pose) PackedRotamerKintree (class in tmol.pack.rotamer) PackerEnergyTables (class in tmol.pack) PackerPalette (class in tmol.pack) PackerPalleteAnnotation (class in tmol.pack) PackerTask (class in tmol.pack) ParameterDatabase (class in tmol.database) PatchedChemicalDatabase (class in tmol.database) polymer_entity_residues() (in module tmol.ligand) polymer_index() (in module tmol.score.na_torsion) pose_stack_from_atom37() (in module tmol.io) pose_stack_from_atom37_and_topology() (in module tmol.io) pose_stack_from_biotite() (in module tmol.io) pose_stack_from_canonical_aa_atom37() (in module tmol.io) pose_stack_from_canonical_form_and_context() (in module tmol.io) pose_stack_from_cif() (in module tmol.io) pose_stack_from_file() (in module tmol.io) pose_stack_from_pdb() (in module tmol.io) pose_stack_to_pdb_string() (in module tmol.io) PoseBuildContext (class in tmol.io) PoseStack (class in tmol.pose) PoseStackBuilder (class in tmol.pose) PoseStackKinematicsModule (class in tmol.kinematics) pre_work_initialization() (tmol.score.ScoreFunction method) prepare_atom37_pose_builder() (in module tmol.io) prepare_ligand_from_cif() (in module tmol.ligand) prepare_ligand_from_mol2() (in module tmol.ligand) prepare_ligand_from_smiles() (in module tmol.ligand) prepare_ligands() (in module tmol.ligand) prepare_ligands_from_smiles() (in module tmol.ligand) prepare_polymer_residue() (in module tmol.ligand) prepare_single_ligand() (in module tmol.ligand) PreparedAtom37PoseBuilder (class in tmol.io) print_row_numbered_tensor() (in module tmol.utility.tensor) pucker_weights() (in module tmol.score.na_torsion) Q qualified_name() (in module tmol.utility) R RawResidueType (class in tmol.database) real_atoms (tmol.pose.PoseStack property) reasonable_fold_forest() (tmol.kinematics.FoldForest class method) recombine_fragmented_ligands() (in module tmol.ligand) RefEnergyTerm (class in tmol.score.ref) RefinedResidueType (class in tmol.chemical) RefTermCreator (class in tmol.score.terms) register_converter() (in module tmol.types) register_validator() (in module tmol.types) relax_pack_min_step() (in module tmol.relax) release_retained_state() (tmol.optimization.CartesianMinimizer method) remove_metal_coordination() (in module tmol.io) remove_term_for_score_type() (tmol.score.ScoreFunction method) render_block_pair_scoring_module() (tmol.score.ScoreFunction method) render_rotamer_scoring_module() (tmol.score.ScoreFunction method) render_whole_pose_scoring_module() (tmol.score.ScoreFunction method) replicate_constraints() (tmol.pose.ConstraintSet static method) res_mask_to_coord_mask() (in module tmol.ops) ResidueTypeSet (class in tmol.chemical) resolve_block_type_names() (in module tmol.pose) resolve_device() (in module tmol.utility) resolve_name3() (tmol.io.CanonicalOrdering method) restrict_absent_name3s() (tmol.pack.PackerTask method) restrict_to_repacking() (tmol.pack.PackerTask method) root_node() (tmol.kinematics.KinForest class method) RotamerKintree (class in tmol.pack.rotamer) RotamerScoringModule (class in tmol.score) RotamerSet (class in tmol.pack.rotamer) run_cart_min() (in module tmol.optimization) run_kin_min() (in module tmol.optimization) run_min() (in module tmol.optimization) S sampler_name() (tmol.pack.rotamer.ChiSampler class method) (tmol.pack.rotamer.ConformerSampler class method) (tmol.pack.rotamer.dunbrack.DunbrackChiSampler class method) (tmol.pack.rotamer.FallbackSampler class method) (tmol.pack.rotamer.FixedAAChiSampler class method) (tmol.pack.rotamer.IncludeCurrentSampler class method) (tmol.pack.rotamer.NaChiRotamerSampler class method) samples_after_other_samplers (tmol.pack.rotamer.ConformerSampler attribute) (tmol.pack.rotamer.FallbackSampler attribute) score_interactions() (tmol.score.BlockPairScoringModule method) score_term_creator() (in module tmol.score.terms) score_type_covered_by_contained_term() (tmol.score.ScoreFunction method) scored_torsion_bonds() (in module tmol.score.na_torsion) ScoreFunction (class in tmol.score) ScoreTermFactory (class in tmol.score.terms) ScoreType (class in tmol.score) ScoringDatabase (class in tmol.database) select_poses() (tmol.pose.InterBlockBondsep method) selection_gallery() (in module tmol.io) SeqToken (class in tmol.pose) set_chi_sample_budget() (tmol.pack.PackerTask method) set_compare() (in module tmol.pack) set_move_all_jump_dofs_for_jump() (tmol.kinematics.MoveMap method) set_move_all_jump_dofs_for_root_jump() (tmol.kinematics.MoveMap method) set_move_all_mc_tors_for_blocks() (tmol.kinematics.MoveMap method) set_move_atom_dof_for_blocks() (tmol.kinematics.MoveMap method) set_move_jump_dof_for_jumps() (tmol.kinematics.MoveMap method) set_move_jump_dof_for_root_jumps() (tmol.kinematics.MoveMap method) set_move_mc_tor_for_blocks() (tmol.kinematics.MoveMap method) set_move_named_torsion_for_blocks() (tmol.kinematics.MoveMap method) set_move_sc_tor_for_blocks() (tmol.kinematics.MoveMap method) set_named_torsions() (in module tmol.kinematics) set_option() (tmol.score.ScoreFunction method) set_options() (tmol.score.ScoreFunction method) set_weight() (tmol.score.ScoreFunction method) SetPackerTask (class in tmol.pack) Shape (class in tmol.types) shape (tmol.pose.InterBlockBondsep property) Shape.Factory (class in tmol.types) SidechainSampler (class in tmol.pack.rotamer) smiles_in_tokens() (in module tmol.pose) split() (tmol.pose.ConstraintSet method) (tmol.pose.PoseStack method) (tmol.pose.SplitBlockMapping method) SplitBlockEntry (class in tmol.pose) SplitBlockMapping (class in tmol.pose) stretch() (in module tmol.utility.tensor) stretch2() (in module tmol.utility.tensor) SubscriptableType (class in tmol.types) sugar_ring_atoms() (in module tmol.score.na_torsion) switchable_view() (in module tmol.io) syn_weight() (in module tmol.score.na_torsion) T Tensor (class in tmol.types) TensorGroup (class in tmol.types) TermCreator (class in tmol.score.terms) three2one() (in module tmol.chemical) tmol module tmol.chemical module tmol.database module tmol.io module tmol.kinematics module tmol.ligand module tmol.numeric module tmol.ops module tmol.optimization module tmol.pack module tmol.pack.rotamer module tmol.pack.rotamer.dunbrack module tmol.pose module tmol.relax module tmol.score module tmol.score.constraint module tmol.score.na_torsion module tmol.score.terms module tmol.types module tmol.utility module tmol.utility.tensor module to() (tmol.pose.ConstraintSet method) (tmol.types.TensorGroup method) to_atom_lines() (in module tmol.io) to_dense() (tmol.pose.InterBlockBondsep method) to_directed() (tmol.score.IndexedBonds class method) to_pdb() (in module tmol.io) to_pdb_lines() (in module tmol.io) tokenize_sequences() (in module tmol.pose) torch_dtype() (in module tmol.types) two_body_terms() (tmol.score.ScoreFunction method) type_idx() (tmol.score.AtomTypeParamResolver method) U u() (in module tmol.utility) union_convert() (in module tmol.types) unique_val() (in module tmol.utility) unsplit_pose_stack() (in module tmol.ligand) V validate() (tmol.types.Shape method) validate_args() (in module tmol.types) validate_convert() (in module tmol.types) validate_fold_forest() (in module tmol.kinematics) validate_isinstance() (in module tmol.types) ValidateAttrs (class in tmol.types) view() (in module tmol.io) W weights_tensor() (tmol.score.ScoreFunction method) WholePoseScoringModule (class in tmol.score) with_added_residues() (tmol.database.PatchedChemicalDatabase method) with_symmetric_gly() (tmol.database.ParameterDatabase method) with_variants_applied() (tmol.database.PatchedChemicalDatabase method) write_params_file() (in module tmol.ligand) write_params_from_mol2() (in module tmol.ligand) write_pose_stack_pdb() (in module tmol.io)
