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Deprecated elements in the API

Name of deprecated class, field or methodDeprecation versionRecommended class, field or method

chemaxon.core.calculations.valencecheck

ValenceCheckOptions.ValenceCheckOptions(boolean localAromatic, boolean traditionalNallowed)Marvin 6.2chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

chemaxon.struc

MolAtom.getRadical()Marvin 6.2chemaxon.struc.MolAtom.getRadicalValue()
MolAtom.setRadical(int r)Marvin 6.2chemaxon.struc.MolAtom.setRadicalValue(Radical)
MolBond.isRemovable()Marvin 6.2Not supported feature.
Molecule.RM_KEEP_LEAVINGGROUPSMarvin 6.2Not supported feature.
Molecule.isGUIContracted()Marvin 6.2chemaxon.struc.Molecule.hasContractedSgroup()
Molecule.mergeAtoms(MolAtom that, MolAtom node)Marvin 6.2chemaxon.struc.util.moleculeutil.MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)
Molecule.setGUIContracted(boolean contract, int opts)Marvin 6.2chemaxon.struc.Molecule.expandSgroups(int)
chemaxon.struc.Molecule.contractSgroups(int)
chemaxon.struc.sgroup.Expandable.LEAVE_COORDS_UNCHANGED
Molecule.setGUIContracted(boolean contract)Marvin 6.2chemaxon.struc.Molecule.expandSgroups(int)
chemaxon.struc.Molecule.contractSgroups(int)
chemaxon.struc.sgroup.Expandable.LEAVE_COORDS_UNCHANGED
MoleculeGraph.createBHtab()Marvin 6.2No replacement.
MoleculeGraph.insertAtom(int i, MolAtom atom)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.add(MolAtom)
MoleculeGraph.insertBond(int i, MolBond bond)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.add(MolBond)
MoleculeGraph.mergeAtoms(MolAtom replacementAtom, MolAtom origAtom)Marvin 6.2chemaxon.struc.util.moleculeutil.MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)
MoleculeGraph.replaceBond(MolBond oldb, MolBond newb)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.removeBond(MolBond)
chemaxon.struc.MoleculeGraph.add(MolBond)
MoleculeGraph.setAtom(int i, MolAtom atom)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.removeAtom(int)
chemaxon.struc.MoleculeGraph.add(MolAtom)
chemaxon.struc.MolAtom
MoleculeGraph.setBond(int i, MolBond b)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.removeBond(MolBond)
chemaxon.struc.MoleculeGraph.add(MolBond)
RgMolecule.mergeAtoms(MolAtom that, MolAtom a)Marvin 6.2chemaxon.struc.util.moleculeutil.MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)
RgMolecule.replaceBond(MolBond olde, MolBond newe)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.RgMolecule.removeBond(MolBond)
chemaxon.struc.RgMolecule.add(MolBond)
RgMolecule.setAtom(int iu, MolAtom node)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.RgMolecule.removeAtom(MolAtom)
chemaxon.struc.RgMolecule.add(MolAtom)
RgMolecule.setBond(int iu, MolBond edge)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.RgMolecule.removeBond(MolBond)
chemaxon.struc.RgMolecule.add(MolBond)
RxnMolecule.mergeAtoms(MolAtom that, MolAtom node)Marvin 6.2

chemaxon.struc.util.moleculeutil.MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)


RxnMolecule.replaceBond(MolBond olde, MolBond newe)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.RxnMolecule.removeBond(MolBond)
chemaxon.struc.RxnMolecule.add(MolBond)
RxnMolecule.setAtom(int iu, MolAtom node)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.RxnMolecule.removeAtom(MolAtom)
chemaxon.struc.RxnMolecule.add(MolAtom)
RxnMolecule.setBond(int iu, MolBond edge)Marvin 6.2chemaxon.struc.MoleculeGraph
chemaxon.struc.RxnMolecule.removeBond(MolBond)
chemaxon.struc.RxnMolecule.add(MolBond)
SelectionMolecule.setBond(int i, MolBond bond)Marvin 6.2chemaxon.struc.SelectionMolecule.removeBond(MolBond)
chemaxon.struc.SelectionMolecule.add(MolBond)
Sgroup.setGUIStateRecursively(boolean contract, int opts)Marvin 6.2chemaxon.struc.Molecule.setGUIContracted(boolean)
chemaxon.struc.Molecule.setGUIContracted(boolean, int)
Sgroup.setGUIStateRecursively(boolean v)Marvin 6.2chemaxon.struc.Molecule.setGUIContracted(boolean)
chemaxon.struc.Molecule.setGUIContracted(boolean, int)
Sgroup.setXState(int state, int opts)Marvin 6.2chemaxon.struc.Sgroup.setXState(int)

chemaxon.struc.sgroup

Expandable.COORDS_UPDATEMarvin 6.2Not supported feature.
Expandable.REVERSIBLE_EXPANDMarvin 6.2chemaxon.struc.sgroup.Expandable.LEAVE_COORDS_UNCHANGED
SuperatomSgroup.cloneLeavingGroups(SuperatomSgroup sasg)Marvin 6.2Not supported feature.
SuperatomSgroup.expandOther(int opts, Molecule moltoexpand)Marvin 6.2chemaxon.struc.sgroup.SuperatomSgroup.expand(int)
SuperatomSgroup.getParentSgroupGraph()Marvin 6.2chemaxon.struc.sgroup.SuperatomSgroup.getSgroupGraph()
SuperatomSgroup.removeLeavingGroup(int order)Marvin 6.2Not supported feature.
SuperatomSgroup.setCrossingBondType(int order, BondType newType)Marvin 6.2Not supported feature.
SuperatomSgroup.setLeavingGroup(int order, int atNo, String alternativeName, BondType crossingBondType)Marvin 6.2Not supported feature.
SuperatomSgroup.setLeavingGroup(int order, int atNo, String alternativeName)Marvin 6.2Not supported feature.
SuperatomSgroup.setLeavingGroup(int order, int atNo)Marvin 6.2Not supported feature.
SuperatomSgroup.setLeavingGroupAlternativeName(int order, String alternativeName)Marvin 6.2Not supported feature.
SuperatomSgroup.updateAttachmentPoints()Marvin 6.2chemaxon.struc.sgroup.SuperatomSgroup.calculateAttachmentPoints()

chemaxon.util.iterator

IteratorFactory.INCLUDE_CHEMICAL_ATOMSMarvin 6.2chemaxon.util.iterator.IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY