All of the Deprecated and Removed Methods¶
| ### 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.struc.interfaces.chemicalgraph.builder.Builder |
ValenceCheckOptions.Builder.setLocalAromatiChecking(boolean localAromaticCheck) |
Marvin 14.7.7 | chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder.setLocalAromaticChecking(boolean) |
| ##### chemaxon.struc | ||
MoleculeGraph.ValenceCheckState |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions) chemaxon.core.calculations.valencecheck.ValenceCheckOptions |
MDocument.exportToBinFormat(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToBinFormat(MDocument, String) |
MDocument.exportToFormat(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToFormat(MDocument, String) |
MDocument.exportToObject(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToObject(MDocument, String) |
MDocument.parseMRV(String sval) |
Marvin 5.7 | chemaxon.formats.MolImporter.parseMRV(String) |
MDocument.setGUIProperyContainer(MPropertyContainer gpc) |
Marvin 6.1 | chemaxon.struc.MDocument.setGUIPropertyContainer(MPropertyContainer) |
MDocument.Prop.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.formats.MolExporter.convertToString(MDocument, String, int) |
MObject.addNotify() |
Marvin 6.1 | chemaxon.struc.MObject.addNotify(MDocument) |
MObject.removeNotify() |
Marvin 6.1 | chemaxon.struc.MObject.removeNotify(MDocument) |
MolAtom.CTSPECIFIC_H |
Marvin 5.11 | Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use. |
MolAtom.getAtomicNumber(String element) |
Marvin 5.9 | chemaxon.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 6.0 | chemaxon.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 5.7 | chemaxon.struc.MolAtom.getQueryString() |
MolAtom.getRadical() |
Marvin 6.2 | chemaxon.struc.MolAtom.getRadicalValue() |
MolAtom.hasSMARTSProps() |
Marvin 5.7 | chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.hasSMARTSProps(MolAtom) |
MolAtom.hasSMARTSPropsExcluding(String exclude) |
Marvin 5.7 | chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom, String) |
MolAtom.numOf(String e) |
Marvin 5.9 | chemaxon.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 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom) chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom, int) |
MolAtom.setAttach(int newOrder, Sgroup sg) |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom) chemaxon.struc.sgroup.SuperatomSgroup.addAttachmentPoint(MolAtom, int) |
MolAtom.setForSpecIsotopeSymbol(String sym) |
Marvin 6.3 | chemaxon.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 5.7 | chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.setQuerystr(MolAtom, String, int) chemaxon.struc.MolAtom.setQueryString(String) |
MolAtom.setQuerystr(String s) |
Marvin 5.7 | chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.setQuerystr(MolAtom, String) chemaxon.struc.MolAtom.setQueryString(String) |
MolAtom.setRadical(int r) |
Marvin 6.2 | chemaxon.struc.MolAtom.setRadicalValue(AtomProperty.Radical) |
MolAtom.setSMARTS(String s) |
Marvin 5.7 | chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier.setSMARTS(MolAtom, String) |
MolBond.getDesiredLength() |
Marvin 5.11 | chemaxon.struc.MolBond.desiredLength(int, int, int, int) |
MolBond.getDesiredLength(boolean shortenHbonds) |
Marvin 5.11 | chemaxon.struc.MolBond.desiredLength(int, int, int, int) |
MolBond.isRemovable() |
Marvin 6.2 | Not supported feature. |
Molecule.RM_KEEP_LEAVINGGROUPS |
Marvin 6.2 | Not supported feature. |
Molecule.checkConsistency() |
Marvin 5.7 | Not intended for public use, it was intended only for internal debugging. |
Molecule.clonelesscopy(MoleculeGraph g) |
Marvin 6.3 | Not supported feature. |
Molecule.exportToBinFormat(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToBinFormat(Molecule, String) |
Molecule.exportToFormat(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToFormat(Molecule, String) |
Molecule.exportToObject(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToObject(Molecule, String) |
Molecule.getProperty(String key) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) Usage: String property = MPropHandler.convertToString(mol.properties(), key); |
Molecule.getPropertyKeys() |
Marvin 4.1 | chemaxon.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 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check); |
Molecule.isGUIContracted() |
Marvin 6.2 | chemaxon.struc.Molecule.hasContractedSgroup() |
Molecule.isSgroup() |
Marvin 14.7.7 | Not supported feature. |
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 |
Molecule.sortSgroupXBonds() |
Marvin 5.12 | Crossing 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 5.7 | chemaxon.formats.MolExporter.exportToBinFormat(Molecule, String) |
Molecule.toFormat(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToFormat(Molecule, String) To get exact replacement use: Usage: try { String out = MolExporter.exportToFormat(this, fmt); catch (IOException e){ |
Molecule.toObject(String fmt) |
Marvin 5.7 | chemaxon.formats.MolExporter.exportToObject(Molecule, String) |
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.CACHE_REMOVE_SSSRMODULE |
Marvin 5.12 | SSSR module is not cached any more. |
MoleculeGraph.VALENCE_CHECK_AMBIGUOUS |
Marvin 6.0 | chemaxon.core.calculations.valencecheck.ValenceCheckOptions |
MoleculeGraph.addExplicitHydrogens(int f, MolAtom[] atoms) |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) Usage: Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f); |
MoleculeGraph.addExplicitHydrogens(int f) |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) Usage: Hydrogenize.convertImplicitHToExplicit(molecule, null, f); |
MoleculeGraph.addExplicitLonePairs() |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) Usage: Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null); |
MoleculeGraph.arrangeComponents() |
Marvin 5.7 | chemaxon.marvin.util.CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean) Usage: CleanUtil.arrangeComponents(molecule, true, true); |
MoleculeGraph.checkConsistency() |
Marvin 5.7 | Not intended for public use, it was intended only for internal debugging. |
MoleculeGraph.clean(int dim, String opts, MProgressMonitor pmon) |
Marvin 5.7 | chemaxon.calculations.clean.Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor) |
MoleculeGraph.clean(int dim, String opts) |
Marvin 5.7 | chemaxon.calculations.clean.Cleaner.clean(MoleculeGraph, int, String) |
MoleculeGraph.clonelesscopy(MoleculeGraph graph) |
Marvin 6.3 | Not supported feature. |
MoleculeGraph.createBHtab() |
Marvin 6.2 | No replacement. |
MoleculeGraph.findComponentIds() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getFragIds(int) chemaxon.struc.MoleculeGraph.FRAG_BASIC Usage: mol.getFragIds(MoleculeGraph.FRAG_BASIC); |
MoleculeGraph.findFrag(int i, MoleculeGraph frag) |
Marvin 5.6 | chemaxon.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 5.6 | chemaxon.struc.MoleculeGraph.findFrags(Class, int) chemaxon.struc.MoleculeGraph.FRAG_KEEPING_MULTICENTERS Usage: mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS); |
MoleculeGraph.getBtab() |
Marvin 5.4 | chemaxon.struc.MoleculeGraph.getBondTable() chemaxon.core.util.BondTable.getMatrixArray() Usage: molecule.getBondTable().getMatrixArray(); |
MoleculeGraph.getDesiredLength(int atno1, int atno2, int type) |
Marvin 5.11 | chemaxon.struc.MolBond.desiredLength(int, int, int, int) chemaxon.struc.MoleculeGraph.getDim() Usage: MolBond.desiredLength(atno1, atno2, type, getDim()); |
MoleculeGraph.getDesiredLength(MolBond b) |
Marvin 5.11 | chemaxon.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 5.6 | chemaxon.struc.MoleculeGraph.getFragCount(int) chemaxon.struc.MoleculeGraph.FRAG_KEEPING_MULTICENTERS Usage: mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS); |
MoleculeGraph.getGrinv(int[] gi, boolean uniqueFlag) |
Marvin 4.0 | chemaxon.struc.MoleculeGraph.getGrinv(int[], int) Usage: getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0); |
MoleculeGraph.getPossibleAttachmentPoints(MolAtom molAtom) |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.getAttachmentPointOrders(MolAtom) chemaxon.struc.MolAtom.getAttachParentSgroup() Usage: SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup()); List<Integer> orders = group.getAttachmentPointOrders(molAtom); |
MoleculeGraph.getStereo2(MolBond b) |
Marvin 6.3 | chemaxon.struc.MoleculeGraph.getEZStereo(MolBond) |
MoleculeGraph.getValenceCheckState() |
Marvin 6.0 | chemaxon.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 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertImplicitHToExplicit(MoleculeGraph) chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph) |
MoleculeGraph.implicitizeHydrogens(int f, MolAtom[] atoms, boolean check) |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check); |
MoleculeGraph.implicitizeHydrogens(int f, MolAtom[] atoms) |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f); |
MoleculeGraph.implicitizeHydrogens(int f) |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int) Usage: Hydrogenize.convertExplicitHToImplicit(molecule, f); |
MoleculeGraph.implicitizeHydrogens0(int f, MolAtom[] atoms, boolean check) |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check); |
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.isAtom() |
Marvin 14.7.7 | Not supported feature. |
MoleculeGraph.isBond() |
Marvin 14.7.7 | Not supported feature. |
MoleculeGraph.isMolecule() |
Marvin 14.7.7 | Usage: use myObject instanceof Molecule instead |
MoleculeGraph.isRing() |
Marvin 14.7.7 | Not supported feature. |
MoleculeGraph.mergeAtoms(MolAtom replacementAtom, MolAtom origAtom) |
Marvin 6.2 | chemaxon.struc.util.moleculeutil.MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) |
MoleculeGraph.partialClean(int dim, int[] fixed, String opts) |
Marvin 5.7 | chemaxon.calculations.clean.Cleaner.partialClean(MoleculeGraph, int, int[], String) |
MoleculeGraph.partialClean(Molecule[] template, String opts) |
Marvin 5.7 | chemaxon.calculations.clean.Cleaner.partialClean(Molecule, Molecule[], String) |
MoleculeGraph.partialClean(MoleculeGraph template, int[] map, String opts) |
Marvin 5.7 | chemaxon.calculations.clean.Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String) |
MoleculeGraph.removeExplicitLonePairs() |
Marvin 5.7 | chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph) |
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) |
MoleculeGraph.setValenceCheckState(ValenceCheckState state) |
Marvin 6.0 | chemaxon.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 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MProp.convertToString(String fmt) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MPropertyContainer.getString(String key) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MPropertyContainer, String) |
PeriodicSystem.getAtomicNumber(String symbol) |
Marvin 5.9 | chemaxon.struc.PeriodicSystem.findAtomicNumber(String) |
RgMolecule.checkConsistency() |
Marvin 5.7 | Not intended for public use, it was intended only for internal debugging. |
RgMolecule.clonelesscopy(MoleculeGraph g) |
Marvin 6.3 | Not supported feature. |
RgMolecule.isAtom() |
Marvin 14.7.7 | Not supported feature. |
RgMolecule.isBond() |
Marvin 14.7.7 | Not supported feature. |
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.clonelesscopy(MoleculeGraph g) |
Marvin 6.3 | Not supported feature. |
RxnMolecule.isAtom() |
Marvin 14.7.7 | Not supported feature. |
RxnMolecule.isBond() |
Marvin 14.7.7 | Not supported feature. |
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.getType() |
Marvin 6.3 | chemaxon.struc.Sgroup.getSgroupType() chemaxon.struc.sgroup.AminoAcidSgroup chemaxon.struc.Sgroup.ST_SUPERATOM chemaxon.struc.Sgroup.getSgroupType() chemaxon.struc.SgroupType.AMINOACID |
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) |
Sgroup.Sgroup(Molecule parent, int t, int xstate) |
Marvin 5.12 | chemaxon.struc.SgroupFactory.createSgroup(Molecule, SgroupType) chemaxon.struc.Sgroup.setXState(int) |
Sgroup.Sgroup(Molecule parent, int t) |
Marvin 5.12 | chemaxon.struc.SgroupFactory.createSgroup(Molecule, SgroupType) |
StereoConstants.CTUNKNOWN |
Marvin 6.1 | Usage: In the specified methods the CIS |
| ##### chemaxon.struc.graphics | ||
MEFlow.getValidSinkAtomPairsForMolecule(Molecule m, MolAtom source) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolAtom) |
MEFlow.getValidSinkAtomPairsForMolecule(Molecule m, MolBond source) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtomPairs(Molecule, MolBond) |
MEFlow.getValidSinkAtomsForMolecule(Molecule m, MolAtom source) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolAtom) |
MEFlow.getValidSinkAtomsForMolecule(Molecule m, MolBond source) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkAtoms(Molecule, MolBond) |
MEFlow.getValidSinkBondsForMolecule(Molecule m, MolAtom source) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkBonds(Molecule, MolAtom) |
MEFlow.getValidSinkBondsForMolecule(Molecule m, MolBond source) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSinkBonds(Molecule, MolBond) |
MEFlow.getValidSourceAtomPairsForMolecule(Molecule m) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSourceAtomPairs(Molecule) |
MEFlow.getValidSourceAtomsForMolecule(Molecule m) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSourceAtoms(Molecule) |
MEFlow.getValidSourceBondsForMolecule(Molecule m) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.getValidSourceBonds(Molecule) |
MEFlow.isValidSourceAndSinkForMolecule(Object source, Object sink, Molecule m) |
Marvin 6.1 | chemaxon.struc.graphics.util.EFlowPlacementValidators.isValidFlow(MolAtom, MolAtom, Molecule) |
MEFlow.isValidSourceForMolecule(Object source, Molecule m) |
Marvin 6.1 | chemaxon.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 6.1 | chemaxon.struc.CTransform3D.setRotation(double, double, double, double) chemaxon.struc.CTransform3D.setRotationCenter(DPoint3) |
| ##### chemaxon.struc.prop | ||
MBooleanProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MDoubleArrayProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MDoubleProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MHashProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MHCoords3DProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MIntegerArrayProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MIntegerProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MListProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MMoleculeProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MObjectProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
MStringProp.convertToString(String fmt, int flags) |
Marvin 5.7 | chemaxon.marvin.io.MPropHandler.convertToString(MProp, String) |
| ##### 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.getAttachAtoms() |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.getBoundAttachAtoms() |
SuperatomSgroup.getFreeLegalAttachAtoms() |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.getFreeAttachAtoms() |
SuperatomSgroup.getLegalAttachAtoms() |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.getAllAttachAtoms() |
SuperatomSgroup.getParentSgroupGraph() |
Marvin 6.2 | chemaxon.struc.sgroup.SuperatomSgroup.getSgroupGraph() |
SuperatomSgroup.isFreeLegalAttachAtom(MolAtom a) |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.isFreeAttachAtom(MolAtom) |
SuperatomSgroup.isLegalAttachment(MolAtom atom) |
Marvin 6.0 | chemaxon.struc.sgroup.SuperatomSgroup.isAttachmentAtom(MolAtom) |
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.sortXBonds() |
Marvin 5.12 | Crossing 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 6.2 | chemaxon.struc.sgroup.SuperatomSgroup.calculateAttachmentPoints() |
| ##### chemaxon.util.iterator | ||
IteratorFactory.INCLUDE_CHEMICAL_ATOMS |
Marvin 6.2 | chemaxon.util.iterator.IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY |
IteratorFactory.AtomIterator.nextAtom() |
Marvin 6.2 | chemaxon.util.iterator.IteratorFactory.AtomIterator.next() |
IteratorFactory.AtomNeighbourIterator.nextAtom() |
Marvin 6.2 | chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator.next() |
IteratorFactory.BondIterator.nextBond() |
Marvin 6.2 | chemaxon.util.iterator.IteratorFactory.BondIterator.next() |
IteratorFactory.BondNeighbourIterator.nextBond() |
Marvin 6.2 | chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator.next() |
IteratorFactory.RgComponentIterator.nextComponent() |
Marvin 6.2 | chemaxon.util.iterator.IteratorFactory.RgComponentIterator.next() |
| ### Removed elements in the API | ||
| Name of removed class, field or method | Removal version | Recommended class, field or method |
| ##### chemaxon.struc | ||
CEdge |
Marvin 6.0 | chemaxon.struc.MolBond |
CGraph |
Marvin 6.0 | chemaxon.struc.MoleculeGraph |
CNode |
Marvin 6.0 | chemaxon.struc.MolAtom |
MDocument.setGUIProperyContainer(MPropertyContainer gpc) |
Marvin 6.0 | chemaxon.struc.MDocument.setGUIPropertyContainer(MPropertyContainer) |
MolAtom.getEdge(int i) |
Marvin 6.0 | chemaxon.struc.MolAtom.getBond(int) |
MolAtom.getEdgeCount() |
Marvin 6.0 | chemaxon.struc.MolAtom.getBondCount() |
MolAtom.getEdgeTo(MolAtom other) |
Marvin 6.0 | chemaxon.struc.MolAtom.getBondTo(MolAtom) |
MolAtom.haveSimilarEdges(MolAtom a) |
Marvin 6.0 | chemaxon.struc.MolAtom.haveSimilarBonds(MolAtom) |
MolAtom.isArrowEnd() |
Marvin 6.0 | chemaxon.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 6.0 | chemaxon.struc.PeriodicSystem.isNobleGas(int) chemaxon.struc.MolAtom.getAtno() Usage: PeriodicSystem.isNobleGas(atom.getAtno()); |
MolAtom.setMassnoIfKnown(String sym) |
Marvin 6.0 | chemaxon.struc.MolAtom.setForSpecIsotopeSymbol(String) |
MolAtom.valenceCheck(int opts) |
Marvin 6.0 | chemaxon.struc.MolAtom.valenceCheck() There are no options for valence check. |
MolBond.ARROW |
Marvin 6.0 | chemaxon.struc.graphics.MRArrow Class MRArrow is used to represent reaction arrows. |
MolBond.cloneEdge(MolAtom a1, MolAtom a2) |
Marvin 6.0 | chemaxon.struc.MolBond.cloneBond(MolAtom, MolAtom) |
MolBond.getNode1() |
Marvin 6.0 | chemaxon.struc.MolBond.getAtom1() |
MolBond.getNode2() |
Marvin 6.0 | chemaxon.struc.MolBond.getAtom2() |
MolBond.getOtherNode(MolAtom node) |
Marvin 6.0 | chemaxon.struc.MolBond.getOtherAtom(MolAtom) |
MolBond.isArrow() |
Marvin 6.0 | chemaxon.struc.graphics.MRArrow MolBond objects cannot represent reaction arrows any more. Class MRArrow is used to represent reaction arrows. |
MolBond.isCoordinative() |
Marvin 6.0 | chemaxon.struc.MolBond.isCoordinate() |
Molecule.mergeFrags() |
Marvin 6.0 | It was used by an internal method, not intended for public usage. |
MoleculeGraph.AROM_CHEMAXON |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.AROM_BASIC |
MoleculeGraph.AROM_DAYLIGHT |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.AROM_GENERAL |
MoleculeGraph.findFragById(int fragId, MoleculeGraph frag) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.findFragById(int, int, MoleculeGraph) To keep the same functionality, use value FRAG_KEEPING_MULTICENTERS for parameter fragmentationType. Usage: Usage: mol.findFragById(fragId, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag); |
MoleculeGraph.getAromrings() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int) Usage: getAromaticAndAliphaticRings(AROM_BASIC, true, false, 18, 1000)[0]; |
MoleculeGraph.getAromrings(int size) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int) Usage: getAromaticAndAliphaticRings(AROM_BASIC, true, false, size, 1000)[0]; |
MoleculeGraph.getEdge(int i) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getBond(int) |
MoleculeGraph.getEdgeArray() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getBondArray() |
MoleculeGraph.getEdgeCount() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getBondCount() |
MoleculeGraph.getEdgeVector() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getBondArray() Usage: Vector |
MoleculeGraph.getFragIds() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getFragIds(int) To keep the same functionality, use value FRAG_KEEPING_MULTICENTERS for parameter fragmentationType. Usage: Usage: mol.getFragIds(MoleculeGraph.FRAG_KEEPING_MULTICENTERS); |
MoleculeGraph.getNode(int i) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAtom(int) |
MoleculeGraph.getNodeCount() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAtomCount() |
MoleculeGraph.getNodeVector() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAtomArray() Usage: Vector |
MoleculeGraph.getNonAromrings() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int) Usage: getAromaticAndAliphaticRings(AROM_BASIC, true, false, 18, 1000)[1]; |
MoleculeGraph.getNonAromrings(int size) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getAromaticAndAliphaticRings(int, boolean, boolean, int, int) Usage: getAromaticAndAliphaticRings(AROM_BASIC, true, false, size, 1000)[1]; |
MoleculeGraph.insertEdge(int i, MolBond edge) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.insertBond(int, MolBond) |
MoleculeGraph.insertEdgeInOrder(MolBond e, MolBond[] order) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.insertBondInOrder(MolBond, MolBond[]) |
MoleculeGraph.insertNode(int i, MolAtom node) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.insertAtom(int, MolAtom) |
MoleculeGraph.isValenceCheckEnabled() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.getValenceCheckState() |
MoleculeGraph.mergeFrags() |
Marvin 6.0 | It 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 6.0 | chemaxon.struc.MoleculeGraph.mergeFrags(int, int, int) To keep the same functionality, use value FRAG_KEEPING_MULTICENTERS for parameter fragmentationType. Usage: Usage: mol.mergeFrags(id1, id2, MoleculeGraph.FRAG_KEEPING_MULTICENTERS); |
MoleculeGraph.mergeNodes(MolAtom that, MolAtom a) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.mergeAtoms(MolAtom, MolAtom) |
MoleculeGraph.regenEdges() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.regenBonds() |
MoleculeGraph.removeAllEdges() |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeAllBonds() |
MoleculeGraph.removeEdge(int i) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeBond(int) |
MoleculeGraph.removeEdge(MolBond edge) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeBond(MolBond) |
MoleculeGraph.removeNode(int i, int cleanupFlags) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeAtom(int, int) |
MoleculeGraph.removeNode(int i) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeAtom(int) |
MoleculeGraph.removeNode(MolAtom node, int cleanupFlags) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeAtom(MolAtom, int) |
MoleculeGraph.removeNode(MolAtom node) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.removeAtom(MolAtom) |
MoleculeGraph.replaceEdge(MolBond olde, MolBond newe) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.replaceBond(MolBond, MolBond) |
MoleculeGraph.setEdge(int i, MolBond edge) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.setBond(int, MolBond) |
MoleculeGraph.setNode(int i, MolAtom node) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.setAtom(int, MolAtom) |
MoleculeGraph.setSetSeqs(int id) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.setAtomSetSeq(int) |
MoleculeGraph.setValenceCheckEnabled(boolean b) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.setValenceCheckState(ValenceCheckState) |
MoleculeGraph.sortEdgesAccordingTo(MolBond[] order) |
Marvin 6.0 | chemaxon.struc.MoleculeGraph.sortBondsAccordingTo(MolBond[]) |
MProp.CONV_SELFREF |
Marvin 6.1 | Option 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 6.0 | chemaxon.com.marvin.help.developer.beans.api.MolImportModule.createMol() Replacement method works for all file formats. |
RgMolecule.getBtab() |
Marvin 6.0 | chemaxon.struc.RgMolecule.getBondTable() chemaxon.core.util.BondTable.getMatrixArray() Usage: molecule.getBondTable().getMatrixArray(); |
RgMolecule.setAbsStereo(boolean c, int i, int j) |
Marvin 6.0 | chemaxon.struc.RgMolecule.getRgroupMember(int, int) chemaxon.struc.MoleculeGraph.setAbsStereo(boolean) Usage: rgMolecule.getRgroupMember(i, j).setAbsStereo©; |
RxnMolecule.addStructure(Molecule m, int type, boolean beNew) |
Marvin 6.0 | chemaxon.struc.RxnMolecule.addComponent(Molecule, int, boolean) |
RxnMolecule.addStructure(Molecule m, int type) |
Marvin 6.0 | chemaxon.struc.RxnMolecule.addComponent(Molecule, int) |
RxnMolecule.getBtab() |
Marvin 6.0 | chemaxon.struc.RxnMolecule.getBondTable() chemaxon.core.util.BondTable.getMatrixArray() Usage: molecule.getBondTable().getMatrixArray(); |
RxnMolecule.getStructure(int flags, int i) |
Marvin 6.0 | chemaxon.struc.RxnMolecule.getComponent(int, int) |
RxnMolecule.getStructureCount(int type) |
Marvin 6.0 | chemaxon.struc.RxnMolecule.getComponentCount(int) |
RxnMolecule.removeStructure(int flags, int i) |
Marvin 6.0 | chemaxon.struc.RxnMolecule.removeComponent(int, int) |
| ##### chemaxon.struc.prop | ||
MMoleculeProp.MMoleculeProp(String sval) |
Marvin 6.0 | chemaxon.com.marvin.help.developer.beans.api.MPropHandler.createMMoleculeProp(String) |
| ##### chemaxon.struc.util.bondutil | ||
MolBondUtil |
Marvin 6.3 | Internal usage only. |