| Name of deprecated class, field or method | Deprecation version | Recommended class, field or method | 
| #####  chemaxon.struc |  |  | 
| MolAtom.setForSpecIsotopeSymbol(String sym) | Marvin 6.3 | chemaxon.struc.MolAtom.setSpecIsotopeSymbolPreferred()  chemaxon.struc.MolAtom.setMassno() | 
| Molecule.clonelesscopy(MoleculeGraph g) | Marvin 6.3 | Not supported feature. | 
| Molecule.ungroupSgroup(int i, int opts) | Marvin 6.3 | chemaxon.struc.Molecule.ungroupSgroup(Sgroup) | 
| Molecule.ungroupSgroup(int i) | Marvin 6.3 | chemaxon.struc.Molecule.ungroupSgroup(Sgroup) | 
| Molecule.ungroupSgroups(int type) | Marvin 6.3 | chemaxon.struc.Molecule.ungroupSgroups(EnumSet) | 
| MoleculeGraph.clonelesscopy(MoleculeGraph graph) | Marvin 6.3 | Not supported feature. | 
| MoleculeGraph.getStereo2(MolBond b) | Marvin 6.3 | chemaxon.struc.MoleculeGraph.getEZStereo(MolBond) | 
| RgMolecule.clonelesscopy(MoleculeGraph g) | Marvin 6.3 | Not supported feature. | 
| RxnMolecule.clonelesscopy(MoleculeGraph g) | Marvin 6.3 | Not supported feature. | 
| Sgroup.getType() | Marvin 6.3 | chemaxon.struc.Sgroup.getSgroupType() | 
| ### Removed elements in the API |  |  | 
| Name of removed class, field or method | Removal version | Recommended class, field or method | 
| #####  chemaxon.struc.util.bondutil |  |  | 
| MolBondUtil | Marvin 6.3 | Internal usage only. |