Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W _ _atom_annotations (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _atoms (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _bonds (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _current_pose (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _KDTrees (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _name (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _pdbqt_filename (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _pose_data (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) _positions (meeko.molecule_pdbqt.PDBQTMolecule attribute) (meeko.PDBQTMolecule attribute) A AA_recipe (class in meeko.chemtempgen) adapt_pdbqt_for_autodock4_flexres() (meeko.PDBQTWriterLegacy static method) add_atom() (meeko.molsetup.MoleculeSetup method) add_atom_types (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) add_bond() (meeko.molsetup.MoleculeSetup method) add_dict() (meeko.polymer.ResidueChemTemplates method) (meeko.ResidueChemTemplates method) add_dihedral_interaction() (meeko.molsetup.MoleculeSetupExternalToolkit method) add_hydrogens() (meeko.rdkit_mol_create.RDKitMolCreate static method) (meeko.RDKitMolCreate static method) add_index_map (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) add_json_file() (meeko.polymer.ResidueChemTemplates method) (meeko.ResidueChemTemplates method) add_molsetup() (meeko.molsetup.UniqAtomParams method) add_parameter() (meeko.molsetup.UniqAtomParams method) add_pose_to_mol() (meeko.rdkit_mol_create.RDKitMolCreate class method) (meeko.RDKitMolCreate class method) add_pseudoatom() (meeko.molsetup.MoleculeSetup method) add_rotamers() (meeko.molsetup.MoleculeSetup method) add_rotamers_to_polymer_molsetups() (in module meeko) (in module meeko.polymer) add_sandbox_coordinates() (meeko.rdkit_mol_create.RDKitMolCreate class method) (meeko.RDKitMolCreate class method) add_variants() (in module meeko.chemtempgen) adjacent_smartsmol (meeko.polymer.ResiduePadder attribute) (meeko.ResiduePadder attribute) adjacent_smartsmol_mapidx (meeko.polymer.ResiduePadder attribute) (meeko.ResiduePadder attribute) ambiguous (meeko.polymer.ResidueChemTemplates attribute) (meeko.ResidueChemTemplates attribute) ambiguous_flexres_choices (meeko.RDKitMolCreate attribute) apply_atom_mappings() (in module meeko.polymer) are_fourier_series_identical() (meeko.molsetup.MoleculeSetupExternalToolkit static method) Atom (class in meeko.molsetup) atom_index (meeko.molsetup.Restraint attribute) (meeko.Restraint attribute) atom_name (meeko.chemtempgen.ChemicalComponent attribute) atom_names (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) (meeko.polymer.ResidueTemplate attribute) (meeko.ResidueTemplate attribute) atom_params (meeko.MoleculePreparation attribute) (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.preparation.MoleculePreparation attribute) atom_to_ring_id (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.RDKitMoleculeSetup attribute) atom_type (meeko.molsetup.Atom attribute) atomic_num (meeko.molsetup.Atom attribute) atoms (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) atoms() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) (meeko.PDBQTReceptor method) atoms_by_properties() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) AtomTyper (class in meeko) available_atom_properties() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) B Bond (class in meeko.molsetup) bond_info (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) bonds_removed (meeko.molsetup.RingClosureInfo attribute) break_long_remark_lines() (meeko.PDBQTWriterLegacy static method) breakable (meeko.molsetup.Bond attribute) build_linked_CCs() (in module meeko.chemtempgen) build_noncovalent_CC() (in module meeko.chemtempgen) C calc_flex() (meeko.MoleculePreparation method) (meeko.preparation.MoleculePreparation method) canon_id (meeko.molsetup.Bond attribute) cap() (in module meeko.chemtempgen) cap_allowed_smarts (meeko.chemtempgen.AA_recipe attribute) (meeko.chemtempgen.NA_recipe attribute) cap_protonate (meeko.chemtempgen.AA_recipe attribute) (meeko.chemtempgen.NA_recipe attribute) charge (meeko.molsetup.Atom attribute) charge_atom_prop (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) charge_model (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) check() (meeko.polymer.ResidueTemplate method) (meeko.ResidueTemplate method) check_external_ring_break() (meeko.MoleculePreparation static method) (meeko.preparation.MoleculePreparation static method) ChemicalComponent (class in meeko.chemtempgen) ChemicalComponent_LoggingControler (class in meeko.chemtempgen) clean_atoms() (meeko.molsetup.MoleculeSetup method) closest_atoms() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) (meeko.PDBQTReceptor method) closest_atoms_from_positions() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) (meeko.PDBQTReceptor method) combine_rdkit_mols() (meeko.rdkit_mol_create.RDKitMolCreate static method) (meeko.RDKitMolCreate static method) coord (meeko.molsetup.Atom attribute) copy() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.molsetup.Restraint method) (meeko.RDKitMoleculeSetup method) (meeko.Restraint method) CovalentBuilder (class in meeko) create_from_defaults() (meeko.polymer.ResidueChemTemplates class method) (meeko.ResidueChemTemplates class method) D defaults (meeko.Hydrate attribute) delay_angstroms (meeko.molsetup.Restraint attribute) (meeko.Restraint attribute) delete_atom() (meeko.molsetup.MoleculeSetup method) delete_bond() (meeko.molsetup.MoleculeSetup method) delete_rotamers() (meeko.molsetup.MoleculeSetup method) deprecated_setup_access (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) deprotonate() (in module meeko.chemtempgen) dihedral_interactions (meeko.molsetup.RDKitMoleculeSetup attribute), [1] (meeko.RDKitMoleculeSetup attribute) dihedral_labels (meeko.molsetup.RDKitMoleculeSetup attribute), [1] (meeko.RDKitMoleculeSetup attribute) dihedral_model (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) dihedral_params (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) dihedral_partaking_atoms (meeko.molsetup.RDKitMoleculeSetup attribute), [1] (meeko.RDKitMoleculeSetup attribute) divide_int_gracefully() (in module meeko.polymer) double_bond_penalty (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) E embed() (in module meeko.chemtempgen) embed_allowed_smarts (meeko.chemtempgen.AA_recipe attribute) (meeko.chemtempgen.NA_recipe attribute) error (meeko.polymer.PolymerCreationError attribute) espaloma_model (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) expected_json_keys (meeko.molsetup.Atom attribute) (meeko.molsetup.Bond attribute) (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.molsetup.Restraint attribute) (meeko.molsetup.Ring attribute) (meeko.Monomer attribute) (meeko.Polymer attribute) (meeko.polymer.Monomer attribute) (meeko.polymer.Polymer attribute) (meeko.polymer.ResidueChemTemplates attribute) (meeko.polymer.ResiduePadder attribute) (meeko.polymer.ResidueTemplate attribute) (meeko.RDKitMoleculeSetup attribute) (meeko.ResidueChemTemplates attribute) (meeko.ResiduePadder attribute) (meeko.ResidueTemplate attribute) (meeko.Restraint attribute) export_chem_templates_to_json() (in module meeko.chemtempgen) export_static_atom_params() (meeko.Polymer method) (meeko.polymer.Polymer method) F fetch_from_pdb() (in module meeko.chemtempgen) filter() (meeko.polymer.NoAtomMapWarning method) find_graph_paths() (in module meeko.polymer) find_inter_mols_bonds() (in module meeko.polymer) find_pattern() (meeko.molsetup.MoleculeSetupExternalToolkit method) (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) find_smarts() (meeko.CovalentBuilder method) flexibility_model (meeko.molsetup.MoleculeSetup attribute) flexibilize_sidechain() (meeko.Polymer method) (meeko.polymer.Polymer method) flexible_amides (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) flexres (meeko.RDKitMolCreate attribute) from_cif() (meeko.chemtempgen.ChemicalComponent class method) from_config() (meeko.MoleculePreparation class method) (meeko.preparation.MoleculePreparation class method) from_dict() (meeko.molsetup.UniqAtomParams class method) from_file() (meeko.molecule_pdbqt.PDBQTMolecule class method) (meeko.PDBQTMolecule class method) from_json_file() (meeko.MoleculePreparation class method) (meeko.polymer.ResidueChemTemplates class method) (meeko.preparation.MoleculePreparation class method) (meeko.ResidueChemTemplates class method) from_mol() (meeko.molsetup.RDKitMoleculeSetup class method) (meeko.RDKitMoleculeSetup class method) from_pdb_string() (meeko.Polymer class method) (meeko.polymer.Polymer class method) from_pdbqt_filename() (meeko.PDBQTReceptor class method) from_pdbqt_mol() (meeko.rdkit_mol_create.RDKitMolCreate class method) (meeko.RDKitMolCreate class method) from_pqr_string() (meeko.Polymer class method) (meeko.polymer.Polymer class method) from_prody() (meeko.Polymer class method) (meeko.polymer.Polymer class method) G get_atom_idx_by_names() (in module meeko.chemtempgen) get_atom_idx_by_patterns() (in module meeko.chemtempgen) get_atom_indices_by_residue() (meeko.PDBQTReceptor static method) get_atom_params() (meeko.MoleculePreparation static method) (meeko.preparation.MoleculePreparation static method) get_atom_type() (meeko.molsetup.MoleculeSetup method) get_atomic_num() (meeko.molsetup.MoleculeSetup method) get_bond_id() (meeko.molsetup.Bond static method) get_bonds_in_ring() (meeko.molsetup.MoleculeSetup static method) get_charge() (meeko.molsetup.MoleculeSetup method) get_conformer_with_modified_positions() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) get_coord() (meeko.molsetup.MoleculeSetup method) get_defaults_dict() (meeko.MoleculePreparation class method) (meeko.preparation.MoleculePreparation class method) get_equivalent_atoms() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) get_ignored_monomers() (meeko.Polymer method) (meeko.polymer.Polymer method) get_indices_from_atom_params() (meeko.molsetup.UniqAtomParams method) get_is_ignore() (meeko.molsetup.MoleculeSetup method) get_mol_name() (meeko.molsetup.MoleculeSetupExternalToolkit method) (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) get_mol_with_modified_positions() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) get_molAtomMapNumbers() (in module meeko.polymer) get_neighbors() (meeko.molsetup.MoleculeSetup method) get_num_mol_atoms() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) get_pdbinfo() (meeko.molsetup.MoleculeSetup method) get_pretty_smiles() (in module meeko.chemtempgen) get_reactive_config() (in module meeko) get_smiles_and_order() (meeko.molsetup.MoleculeSetupExternalToolkit method) (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) get_smiles_with_atom_names() (in module meeko.chemtempgen) get_symmetries_for_rmsd() (meeko.molsetup.RDKitMoleculeSetup static method) (meeko.RDKitMoleculeSetup static method) get_updated_positions() (in module meeko.polymer) get_valid_monomers() (meeko.Polymer method) (meeko.polymer.Polymer method) graph (meeko.molsetup.Atom attribute) guess_flexres_smiles() (meeko.rdkit_mol_create.RDKitMolCreate class method) (meeko.RDKitMolCreate class method) H handle_parsing_situations() (in module meeko.polymer) has_flexible_residues() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) has_implicit_hydrogens() (meeko.molsetup.RDKitMoleculeSetup static method) (meeko.RDKitMoleculeSetup static method) has_water_molecules() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) Hydrate (class in meeko) hydrate (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) I index (meeko.molsetup.Atom attribute) index1 (meeko.molsetup.Bond attribute) index2 (meeko.molsetup.Bond attribute) init_atom() (meeko.molsetup.MoleculeSetupExternalToolkit method) (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) init_bond() (meeko.molsetup.MoleculeSetupExternalToolkit method) (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) input_atom_params (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) input_resname (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) is_dummy (meeko.molsetup.Atom attribute) is_flexres_atom (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) is_ignore (meeko.molsetup.Atom attribute) is_movable (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) is_pseudo_atom (meeko.molsetup.Atom attribute) J json_encoder() (meeko.molsetup.Atom class method) (meeko.molsetup.Bond class method) (meeko.molsetup.MoleculeSetup class method) (meeko.molsetup.RDKitMoleculeSetup class method) (meeko.molsetup.Restraint class method) (meeko.molsetup.Ring class method) (meeko.Monomer class method) (meeko.Polymer class method) (meeko.polymer.Monomer class method) (meeko.polymer.Polymer class method) (meeko.polymer.ResidueChemTemplates class method) (meeko.polymer.ResiduePadder class method) (meeko.polymer.ResidueTemplate class method) (meeko.RDKitMoleculeSetup class method) (meeko.ResidueChemTemplates class method) (meeko.ResiduePadder class method) (meeko.ResidueTemplate class method) (meeko.Restraint class method) K kcal_per_angstrom_square (meeko.molsetup.Restraint attribute) (meeko.Restraint attribute) keep_chorded_rings (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) keep_equivalent_rings (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) L link_labels (meeko.chemtempgen.ChemicalComponent attribute) (meeko.polymer.ResidueTemplate attribute) (meeko.ResidueTemplate attribute) load_atom_params (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) log (meeko.Polymer attribute) (meeko.polymer.Polymer attribute) lookup_filename() (meeko.polymer.ResidueChemTemplates static method) (meeko.ResidueChemTemplates static method) M macrocycle_allow_A (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) make_canonical() (meeko.chemtempgen.ChemicalComponent method) make_capped() (meeko.chemtempgen.ChemicalComponent method) make_embedded() (meeko.chemtempgen.ChemicalComponent method) make_link_labels_from_names() (meeko.chemtempgen.ChemicalComponent method) make_link_labels_from_patterns() (meeko.chemtempgen.ChemicalComponent method) make_pretty_smiles() (meeko.chemtempgen.ChemicalComponent method) mapidx_from_raw (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) mapidx_to_raw (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) mapping_by_mcs() (in module meeko.polymer) match() (meeko.polymer.ResidueTemplate method) (meeko.ResidueTemplate method) max_ring_size (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) meeko module meeko.chemtempgen module meeko.molecule_pdbqt module meeko.molsetup module meeko.polymer module merge_terminal_atoms() (meeko.molsetup.MoleculeSetup method) merge_these_atom_types (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) min_ring_size (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) modified_atom_positions (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.RDKitMoleculeSetup attribute) module meeko meeko.chemtempgen meeko.molecule_pdbqt meeko.molsetup meeko.polymer mol (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.polymer.ResidueTemplate attribute) (meeko.RDKitMoleculeSetup attribute) (meeko.ResidueTemplate attribute) mol_contains_unexpected_element() (in module meeko.chemtempgen) MoleculePreparation (class in meeko) (class in meeko.preparation) MoleculeSetup (class in meeko.molsetup) MoleculeSetupExternalToolkit (class in meeko.molsetup) molsetup (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) molsetup_mapidx (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) Monomer (class in meeko) (class in meeko.polymer) monomers (meeko.Polymer attribute) (meeko.polymer.Polymer attribute) N NA_recipe (class in meeko.chemtempgen) name (meeko.molecule_pdbqt.PDBQTMolecule property) (meeko.MoleculePreparation attribute) (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.PDBQTMolecule property) neighbor_atoms() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) (meeko.PDBQTReceptor method) NoAtomMapWarning (class in meeko.polymer) O offatom_params (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) oids_block_from_setup() (in module meeko) orient_water() (meeko.Hydrate static method) P packaged_params (meeko.MoleculePreparation attribute) padded_mol (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) padders (meeko.polymer.ResidueChemTemplates attribute) (meeko.ResidueChemTemplates attribute) param_names (meeko.molsetup.UniqAtomParams attribute) parameterize() (meeko.Monomer method) (meeko.Polymer method) (meeko.polymer.Monomer method) (meeko.polymer.Polymer method) params (meeko.molsetup.UniqAtomParams attribute) parent (meeko.chemtempgen.ChemicalComponent attribute) parse_offxml() (in module meeko) parse_residue_string() (meeko.CovalentBuilder class method) path (meeko.MoleculePreparation attribute) pattern_to_label_mapping_standard (meeko.chemtempgen.AA_recipe attribute) (meeko.chemtempgen.NA_recipe attribute) pdbinfo (meeko.molsetup.Atom attribute) PDBQTMolecule (class in meeko) (class in meeko.molecule_pdbqt) PDBQTReceptor (class in meeko) PDBQTWriterLegacy (class in meeko) perceive_rings() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) Polymer (class in meeko) (class in meeko.polymer) PolymerCreationError pose_id (meeko.molecule_pdbqt.PDBQTMolecule property) (meeko.PDBQTMolecule property) positions() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.PDBQTMolecule method) (meeko.PDBQTReceptor method) prepare() (meeko.MoleculePreparation method) (meeko.preparation.MoleculePreparation method) process() (meeko.CovalentBuilder method) PSEUDOATOM_ATOMIC_NUM (meeko.molsetup.MoleculeSetup attribute) pseudoatom_count (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) pseudos_by_atom (meeko.molsetup.RingClosureInfo attribute) R raw_input_mols (meeko.Polymer attribute) (meeko.polymer.Polymer attribute) raw_rdkit_mol (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) rdkit_mol (meeko.chemtempgen.ChemicalComponent attribute) (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) RDKitMolCreate (class in meeko) (class in meeko.rdkit_mol_create) RDKitMoleculeSetup (class in meeko) (class in meeko.molsetup) reactive_smarts (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) reactive_smarts_idx (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) rec (meeko.CovalentBuilder attribute) recharge() (in module meeko.chemtempgen) recommendations (meeko.polymer.PolymerCreationError attribute) rectify_charges() (in module meeko.polymer) remark_index_map() (meeko.PDBQTWriterLegacy class method) remove_atoms_with_mapping() (in module meeko.polymer) remove_elements() (meeko.molsetup.RDKitMoleculeSetup static method) (meeko.RDKitMoleculeSetup static method) remove_smiles (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) remove_unmapped_atoms_from_mol() (in module meeko.polymer) residue_chem_templates (meeko.Polymer attribute) (meeko.polymer.Polymer attribute) residue_template_key (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) residue_templates (meeko.polymer.ResidueChemTemplates attribute) (meeko.ResidueChemTemplates attribute) ResidueChemTemplates (class in meeko) (class in meeko.polymer) ResiduePadder (class in meeko) (class in meeko.polymer) residues (meeko.CovalentBuilder attribute) ResidueTemplate (class in meeko) (class in meeko.polymer) ResidueTemplate_check() (meeko.chemtempgen.ChemicalComponent method) resname (meeko.chemtempgen.ChemicalComponent attribute) restrain_to() (meeko.molsetup.RDKitMoleculeSetup method) (meeko.RDKitMoleculeSetup method) Restraint (class in meeko) (class in meeko.molsetup) restraints (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) rigid_macrocycles (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) rigidify_bonds_indices (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) rigidify_bonds_smarts (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) Ring (class in meeko.molsetup) ring_closure_info (meeko.molsetup.MoleculeSetup attribute) ring_id (meeko.molsetup.Ring attribute) RingClosureInfo (class in meeko.molsetup) rings (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) rmsd_symmetry_indices (meeko.molsetup.RDKitMoleculeSetup attribute) (meeko.RDKitMoleculeSetup attribute) rotamers (meeko.molsetup.MoleculeSetup attribute) (meeko.molsetup.RDKitMoleculeSetup attribute) rotatable (meeko.molsetup.Bond attribute) rxn (meeko.polymer.ResiduePadder attribute) (meeko.ResiduePadder attribute) S score (meeko.molecule_pdbqt.PDBQTMolecule property) (meeko.PDBQTMolecule property) set_atom_names() (meeko.Monomer method) (meeko.polymer.Monomer method) set_atom_type() (meeko.molsetup.MoleculeSetup method) set_atom_type_from_uniq_atom_params() (meeko.molsetup.MoleculeSetup method) setup (meeko.MoleculePreparation property) (meeko.preparation.MoleculePreparation property) show() (meeko.molsetup.MoleculeSetup method) skip_types (meeko.PDBQTReceptor attribute) smiles_exh (meeko.chemtempgen.ChemicalComponent attribute) stitch() (meeko.Polymer method) (meeko.polymer.Polymer method) T target_coords (meeko.molsetup.Restraint attribute) (meeko.Restraint attribute) template (meeko.Monomer attribute) (meeko.polymer.Monomer attribute) to_pdb() (meeko.Polymer method) (meeko.polymer.Polymer method) traceback (meeko.polymer.PolymerCreationError attribute) transform() (meeko.CovalentBuilder method) true_atom_count (meeko.molsetup.MoleculeSetup property) type_everything() (meeko.AtomTyper class method) U UniqAtomParams (class in meeko.molsetup) untyped_macrocycles (meeko.MoleculePreparation attribute) (meeko.preparation.MoleculePreparation attribute) update_H_positions() (in module meeko.polymer) V variant_dict (meeko.chemtempgen.AA_recipe attribute) (meeko.chemtempgen.NA_recipe attribute) W write_coord_string() (meeko.molsetup.MoleculeSetup method) write_from_polymer() (meeko.PDBQTWriterLegacy class method) write_pdbqt_file() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.MoleculePreparation method) (meeko.PDBQTMolecule method) (meeko.preparation.MoleculePreparation method) write_pdbqt_string() (meeko.molecule_pdbqt.PDBQTMolecule method) (meeko.MoleculePreparation method) (meeko.PDBQTMolecule method) (meeko.preparation.MoleculePreparation method) write_sd_string() (meeko.rdkit_mol_create.RDKitMolCreate static method) (meeko.RDKitMolCreate static method) write_string() (meeko.PDBQTWriterLegacy class method) write_string_from_polymer() (meeko.PDBQTWriterLegacy class method)
