Package chemaxon.struc.sgroup

Class MulticenterSgroup

java.lang.Object

chemaxon.struc.Sgroup

chemaxon.struc.sgroup.MulticenterSgroup

All Implemented Interfaces:

Serializable

@PublicApi
public class MulticenterSgroup
extends Sgroup

Multicenter S-group to represent complexes like markush ring structures, ferrocenes, metallocenes...
This sgroup represents a group of atoms with an atom called central atom. The atomic number of this central atom is MolAtom.MULTICENTER. The represented atoms are in the sgroup graph. Only the parent molecule of the sgroup contains the central atom, the sgroup graph doesn't.

Since:

Marvin 5.0, 01/09/2007

See Also:

• getCentralAtom()
• setCentralAtom(MolAtom)
• MolAtom.MULTICENTER
• MolAtom.getAtno()
• Sgroup.getParentMolecule()
• Sgroup.getSgroupGraph()
• Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.Sgroup

atomSet, brackets, CHARGE_ON_ATOMS, CHARGE_ON_GROUP, parentSgroup, PR_ATSYMS, RA_IN_EXPAND, RA_REMOVE_EXCEPT_RU, SCN_EITHER_UNKNOWN, SCN_HEAD_TO_HEAD, SCN_HEAD_TO_TAIL, SGROUP_TYPE_COUNT, sgroupGraph, sgroupType, SORT_CHILD_PARENT, SORT_PARENT_CHILD, SST_ALTERNATING, SST_BLOCK, SST_RANDOM, ST_AMINOACID, ST_ANY, ST_COMPONENT, ST_COPOLYMER, ST_CROSSLINK, ST_DATA, ST_FORMULATION, ST_GENERIC, ST_GRAFT, ST_MER, ST_MIXTURE, ST_MODIFICATION, ST_MONOMER, ST_MULTICENTER, ST_MULTIPLE, ST_SRU, ST_SUPERATOM, XSTATE_C, XSTATE_NONE, XSTATE_X, XSTATE_XC

Constructor Summary

Constructors

Modifier	Constructor	Description
	MulticenterSgroup(Molecule parent)	Constructs a Multicenter S-group.
protected	MulticenterSgroup(MulticenterSgroup sg, Molecule m, Sgroup psg)	Copy constructor.
protected	MulticenterSgroup(MulticenterSgroup sg, Molecule m, Sgroup psg, int[] atomIndexMap)	Copy constructor.

Method Summary

Modifier and Type	Method	Description
void	addCentralAtom()	Adds a central atom to this sgroup.
protected Sgroup	cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap)	Gets a new Sgroup instance.
MolAtom	getCentralAtom()	Gets the central atom of this sgroup.
boolean	hasBrackets()	Does a bracket belong to this sgroup?
boolean	hasNonCoordinateBond()	Decides whether the central atom of the sgroup has a non-coordinate bond.
DPoint3	recalcCentralAtom()	Recalculates and sets the coordinates of the central atom of this sgroup.
void	replaceAtom(MolAtom oldAtom, MolAtom newAtom, int opts)	Replace an existing atom by a new one in this S-group and its parent (recursively).
void	replaceMulticenterAtom(MolAtom atom, MolAtom atom2)	Deprecated, for removal: This API element is subject to removal in a future version. as of Marvin 2014.08.25.0, use setCentralAtom(chemaxon.struc.MolAtom) instead
void	setCentralAtom(MolAtom atom)	Sets the central atom of this sgroup.

Methods inherited from class chemaxon.struc.Sgroup

add, addBracket, addChildSgroup, areChildSgroupsVisible, checkBondConsistency, checkBonds, checkConsistencyInEmbeddings, checkSgroupGraphConsistency, clearObjects, cloneSgroup, cloneStructure, contains, containsAllAtomsOf, contract, countAllAtoms, createMolecule, createMolecule, expand, findCrossingBonds, findSmallestSgroupContaining, findSmallestSgroupOf, getAtom, getAtomArray, getAtomCount, getAtomSymbolListAsString, getAttach, getBondArray, getBracketCount, getBrackets, getChargeLocation, getChildSgroup, getChildSgroupCount, getChildSgroups, getConnectivity, getCrossingAtoms, getId, getParentMolecule, getParentSgroup, getSgroupGraph, getSgroupType, getSubscript, getSubType, getSuperscript, getTotalCharge, getType, getXState, hasAtom, indexOf, indexOf, initBrackets, isBracketCrossingBond, isBracketVisible, isDescendantOf, isEmpty, isOrderedComponentSgroup, isPartSelected, isRemovable, isSelected, isTotalSelected, isVisible, removeAtom, removeAtom, removeAtom, removeBond, removeBonds, removeChildSgroup, removeGroupedAtom, removeObject, replaceAtom, selectAllObjects, setAtom, setChargeLocation, setConnectivity, setGUIStateRecursively, setGUIStateRecursively, setId, setParentMolecule, setSgroupGraph, setSubscript, setSubType, setXState, setXState, setXState0, sort, toString, toString, transformByParent

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

MulticenterSgroup

public MulticenterSgroup(Molecule parent)

Constructs a Multicenter S-group. Please note the S-group is not added automatically to the parent molecule.

Parameters:

parent - the parent molecule

Since:

Marvin 5.0

See Also:

• Molecule.addSgroup(Sgroup, boolean)

MulticenterSgroup

protected MulticenterSgroup(MulticenterSgroup sg,
 Molecule m,
 Sgroup psg)

Copy constructor.

Parameters:

sg - the S-group to copy

m - the new parent molecule

psg - the new parent S-group or null

Since:

Marvin 5.0

MulticenterSgroup

protected MulticenterSgroup(MulticenterSgroup sg,
 Molecule m,
 Sgroup psg,
 int[] atomIndexMap)

Copy constructor.

Parameters:

sg - the S-group to copy

m - the new parent molecule

psg - the new parent S-group or null

atomIndexMap - indices of cloned atoms in the original molecule or null

Since:

Marvin 5.0

Method Details

cloneSgroup

protected Sgroup cloneSgroup(Molecule m,
 Sgroup psg,
 int[] atomIndexMap)

Gets a new Sgroup instance.

Overrides:

cloneSgroup in class Sgroup

Parameters:

m - the new parent molecule

psg - the new parent S-group

atomIndexMap - indices of cloned atoms in the original molecule or null

Returns:

the new object

Since:

Marvin 5.0.2

addCentralAtom

public void addCentralAtom()

Adds a central atom to this sgroup.

recalcCentralAtom

public DPoint3 recalcCentralAtom()

Recalculates and sets the coordinates of the central atom of this sgroup.

Returns:

the recalculated coordinates of the central atom

hasBrackets

public boolean hasBrackets()

Does a bracket belong to this sgroup?

Overrides:

hasBrackets in class Sgroup

Returns:

returns false

hasNonCoordinateBond

public boolean hasNonCoordinateBond()

Decides whether the central atom of the sgroup has a non-coordinate bond.

Returns:

returns true if the central atom of the sgroup has at least one non-coordinate bond, false otherwise.

getCentralAtom

public MolAtom getCentralAtom()

Gets the central atom of this sgroup.

Returns:

the central atom

setCentralAtom

public void setCentralAtom(MolAtom atom)

Sets the central atom of this sgroup.

Parameters:

atom - the central atom

replaceMulticenterAtom

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void replaceMulticenterAtom(MolAtom atom,
 MolAtom atom2)

Deprecated, for removal: This API element is subject to removal in a future version.

as of Marvin 2014.08.25.0, use setCentralAtom(chemaxon.struc.MolAtom) instead

Replace an existing central atom by a new one in this S-group and its parent (recursively).

Parameters:

atom - the original atom

atom2 - the new atom

replaceAtom

public void replaceAtom(MolAtom oldAtom,
 MolAtom newAtom,
 int opts)

Description copied from class: Sgroup

Replace an existing atom by a new one in this S-group and its parent (recursively).

Overrides:

replaceAtom in class Sgroup

Parameters:

oldAtom - the original atom

newAtom - the new atom

opts - options

See Also:

• Sgroup.RA_REMOVE_EXCEPT_RU