| ### 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 | TRANS or CIS | TRANS | CTUNSPEC values are used instead. |
| ##### 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<MolBond> v = new Vector<MolBond>(getBondCount()); v.addAll(Arrays.asList(getBondArray())). | |||
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<MolAtom> v = new Vector<MolAtom>(getAtomCount()); v.addAll(Arrays.asList(getAtomArray())); | |||
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(c); | |||
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. |