Deprecated and removed elements in the API

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

MDocument.exportToBinFormat(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToBinFormat(MDocument, String)
MDocument.exportToFormat(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToFormat(MDocument, String)
MDocument.exportToObject(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToObject(MDocument, String)
MDocument.parseMRV(String sval)Marvin 5.7chemaxon.formats.MolImporter.parseMRV(String)
MDocument.setGUIProperyContainer(MPropertyContainer gpc)Marvin 6.1chemaxon.struc.MDocument.setGUIPropertyContainer(MPropertyContainer)
MObject.addNotify()Marvin 6.1chemaxon.struc.MObject.addNotify(MDocument)
MObject.removeNotify()Marvin 6.1chemaxon.struc.MObject.removeNotify(MDocument)
MolAtom.CTSPECIFIC_HMarvin 5.11Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.
MolAtom.getAtomicNumber(String element)Marvin 5.9chemaxon.struc.PeriodicSystem.findAtomicNumber(String)
The recommended method does not work for symbol not representing a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
MolAtom.getAttach()Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.getAttachmentPointOrders(MolAtom)
If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.
MolAtom.getQuerystr()Marvin 5.7chemaxon.struc.MolAtom.getQueryString()
MolAtom.getRadical()Marvin 6.2chemaxon.struc.MolAtom.getRadicalValue()
MolAtom.hasSMARTSProps()Marvin 5.7chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.hasSMARTSProps(MolAtom)
MolAtom.hasSMARTSPropsExcluding(String exclude)Marvin 5.7chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom, String)
MolAtom.numOf(String e)Marvin 5.9chemaxon.struc.PeriodicSystem.findAtomicNumber(String)
The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
MolAtom.setAttach(int a)Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom)
chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom, int)
MolAtom.setAttach(int newOrder, Sgroup sg)Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom)
chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom, int)
MolAtom.setForSpecIsotopeSymbol(String sym)Marvin 6.3chemaxon.struc.MolAtom.setSpecIsotopeSymbolPreferred()
chemaxon.struc.MolAtom.setMassno()
MolAtom.setImplicitHBasedOnValence(Valence v)Marvin 6.0.1

Usage: 

Internal usage only.
MolAtom.setQuerystr(String s, int options)Marvin 5.7chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.setQuerystr(MolAtom, String, int)
chemaxon.struc.MolAtom.setQueryString(String)
MolAtom.setQuerystr(String s)Marvin 5.7chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.setQuerystr(MolAtom, String)
chemaxon.struc.MolAtom.setQueryString(String)
MolAtom.setRadical(int r)Marvin 6.2chemaxon.struc.MolAtom.setRadicalValue(AtomProperty.Radical)
MolAtom.setSMARTS(String s)Marvin 5.7chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.setSMARTS(MolAtom, String)
MolBond.getDesiredLength()Marvin 5.11chemaxon.struc.MolBond.desiredLength(int, int, int, int)
MolBond.getDesiredLength(boolean shortenHbonds)Marvin 5.11chemaxon.struc.MolBond.desiredLength(int, int, int, int)
MolBond.isRemovable()Marvin 6.2Not supported feature.
Molecule.RM_KEEP_LEAVINGGROUPSMarvin 6.2Not supported feature.
Molecule.checkConsistency()Marvin 5.7Not intended for public use, it was intended only for internal debugging.
Molecule.clonelesscopy(MoleculeGraph g)Marvin 6.3Not supported feature.
Molecule.exportToBinFormat(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToBinFormat(Molecule, String)
Molecule.exportToFormat(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToFormat(Molecule, String)
Molecule.exportToObject(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToObject(Molecule, String)
Molecule.getProperty(String key)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)

Usage: 

String property = MPropHandler.convertToString(mol.properties(), key);
Molecule.getPropertyKeys()Marvin 4.1chemaxon.struc.Molecule.properties()
chemaxon.struc.MPropertyContainer.getKeys()
chemaxon.struc.Molecule.properties()
chemaxon.struc.MPropertyContainer.getKeyEnumeration()
One-to-one replacement is method getKeyEnumeration() but method getKeys() is simpler to use.
Molecule.implicitizeHydrogens0(int f, MolAtom[] atoms, boolean check)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)

Usage: 

Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
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
Molecule.sortSgroupXBonds()Marvin 5.12Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
Molecule.toBinFormat(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToBinFormat(Molecule, String)
Molecule.toFormat(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToFormat(Molecule, String)
To get exact replacement use:<br>

Usage: 

try {
String out = MolExporter.exportToFormat(this, fmt);
 catch (IOException e){
Molecule.toObject(String fmt)Marvin 5.7chemaxon.formats.MolExporter.exportToObject(Molecule, String)
Molecule.ungroupSgroup(int i, int opts)Marvin 6.3chemaxon.struc.Molecule.ungroupSgroup(Sgroup)
Molecule.ungroupSgroup(int i)Marvin 6.3chemaxon.struc.Molecule.ungroupSgroup(Sgroup)
Molecule.ungroupSgroups(int type)Marvin 6.3chemaxon.struc.Molecule.ungroupSgroups(EnumSet)
MoleculeGraph.CACHE_REMOVE_SSSRMODULEMarvin 5.12SSSR module is not cached any more.
MoleculeGraph.VALENCE_CHECK_AMBIGUOUSMarvin 6.0chemaxon.core.calculations.valencecheck.ValenceCheckOptions
MoleculeGraph.addExplicitHydrogens(int f, MolAtom[] atoms)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)

Usage: 

Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
MoleculeGraph.addExplicitHydrogens(int f)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)

Usage: 

Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
MoleculeGraph.addExplicitLonePairs()Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])

Usage: 

Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
MoleculeGraph.arrangeComponents()Marvin 5.7chemaxon.marvin.util.CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean)

Usage: 

CleanUtil.arrangeComponents(molecule, true, true);
MoleculeGraph.checkConsistency()Marvin 5.7Not intended for public use, it was intended only for internal debugging.
MoleculeGraph.clean(int dim, String opts, MProgressMonitor pmon)Marvin 5.7chemaxon.calculations.clean.Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor)
MoleculeGraph.clean(int dim, String opts)Marvin 5.7chemaxon.calculations.clean.Cleaner.clean(MoleculeGraph, int, String)
MoleculeGraph.clonelesscopy(MoleculeGraph graph)Marvin 6.3Not supported feature.
MoleculeGraph.createBHtab()Marvin 6.2No replacement.
MoleculeGraph.findComponentIds()Marvin 6.0chemaxon.struc.MoleculeGraph.getFragIds(int)
chemaxon.struc.MoleculeGraph.FRAG_BASIC

Usage: 

mol.getFragIds(MoleculeGraph.FRAG_BASIC);
MoleculeGraph.findFrag(int i, MoleculeGraph frag)Marvin 5.6chemaxon.struc.MoleculeGraph.findFrag(int, int, MoleculeGraph)
chemaxon.struc.MoleculeGraph.FRAG_KEEPING_MULTICENTERS

Usage: 

mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
MoleculeGraph.findFrags(Class<C> cl)Marvin 5.6chemaxon.struc.MoleculeGraph.findFrags(Class, int)
chemaxon.struc.MoleculeGraph.FRAG_KEEPING_MULTICENTERS

Usage: 

mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.getBtab()Marvin 5.4chemaxon.struc.MoleculeGraph.getBondTable()
chemaxon.core.util.BondTable.getMatrixArray()

Usage: 

molecule.getBondTable().getMatrixArray();
MoleculeGraph.getDesiredLength(int atno1, int atno2, int type)Marvin 5.11chemaxon.struc.MolBond.desiredLength(int, int, int, int)
chemaxon.struc.MoleculeGraph.getDim()

Usage: 

MolBond.desiredLength(atno1, atno2, type, getDim());
MoleculeGraph.getDesiredLength(MolBond b)Marvin 5.11chemaxon.struc.MolBond.desiredLength(int, int, int, int)
chemaxon.struc.MolBond.getType()
chemaxon.struc.MoleculeGraph.getDim()

Usage: 

MolBond.desiredLength(atno1, atno2, b.getType, getDim());
MoleculeGraph.getFragCount()Marvin 5.6chemaxon.struc.MoleculeGraph.getFragCount(int)
chemaxon.struc.MoleculeGraph.FRAG_KEEPING_MULTICENTERS

Usage: 

mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.getGrinv(int[] gi, boolean uniqueFlag)Marvin 4.0chemaxon.struc.MoleculeGraph.getGrinv(int[], int)

Usage: 

getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
MoleculeGraph.getPossibleAttachmentPoints(MolAtom molAtom)Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.getAttachmentPointOrders(MolAtom)
chemaxon.struc.MolAtom.getAttachParentSgroup()

Usage: 

SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup());
List&ltInteger&gt orders = group.getAttachmentPointOrders(molAtom);
MoleculeGraph.getStereo2(MolBond b)Marvin 6.3chemaxon.struc.MoleculeGraph.getEZStereo(MolBond)
MoleculeGraph.getValenceCheckState()Marvin 6.0chemaxon.struc.MoleculeGraph.getValenceCheckOptions()
chemaxon.struc.MoleculeGraph.isValenceCheckEnabled()

Usage: 

// Same as getValenceCheckState() == ValenceCheckState.OFF:
isValenceCheckEnabled() == true;
// Same as getValenceCheckState() == ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED:
getValenceCheckOptions.isLocalAromatic() == true;
// Same as getValenceCheckState() == ValenceCheckState.FULL:
getValenceCheckOptions.isLocalAromatic() == false;
MoleculeGraph.hydrogenize(boolean add)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitHToExplicit(MoleculeGraph)
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph)
MoleculeGraph.implicitizeHydrogens(int f, MolAtom[] atoms, boolean check)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)

Usage: 

Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
MoleculeGraph.implicitizeHydrogens(int f, MolAtom[] atoms)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int)

Usage: 

Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
MoleculeGraph.implicitizeHydrogens(int f)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)

Usage: 

Hydrogenize.convertExplicitHToImplicit(molecule, f);
MoleculeGraph.implicitizeHydrogens0(int f, MolAtom[] atoms, boolean check)Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)

Usage: 

Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
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.partialClean(int dim, int[] fixed, String opts)Marvin 5.7chemaxon.calculations.clean.Cleaner.partialClean(MoleculeGraph, int, int[], String)
MoleculeGraph.partialClean(Molecule[] template, String opts)Marvin 5.7chemaxon.calculations.clean.Cleaner.partialClean(Molecule, Molecule[], String)
MoleculeGraph.partialClean(MoleculeGraph template, int[] map, String opts)Marvin 5.7chemaxon.calculations.clean.Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String)
MoleculeGraph.removeExplicitLonePairs()Marvin 5.7chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph)
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)
MoleculeGraph.setValenceCheckState(ValenceCheckState state)Marvin 6.0chemaxon.struc.MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)
chemaxon.struc.MoleculeGraph.setValenceCheckEnabled(boolean)

Usage: 

// Same as setValenceCheckState(ValenceCheckState.OFF):
setValenceCheckEnabled(false);
// Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED):
setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
// Same as setValenceCheckState(ValenceCheckState.FULL):
setValenceCheckOptions(new ValenceCheckOptions(false, true));
MProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MProp.convertToString(String fmt)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MPropertyContainer.getString(String key)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MPropertyContainer, String)
PeriodicSystem.getAtomicNumber(String symbol)Marvin 5.9chemaxon.struc.PeriodicSystem.findAtomicNumber(String)
RgMolecule.checkConsistency()Marvin 5.7Not intended for public use, it was intended only for internal debugging.
RgMolecule.clonelesscopy(MoleculeGraph g)Marvin 6.3Not supported feature.
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.clonelesscopy(MoleculeGraph g)Marvin 6.3Not supported feature.
RxnMolecule.mergeAtoms(MolAtom that, MolAtom node)Marvin 6.2chemaxon.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.getType()Marvin 6.3chemaxon.struc.Sgroup.getSgroupType()
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)
Sgroup.Sgroup(Molecule parent, int t, int xstate)Marvin 5.12chemaxon.struc.SgroupFactory.createSgroup(Molecule, SgroupType)
chemaxon.struc.Sgroup.setXState(int)
Sgroup.Sgroup(Molecule parent, int t)Marvin 5.12chemaxon.struc.SgroupFactory.createSgroup(Molecule, SgroupType)
StereoConstants.CTUNKNOWNMarvin 6.1

Usage: 

In the specified methods the CIS|TRANS or 
CIS|TRANS|CTUNSPEC values are used instead.

chemaxon.struc.graphics

MEFlow.getValidSinkAtomPairsForMolecule(Molecule m, MolAtom source)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom)
MEFlow.getValidSinkAtomPairsForMolecule(Molecule m, MolBond source)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond)
MEFlow.getValidSinkAtomsForMolecule(Molecule m, MolAtom source)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom)
MEFlow.getValidSinkAtomsForMolecule(Molecule m, MolBond source)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond)
MEFlow.getValidSinkBondsForMolecule(Molecule m, MolAtom source)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom)
MEFlow.getValidSinkBondsForMolecule(Molecule m, MolBond source)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond)
MEFlow.getValidSourceAtomPairsForMolecule(Molecule m)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSourceAtomPairs(Molecule)
MEFlow.getValidSourceAtomsForMolecule(Molecule m)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSourceAtoms(Molecule)
MEFlow.getValidSourceBondsForMolecule(Molecule m)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSourceBonds(Molecule)
MEFlow.isValidSourceAndSinkForMolecule(Object source, Object sink, Molecule m)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule)
MEFlow.isValidSourceForMolecule(Object source, Molecule m)Marvin 6.1chemaxon.struc.graphics.util.EFlowPlacementValidators.isValidSource(MolAtom, Molecule)
chemaxon.struc.graphics.util.EFlowPlacementValidators.isValidSource(MolAtom[], Molecule)
chemaxon.struc.graphics.util.EFlowPlacementValidators.isValidSource(MolBond, Molecule)
MPolyline.rotate(DPoint3 center, double dphi, DPoint3 p)Marvin 6.1chemaxon.struc.CTransform3D.setRotation(double, double, double, double)
chemaxon.struc.CTransform3D.setRotationCenter(DPoint3)

chemaxon.struc.prop

MBooleanProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MDoubleArrayProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MDoubleProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MHashProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MHCoords3DProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MIntegerArrayProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MIntegerProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MListProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MMoleculeProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MObjectProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)
MStringProp.convertToString(String fmt, int flags)Marvin 5.7chemaxon.marvin.io.MPropHandler.convertToString(MProp, String)

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.getAttachAtoms()Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.getBoundAttachAtoms()
SuperatomSgroup.getFreeLegalAttachAtoms()Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.getFreeAttachAtoms()
SuperatomSgroup.getLegalAttachAtoms()Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.getAllAttachAtoms()
SuperatomSgroup.getParentSgroupGraph()Marvin 6.2chemaxon.struc.sgroup.SuperatomSgroup.getSgroupGraph()
SuperatomSgroup.isFreeLegalAttachAtom(MolAtom a)Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.isFreeAttachAtom(MolAtom)
SuperatomSgroup.isLegalAttachment(MolAtom atom)Marvin 6.0chemaxon.struc.sgroup.SuperatomSgroup.isAttachmentAtom(MolAtom)
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.sortXBonds()Marvin 5.12Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
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

Removed elements in the API
Name of removed class, field or methodRemoval versionRecommended class, field or method

chemaxon.struc

CEdgeMarvin 6.0chemaxon.struc.MolBond
CGraphMarvin 6.0chemaxon.struc.MoleculeGraph
CNodeMarvin 6.0chemaxon.struc.MolAtom
MDocument.setGUIProperyContainer(MPropertyContainer gpc)Marvin 6.0chemaxon.struc.MDocument.setGUIPropertyContainer(MPropertyContainer)
MolAtom.getEdge(int i)Marvin 6.0chemaxon.struc.MolAtom.getBond(int)
MolAtom.getEdgeCount()Marvin 6.0chemaxon.struc.MolAtom.getBondCount()
MolAtom.getEdgeTo(MolAtom other)Marvin 6.0chemaxon.struc.MolAtom.getBondTo(MolAtom)
MolAtom.haveSimilarEdges(MolAtom a)Marvin 6.0chemaxon.struc.MolAtom.haveSimilarBonds(MolAtom)
MolAtom.isArrowEnd()Marvin 6.0chemaxon.struc.MPoint
chemaxon.struc.graphics.MRArrow
MolAtom objects cannot represent end-points of reaction arrows any more. Class chemaxon.struc.graphics.MRArrow is used to represent reaction arrows and class MPoint represents the end-points of a reaction arrow.
MolAtom.isNobleGas()Marvin 6.0chemaxon.struc.PeriodicSystem.isNobleGas(int)
chemaxon.struc.MolAtom.getAtno()

Usage: 

PeriodicSystem.isNobleGas(atom.getAtno());
MolAtom.setMassnoIfKnown(String sym)Marvin 6.0chemaxon.struc.MolAtom.setForSpecIsotopeSymbol(String)
MolAtom.valenceCheck(int opts)Marvin 6.0chemaxon.struc.MolAtom.valenceCheck()
There are no options for valence check.
MolBond.ARROWMarvin 6.0chemaxon.struc.graphics.MRArrow
Class MRArrow is used to represent reaction arrows.
MolBond.cloneEdge(MolAtom a1, MolAtom a2)Marvin 6.0chemaxon.struc.MolBond.cloneBond(MolAtom, MolAtom)
MolBond.getNode1()Marvin 6.0chemaxon.struc.MolBond.getAtom1()
MolBond.getNode2()Marvin 6.0chemaxon.struc.MolBond.getAtom2()
MolBond.getOtherNode(MolAtom node)Marvin 6.0chemaxon.struc.MolBond.getOtherAtom(MolAtom)
MolBond.isArrow()Marvin 6.0chemaxon.struc.graphics.MRArrow
MolBond objects cannot represent reaction arrows any more. Class MRArrow is used to represent reaction arrows.
MolBond.isCoordinative()Marvin 6.0chemaxon.struc.MolBond.isCoordinate()
Molecule.mergeFrags()Marvin 6.0It was used by an internal method, not intended for public usage.
MoleculeGraph.AROM_CHEMAXONMarvin 6.0chemaxon.struc.MoleculeGraph.AROM_BASIC
MoleculeGraph.AROM_DAYLIGHTMarvin 6.0chemaxon.struc.MoleculeGraph.AROM_GENERAL
MoleculeGraph.findFragById(int fragId, MoleculeGraph frag)Marvin 6.0chemaxon.struc.MoleculeGraph.findFragById(int, int, MoleculeGraph)
To keep the same functionality, use value FRAG_KEEPING_MULTICENTERS for parameter fragmentationType.

Usage: 

mol.findFragById(fragId, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
MoleculeGraph.getAromrings()Marvin 6.0chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int)

Usage: 

getAromaticAndAliphaticRings(AROM_BASIC, true, false, 18, 1000)[0];
MoleculeGraph.getAromrings(int size)Marvin 6.0chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int)

Usage: 

getAromaticAndAliphaticRings(AROM_BASIC, true, false, size, 1000)[0];
MoleculeGraph.getEdge(int i)Marvin 6.0chemaxon.struc.MoleculeGraph.getBond(int)
MoleculeGraph.getEdgeArray()Marvin 6.0chemaxon.struc.MoleculeGraph.getBondArray()
MoleculeGraph.getEdgeCount()Marvin 6.0chemaxon.struc.MoleculeGraph.getBondCount()
MoleculeGraph.getEdgeVector()Marvin 6.0chemaxon.struc.MoleculeGraph.getBondArray()

Usage: 

Vector<MolBond> v = new Vector<MolBond>(getBondCount());
v.addAll(Arrays.asList(getBondArray())).
MoleculeGraph.getFragIds()Marvin 6.0chemaxon.struc.MoleculeGraph.getFragIds(int)
To keep the same functionality, use value FRAG_KEEPING_MULTICENTERS for parameter fragmentationType.

Usage: 

mol.getFragIds(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.getNode(int i)Marvin 6.0chemaxon.struc.MoleculeGraph.getAtom(int)
MoleculeGraph.getNodeCount()Marvin 6.0chemaxon.struc.MoleculeGraph.getAtomCount()
MoleculeGraph.getNodeVector()Marvin 6.0chemaxon.struc.MoleculeGraph.getAtomArray()

Usage: 

Vector<MolAtom> v = new Vector<MolAtom>(getAtomCount());
v.addAll(Arrays.asList(getAtomArray()));
MoleculeGraph.getNonAromrings()Marvin 6.0chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int)

Usage: 

getAromaticAndAliphaticRings(AROM_BASIC, true, false, 18, 1000)[1];
MoleculeGraph.getNonAromrings(int size)Marvin 6.0chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int)

Usage: 

getAromaticAndAliphaticRings(AROM_BASIC, true, false, size, 1000)[1];
MoleculeGraph.insertEdge(int i, MolBond edge)Marvin 6.0chemaxon.struc.MoleculeGraph.insertBond(int, MolBond)
MoleculeGraph.insertEdgeInOrder(MolBond e, MolBond[] order)Marvin 6.0chemaxon.struc.MoleculeGraph.insertBondInOrder(MolBond, MolBond[])
MoleculeGraph.insertNode(int i, MolAtom node)Marvin 6.0chemaxon.struc.MoleculeGraph.insertAtom(int, MolAtom)
MoleculeGraph.isValenceCheckEnabled()Marvin 6.0chemaxon.struc.MoleculeGraph.getValenceCheckState()
MoleculeGraph.mergeFrags()Marvin 6.0It was an empty method in this class which is not required any more, it's usage can simply be deleted.
MoleculeGraph.mergeFrags(int id1, int id2)Marvin 6.0chemaxon.struc.MoleculeGraph.mergeFrags(int, int, int)
To keep the same functionality, use value FRAG_KEEPING_MULTICENTERS for parameter fragmentationType.

Usage: 

mol.mergeFrags(id1, id2, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.mergeNodes(MolAtom that, MolAtom a)Marvin 6.0chemaxon.struc.MoleculeGraph.mergeAtoms(MolAtom, MolAtom)
MoleculeGraph.regenEdges()Marvin 6.0chemaxon.struc.MoleculeGraph.regenBonds()
MoleculeGraph.removeAllEdges()Marvin 6.0chemaxon.struc.MoleculeGraph.removeAllBonds()
MoleculeGraph.removeEdge(int i)Marvin 6.0chemaxon.struc.MoleculeGraph.removeBond(int)
MoleculeGraph.removeEdge(MolBond edge)Marvin 6.0chemaxon.struc.MoleculeGraph.removeBond(MolBond)
MoleculeGraph.removeNode(int i, int cleanupFlags)Marvin 6.0chemaxon.struc.MoleculeGraph.removeAtom(int, int)
MoleculeGraph.removeNode(int i)Marvin 6.0chemaxon.struc.MoleculeGraph.removeAtom(int)
MoleculeGraph.removeNode(MolAtom node, int cleanupFlags)Marvin 6.0chemaxon.struc.MoleculeGraph.removeAtom(MolAtom, int)
MoleculeGraph.removeNode(MolAtom node)Marvin 6.0chemaxon.struc.MoleculeGraph.removeAtom(MolAtom)
MoleculeGraph.replaceEdge(MolBond olde, MolBond newe)Marvin 6.0chemaxon.struc.MoleculeGraph.replaceBond(MolBond, MolBond)
MoleculeGraph.setEdge(int i, MolBond edge)Marvin 6.0chemaxon.struc.MoleculeGraph.setBond(int, MolBond)
MoleculeGraph.setNode(int i, MolAtom node)Marvin 6.0chemaxon.struc.MoleculeGraph.setAtom(int, MolAtom)
MoleculeGraph.setSetSeqs(int id)Marvin 6.0chemaxon.struc.MoleculeGraph.setAtomSetSeq(int)
MoleculeGraph.setValenceCheckEnabled(boolean b)Marvin 6.0chemaxon.struc.MoleculeGraph.setValenceCheckState(ValenceCheckState)
MoleculeGraph.sortEdgesAccordingTo(MolBond[] order)Marvin 6.0chemaxon.struc.MoleculeGraph.sortBondsAccordingTo(MolBond[])
MProp.CONV_SELFREFMarvin 6.1Option for converting self-referring properties is passed to chemaxon.marvin.io.MPropHandle.convertToString(MProp,String) in the format string as 'format' + ":-selfrefprops".
RgMolecule.createMol(String fmt)Marvin 6.0chemaxon.marvin.io.MolImportModule.createMol()
Replacement method works for all file formats.
RgMolecule.getBtab()Marvin 6.0chemaxon.struc.RgMolecule.getBondTable()
chemaxon.core.util.BondTable.getMatrixArray()

Usage: 

molecule.getBondTable().getMatrixArray();
RgMolecule.setAbsStereo(boolean c, int i, int j)Marvin 6.0chemaxon.struc.RgMolecule.getRgroupMember(int, int)
chemaxon.struc.MoleculeGraph.setAbsStereo(boolean)

Usage: 

rgMolecule.getRgroupMember(i, j).setAbsStereo(c);
RxnMolecule.addStructure(Molecule m, int type, boolean beNew)Marvin 6.0chemaxon.struc.RxnMolecule.addComponent(Molecule, int, boolean)
RxnMolecule.addStructure(Molecule m, int type)Marvin 6.0chemaxon.struc.RxnMolecule.addComponent(Molecule, int)
RxnMolecule.getBtab()Marvin 6.0chemaxon.struc.RxnMolecule.getBondTable()
chemaxon.core.util.BondTable.getMatrixArray()

Usage: 

molecule.getBondTable().getMatrixArray();
RxnMolecule.getStructure(int flags, int i)Marvin 6.0chemaxon.struc.RxnMolecule.getComponent(int, int)
RxnMolecule.getStructureCount(int type)Marvin 6.0chemaxon.struc.RxnMolecule.getComponentCount(int)
RxnMolecule.removeStructure(int flags, int i)Marvin 6.0chemaxon.struc.RxnMolecule.removeComponent(int, int)

chemaxon.struc.prop

MMoleculeProp.MMoleculeProp(String sval)Marvin 6.0chemaxon.marvin.io.MPropHandler.createMMoleculeProp(String)

chemaxon.struc.util.bondutil

MolBondUtilMarvin 6.3Internal usage only.