Methods Deprecated or Removed in version 6.2

Deprecated elements in the API

Name of deprecated class, field or method

Deprecation version

Recommended class, field or method

chemaxon.core.calculations.valencecheck

ValenceCheckOptions.ValenceCheckOptions(boolean localAromatic, boolean traditionalNallowed)

Marvin 6.2

chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder

chemaxon.struc

MolAtom.getRadical()

Marvin 6.2

chemaxon.struc.MolAtom.getRadicalValue()

MolAtom.setRadical(int r)

Marvin 6.2

chemaxon.struc.MolAtom.setRadicalValue(Radical)

MolBond.isRemovable()

Marvin 6.2

Not supported feature.

Molecule.RM_KEEP_LEAVINGGROUPS

Marvin 6.2

Not supported feature.

Molecule.isGUIContracted()

Marvin 6.2

chemaxon.struc.Molecule.hasContractedSgroup()

Molecule.mergeAtoms(MolAtom that, MolAtom node)

Marvin 6.2

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

Molecule.setGUIContracted(boolean contract, int opts)

Marvin 6.2

chemaxon.struc.Molecule.expandSgroups(int)
chemaxon.struc.Molecule.contractSgroups(int)
chemaxon.struc.sgroup.Expandable.LEAVE_COORDS_UNCHANGED

Molecule.setGUIContracted(boolean contract)

Marvin 6.2

chemaxon.struc.Molecule.expandSgroups(int)
chemaxon.struc.Molecule.contractSgroups(int)
chemaxon.struc.sgroup.Expandable.LEAVE_COORDS_UNCHANGED

MoleculeGraph.createBHtab()

Marvin 6.2

No replacement.

MoleculeGraph.insertAtom(int i, MolAtom atom)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.add(MolAtom)

MoleculeGraph.insertBond(int i, MolBond bond)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.add(MolBond)

MoleculeGraph.mergeAtoms(MolAtom replacementAtom, MolAtom origAtom)

Marvin 6.2

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

MoleculeGraph.replaceBond(MolBond oldb, MolBond newb)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.removeBond(MolBond)
chemaxon.struc.MoleculeGraph.add(MolBond)

MoleculeGraph.setAtom(int i, MolAtom atom)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.removeAtom(int)
chemaxon.struc.MoleculeGraph.add(MolAtom)
chemaxon.struc.MolAtom

MoleculeGraph.setBond(int i, MolBond b)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.MoleculeGraph.removeBond(MolBond)
chemaxon.struc.MoleculeGraph.add(MolBond)

RgMolecule.mergeAtoms(MolAtom that, MolAtom a)

Marvin 6.2

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

RgMolecule.replaceBond(MolBond olde, MolBond newe)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.RgMolecule.removeBond(MolBond)
chemaxon.struc.RgMolecule.add(MolBond)

RgMolecule.setAtom(int iu, MolAtom node)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.RgMolecule.removeAtom(MolAtom)
chemaxon.struc.RgMolecule.add(MolAtom)

RgMolecule.setBond(int iu, MolBond edge)

Marvin 6.2

chemaxon.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 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.RxnMolecule.removeBond(MolBond)
chemaxon.struc.RxnMolecule.add(MolBond)

RxnMolecule.setAtom(int iu, MolAtom node)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.RxnMolecule.removeAtom(MolAtom)
chemaxon.struc.RxnMolecule.add(MolAtom)

RxnMolecule.setBond(int iu, MolBond edge)

Marvin 6.2

chemaxon.struc.MoleculeGraph
chemaxon.struc.RxnMolecule.removeBond(MolBond)
chemaxon.struc.RxnMolecule.add(MolBond)

SelectionMolecule.setBond(int i, MolBond bond)

Marvin 6.2

chemaxon.struc.SelectionMolecule.removeBond(MolBond)
chemaxon.struc.SelectionMolecule.add(MolBond)

Sgroup.setGUIStateRecursively(boolean contract, int opts)

Marvin 6.2

chemaxon.struc.Molecule.setGUIContracted(boolean)
chemaxon.struc.Molecule.setGUIContracted(boolean, int)

Sgroup.setGUIStateRecursively(boolean v)

Marvin 6.2

chemaxon.struc.Molecule.setGUIContracted(boolean)
chemaxon.struc.Molecule.setGUIContracted(boolean, int)

Sgroup.setXState(int state, int opts)

Marvin 6.2

chemaxon.struc.Sgroup.setXState(int)

chemaxon.struc.sgroup

Expandable.COORDS_UPDATE

Marvin 6.2

Not supported feature.

Expandable.REVERSIBLE_EXPAND

Marvin 6.2

chemaxon.struc.sgroup.Expandable.LEAVE_COORDS_UNCHANGED

SuperatomSgroup.cloneLeavingGroups(SuperatomSgroup sasg)

Marvin 6.2

Not supported feature.

SuperatomSgroup.expandOther(int opts, Molecule moltoexpand)

Marvin 6.2

chemaxon.struc.sgroup.SuperatomSgroup.expand(int)

SuperatomSgroup.getParentSgroupGraph()

Marvin 6.2

chemaxon.struc.sgroup.SuperatomSgroup.getSgroupGraph()

SuperatomSgroup.removeLeavingGroup(int order)

Marvin 6.2

Not supported feature.

SuperatomSgroup.setCrossingBondType(int order, BondType newType)

Marvin 6.2

Not supported feature.

SuperatomSgroup.setLeavingGroup(int order, int atNo, String alternativeName, BondType crossingBondType)

Marvin 6.2

Not supported feature.

SuperatomSgroup.setLeavingGroup(int order, int atNo, String alternativeName)

Marvin 6.2

Not supported feature.

SuperatomSgroup.setLeavingGroup(int order, int atNo)

Marvin 6.2

Not supported feature.

SuperatomSgroup.setLeavingGroupAlternativeName(int order, String alternativeName)

Marvin 6.2

Not supported feature.

SuperatomSgroup.updateAttachmentPoints()

Marvin 6.2

chemaxon.struc.sgroup.SuperatomSgroup.calculateAttachmentPoints()

chemaxon.util.iterator

IteratorFactory.INCLUDE_CHEMICAL_ATOMS

Marvin 6.2

chemaxon.util.iterator.IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY