Index A | C | D | E | F | G | H | I | K | L | M | O | P | R | S | T | U | W A add_angle_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) add_distance_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) add_torsion_constraint() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) AddNullConformer() (rdmc.mol.RDKitMol method) AddRedundantBonds() (rdmc.mol.RDKitMol method) AlignMol() (rdmc.mol.RDKitMol method) AssignStereochemistryFrom3D() (rdmc.mol.RDKitMol method) available_force_field (rdmc.forcefield.OpenBabelFF attribute) (rdmc.forcefield.RDKitFF attribute) available_solver (rdmc.forcefield.OpenBabelFF attribute) C CalcRMSD() (rdmc.mol.RDKitMol method) check_isomorphic_molecules() (in module rdmc.external.rmg) CombineMol() (rdmc.mol.RDKitMol method) Copy() (rdmc.mol.RDKitMol method) D determine_smallest_atom_index_in_torsion() (in module rdmc.utils) E EmbedConformer() (rdmc.mol.RDKitMol method) EmbedMultipleConfs() (rdmc.mol.RDKitMol method) EmbedMultipleNullConfs() (rdmc.mol.RDKitMol method) EmbedNullConformer() (rdmc.mol.RDKitMol method) F find_internal_torsions() (in module rdmc.utils) find_reaction_family() (in module rdmc.external.rmg) find_ring_torsions() (in module rdmc.utils) fix_atom() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) from_rdkit_mol() (in module rdmc.external.rmg) FromFile() (rdmc.mol.RDKitMol class method) FromInchi() (rdmc.mol.RDKitMol class method) FromMol() (rdmc.mol.RDKitMol class method) FromOBMol() (rdmc.mol.RDKitMol class method) FromRMGMol() (rdmc.mol.RDKitMol class method) FromSDF() (rdmc.mol.RDKitMol class method) FromSmarts() (rdmc.mol.RDKitMol class method) FromSmiles() (rdmc.mol.RDKitMol class method) FromXYZ() (rdmc.mol.RDKitMol class method) G generate_reaction_complex() (in module rdmc.external.rmg) generate_vdw_mat() (in module rdmc.mol) get_atom_masses() (in module rdmc.utils) get_closed_shell_by_add_hs() (in module rdmc.utils) get_closed_shell_cheap() (in module rdmc.utils) get_conformer_energies() (rdmc.forcefield.RDKitFF method) get_element_symbols() (in module rdmc.utils) get_energy() (rdmc.forcefield.RDKitFF method) get_internal_coords() (in module rdmc.utils) get_obmol_coords() (in module rdmc.utils) get_optimized_mol() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) get_roo_radical_atoms() (in module rdmc.forcefield) get_substruct_match_and_recover_recipe() (in module rdmc.utils) GetAdjacencyMatrix() (rdmc.mol.RDKitMol method) GetAllConformers() (rdmc.mol.RDKitMol method) GetAtomicNumbers() (rdmc.mol.RDKitMol method) GetAtomMapNumbers() (rdmc.mol.RDKitMol method) GetAtomMasses() (rdmc.mol.RDKitMol method) GetAtoms() (rdmc.mol.RDKitMol method) GetBestAlign() (rdmc.mol.RDKitMol method) GetBondsAsTuples() (rdmc.mol.RDKitMol method) GetClosedShellMol() (rdmc.mol.RDKitMol method) GetConformer() (rdmc.mol.RDKitMol method) GetConformers() (rdmc.mol.RDKitMol method) GetDistanceMatrix() (rdmc.mol.RDKitMol method) GetElementCounts() (rdmc.mol.RDKitMol method) GetElementSymbols() (rdmc.mol.RDKitMol method) GetFingerprint() (rdmc.mol.RDKitMol method) GetFormalCharge() (rdmc.mol.RDKitMol method) GetHeavyAtoms() (rdmc.mol.RDKitMol method) GetInternalCoordinates() (rdmc.mol.RDKitMol method) GetMolFrags() (rdmc.mol.RDKitMol method) GetPositions() (rdmc.mol.RDKitMol method) GetSpinMultiplicity() (rdmc.mol.RDKitMol method) GetSubstructMatch() (rdmc.mol.RDKitMol method) GetSubstructMatchAndRecipe() (rdmc.mol.RDKitMol method) GetSubstructMatches() (rdmc.mol.RDKitMol method) GetSymmSSSR() (rdmc.mol.RDKitMol method) GetTorsionalModes() (rdmc.mol.RDKitMol method) GetTorsionTops() (rdmc.mol.RDKitMol method) GetVdwMatrix() (rdmc.mol.RDKitMol method) H HasCollidingAtoms() (rdmc.mol.RDKitMol method) HasSameConnectivity() (rdmc.mol.RDKitMol method) HasSameConnectivityConformer() (rdmc.mol.RDKitMol method) I is_optimizable() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) K Kekulize() (rdmc.mol.RDKitMol method) L load_rmg_database() (in module rdmc.external.rmg) load_rxn_family_database() (in module rdmc.external.rmg) M make_optimizable() (rdmc.forcefield.RDKitFF method) module rdmc.external rdmc.external.inpwriter rdmc.external.inpwriter.gaussian rdmc.external.inpwriter.orca rdmc.external.inpwriter.qchem rdmc.external.inpwriter.utils rdmc.external.rmg rdmc.forcefield rdmc.mol rdmc.utils mol (rdmc.forcefield.OpenBabelFF property) (rdmc.forcefield.RDKitFF property) O openbabel_mol_to_rdkit_mol() (in module rdmc.utils) OpenBabelFF (class in rdmc.forcefield) optimize() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) optimize_confs() (rdmc.forcefield.RDKitFF method) optimize_mol() (in module rdmc.forcefield) P parse_xyz_by_jensen() (in module rdmc.utils) parse_xyz_by_openbabel() (in module rdmc.utils) parse_xyz_or_smiles_list() (in module rdmc.mol) PrepareOutputMol() (rdmc.mol.RDKitMol method) R rdkit_mol_to_openbabel_mol() (in module rdmc.utils) rdkit_mol_to_openbabel_mol_manual() (in module rdmc.utils) RDKitFF (class in rdmc.forcefield) RDKitMol (class in rdmc.mol) rdmc.external module rdmc.external.inpwriter module rdmc.external.inpwriter.gaussian module rdmc.external.inpwriter.orca module rdmc.external.inpwriter.qchem module rdmc.external.inpwriter.utils module rdmc.external.rmg module rdmc.forcefield module rdmc.mol module rdmc.utils module recover_mol() (rdmc.forcefield.RDKitFF method) Reflect() (rdmc.mol.RDKitMol method) RemoveHs() (rdmc.mol.RDKitMol method) RenumberAtoms() (rdmc.mol.RDKitMol method) reverse_map() (in module rdmc.utils) rmg_mol_to_rdkit_mol() (in module rdmc.utils) S Sanitize() (rdmc.mol.RDKitMol method) SaturateBiradicalSites12() (rdmc.mol.RDKitMol method) SaturateBiradicalSitesCDB() (rdmc.mol.RDKitMol method) SaturateCarbene() (rdmc.mol.RDKitMol method) SaturateMol() (rdmc.mol.RDKitMol method) set_obmol_coords() (in module rdmc.utils) set_rdconf_coordinates() (in module rdmc.utils) set_solver() (rdmc.forcefield.OpenBabelFF method) SetAtomMapNumbers() (rdmc.mol.RDKitMol method) SetPositions() (rdmc.mol.RDKitMol method) setup() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) SetVdwMatrix() (rdmc.mol.RDKitMol method) T ToAtoms() (rdmc.mol.RDKitMol method) ToGraph() (rdmc.mol.RDKitMol method) ToInchi() (rdmc.mol.RDKitMol method) ToMolBlock() (rdmc.mol.RDKitMol method) ToOBMol() (rdmc.mol.RDKitMol method) torsional_scan_1d() (rdmc.forcefield.RDKitFF method) ToRWMol() (rdmc.mol.RDKitMol method) ToSDFFile() (rdmc.mol.RDKitMol method) ToSmiles() (rdmc.mol.RDKitMol method) ToXYZ() (rdmc.mol.RDKitMol method) type (rdmc.forcefield.OpenBabelFF property) (rdmc.forcefield.RDKitFF property) U update_atom_idx() (rdmc.forcefield.OpenBabelFF method) (rdmc.forcefield.RDKitFF method) W write_gaussian_config() (in module rdmc.external.inpwriter.gaussian) write_gaussian_freq() (in module rdmc.external.inpwriter.gaussian) write_gaussian_gsm() (in module rdmc.external.inpwriter.gaussian) write_gaussian_inp() (in module rdmc.external.inpwriter.gaussian) write_gaussian_irc() (in module rdmc.external.inpwriter.gaussian) write_gaussian_opt() (in module rdmc.external.inpwriter.gaussian) write_orca_freq() (in module rdmc.external.inpwriter.orca) write_orca_gsm() (in module rdmc.external.inpwriter.orca) write_orca_irc() (in module rdmc.external.inpwriter.orca) write_orca_opt() (in module rdmc.external.inpwriter.orca) write_qchem_freq() (in module rdmc.external.inpwriter.qchem) write_qchem_irc() (in module rdmc.external.inpwriter.qchem) write_qchem_opt() (in module rdmc.external.inpwriter.qchem)
