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:<br>

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&ltInteger&gt 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()

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.<p> <i>Usage:</i> </p>

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.<p> <i>Usage:</i> </p>

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.<p> <i>Usage:</i> </p>

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.