RDMC APIs#
- rdmc.external
- rdmc.mathlib
- rdmc.conformer_generation
- rdmc.mol
RDKitMolRDKitMol.AddNullConformer()RDKitMol.AddRedundantBonds()RDKitMol.AlignMol()RDKitMol.AssignStereochemistryFrom3D()RDKitMol.CalcRMSD()RDKitMol.CombineMol()RDKitMol.Copy()RDKitMol.EmbedConformer()RDKitMol.EmbedMultipleConfs()RDKitMol.EmbedMultipleNullConfs()RDKitMol.EmbedNullConformer()RDKitMol.FromFile()RDKitMol.FromInchi()RDKitMol.FromMol()RDKitMol.FromOBMol()RDKitMol.FromRMGMol()RDKitMol.FromSDF()RDKitMol.FromSmarts()RDKitMol.FromSmiles()RDKitMol.FromXYZ()RDKitMol.GetAdjacencyMatrix()RDKitMol.GetAllConformers()RDKitMol.GetAtomMapNumbers()RDKitMol.GetAtomMasses()RDKitMol.GetAtomicNumbers()RDKitMol.GetAtoms()RDKitMol.GetBestAlign()RDKitMol.GetBondsAsTuples()RDKitMol.GetClosedShellMol()RDKitMol.GetConformer()RDKitMol.GetConformers()RDKitMol.GetDistanceMatrix()RDKitMol.GetElementCounts()RDKitMol.GetElementSymbols()RDKitMol.GetFingerprint()RDKitMol.GetFormalCharge()RDKitMol.GetHeavyAtoms()RDKitMol.GetInternalCoordinates()RDKitMol.GetMolFrags()RDKitMol.GetPositions()RDKitMol.GetSpinMultiplicity()RDKitMol.GetSubstructMatch()RDKitMol.GetSubstructMatchAndRecipe()RDKitMol.GetSubstructMatches()RDKitMol.GetSymmSSSR()RDKitMol.GetTorsionTops()RDKitMol.GetTorsionalModes()RDKitMol.GetVdwMatrix()RDKitMol.HasCollidingAtoms()RDKitMol.HasSameConnectivity()RDKitMol.HasSameConnectivityConformer()RDKitMol.Kekulize()RDKitMol.PrepareOutputMol()RDKitMol.Reflect()RDKitMol.RemoveHs()RDKitMol.RenumberAtoms()RDKitMol.Sanitize()RDKitMol.SaturateBiradicalSites12()RDKitMol.SaturateBiradicalSitesCDB()RDKitMol.SaturateCarbene()RDKitMol.SaturateMol()RDKitMol.SetAtomMapNumbers()RDKitMol.SetPositions()RDKitMol.SetVdwMatrix()RDKitMol.ToAtoms()RDKitMol.ToGraph()RDKitMol.ToInchi()RDKitMol.ToMolBlock()RDKitMol.ToOBMol()RDKitMol.ToRWMol()RDKitMol.ToSDFFile()RDKitMol.ToSmiles()RDKitMol.ToXYZ()
generate_vdw_mat()parse_xyz_or_smiles_list()
- rdmc.mol_compare
- rdmc.fix
- rdmc.reaction
- rdmc.ts
- rdmc.view
- rdmc.conf
- rdmc.forcefield
OpenBabelFFOpenBabelFF.add_angle_constraint()OpenBabelFF.add_distance_constraint()OpenBabelFF.add_torsion_constraint()OpenBabelFF.available_force_fieldOpenBabelFF.available_solverOpenBabelFF.fix_atom()OpenBabelFF.get_optimized_mol()OpenBabelFF.is_optimizable()OpenBabelFF.molOpenBabelFF.optimize()OpenBabelFF.set_solver()OpenBabelFF.setup()OpenBabelFF.typeOpenBabelFF.update_atom_idx()
RDKitFFRDKitFF.add_angle_constraint()RDKitFF.add_distance_constraint()RDKitFF.add_torsion_constraint()RDKitFF.available_force_fieldRDKitFF.fix_atom()RDKitFF.get_conformer_energies()RDKitFF.get_energy()RDKitFF.get_optimized_mol()RDKitFF.is_optimizable()RDKitFF.make_optimizable()RDKitFF.molRDKitFF.optimize()RDKitFF.optimize_confs()RDKitFF.recover_mol()RDKitFF.setup()RDKitFF.torsional_scan_1d()RDKitFF.typeRDKitFF.update_atom_idx()
get_roo_radical_atoms()optimize_mol()
- rdmc.utils
determine_smallest_atom_index_in_torsion()find_internal_torsions()find_ring_torsions()get_atom_masses()get_closed_shell_by_add_hs()get_closed_shell_cheap()get_element_symbols()get_internal_coords()get_obmol_coords()get_substruct_match_and_recover_recipe()openbabel_mol_to_rdkit_mol()parse_xyz_by_jensen()parse_xyz_by_openbabel()rdkit_mol_to_openbabel_mol()rdkit_mol_to_openbabel_mol_manual()reverse_map()rmg_mol_to_rdkit_mol()set_obmol_coords()set_rdconf_coordinates()