Package chemaxon.struc.sgroup

Class MultipleSgroup

java.lang.Object

chemaxon.struc.Sgroup

chemaxon.struc.sgroup.MultipleSgroup

All Implemented Interfaces:

Expandable, Serializable

@PublicAPI
public class MultipleSgroup
extends Sgroup
implements Expandable

Multiple S-group.

Since:

Marvin 3.3, 08/17/2003

See Also:

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

Fields inherited from interface chemaxon.struc.sgroup.Expandable

COORDS_UPDATE, DEFAULT_OPTIONS, FAST_COORDS, LEAVE_COORDS_UNCHANGED, MDL_EXPAND, NONRECURSIVE_EXPAND, REVERSIBLE_EXPAND

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	add(MolAtom a)	Adds a new atom to the S-group.
void	addRepeatingUnitAtom(MolAtom a)	Adds an atom to the list of paradigmatic repeating unit atoms.
protected Sgroup	cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap)	Gets a new Sgroup instance.
boolean	contract(int opts)	Contracts this S-group.
boolean	expand(int opts)	Expands this S-group unless it has expandable child s-group because in that case our calculations' behaviour can not be predicted.
int	getMultiplier()	Gets the multiplier.
MolAtom	getRepeatingUnitAtom(int i)	Gets a paradigmatic repeating unit atom.
int	getRepeatingUnitAtomCount()	Gets the number of atoms in the pararadigmatic repeating unit.
MolAtom[]	getRepeatingUnitAtoms()	Gets the repeating unit atoms.
String	getSubscript()	Gets the subscript.
static boolean	isAcceptableGraph(MoleculeGraph molGraph)	Decides whether the given molecule graph can be the graph of a multiple s-group.
boolean	isBracketVisible()	Tests whether the bracket is visible.
boolean	isContracted()	Is this S-group contracted?
boolean	isExpanded()	Is this S-group expanded?
boolean	isRepeatingUnitAtom(MolAtom a)	Checks if the specified atom object is in the paradigmatic repeating unit or not.
Sgroup	newInstance()	Gets a new MultipleSgroup instance.
protected void	removeAtom(MolAtom a, int opts)	Removes an atom from the S-group.
void	removeRepeatingUnitAtom(MolAtom a)	Removes an atom from the list of paradigmatic repeating unit atoms.
void	replaceAtom(MolAtom olda, MolAtom newa, int opts)	Replace an existing atom by a new one.
void	setAtom(int i, MolAtom a)	Sets the specified atom in the S-group graph.
void	setMultiplier(int m)	Sets the multiplier.
void	setRepeatingUnitAtom(MolAtom a, boolean set)	Adds or removes an atom to/from the list of paradigmatic repeating unit atoms.
void	setSubscript(String s)	Sets the subscript.
String	toString(int opts)	Returns a string representation of the group.

Methods inherited from class chemaxon.struc.Sgroup

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

Methods inherited from class java.lang.Object

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

Constructor Detail

MultipleSgroup

public MultipleSgroup(Molecule parent,
                      boolean expanded)

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

Parameters:

parent - the parent molecule

expanded - whether the S-group is created in expanded state or not

See Also:

Molecule.addSgroup(Sgroup, boolean)

MultipleSgroup

protected MultipleSgroup(MultipleSgroup 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

Since:

Marvin 3.4

Method Detail

isRepeatingUnitAtom

public final boolean isRepeatingUnitAtom(MolAtom a)

Checks if the specified atom object is in the paradigmatic repeating unit or not.

Parameters:

a - the atom to check

Returns:

true if it is in the paradigmatic repeating unit, false otherwise

isAcceptableGraph

public static boolean isAcceptableGraph(MoleculeGraph molGraph)

Decides whether the given molecule graph can be the graph of a multiple s-group.

Parameters:

molGraph - molecule graph to check

Returns:

true if the graph is acceptable as a multiple sgroup

Since:

Marvin 5.4.0, 01/27/2010

getRepeatingUnitAtomCount

public final int getRepeatingUnitAtomCount()

Gets the number of atoms in the pararadigmatic repeating unit.

Returns:

the number of atoms in the paradigmatic repeating unit

getRepeatingUnitAtom

public final MolAtom getRepeatingUnitAtom(int i)

Gets a paradigmatic repeating unit atom.

Parameters:

i - the paradigmatic repeating unit atom index

Returns:

the paradigmatic repeating unit atom

getRepeatingUnitAtoms

public final MolAtom[] getRepeatingUnitAtoms()

Gets the repeating unit atoms.

Returns:

the paradigmatic repeating unit atoms

addRepeatingUnitAtom

public final void addRepeatingUnitAtom(MolAtom a)

Adds an atom to the list of paradigmatic repeating unit atoms.

Parameters:

a - the atom to add

removeRepeatingUnitAtom

public final void removeRepeatingUnitAtom(MolAtom a)

Removes an atom from the list of paradigmatic repeating unit atoms.

Parameters:

a - the atom to remove

setRepeatingUnitAtom

public final void setRepeatingUnitAtom(MolAtom a,
                                       boolean set)

Adds or removes an atom to/from the list of paradigmatic repeating unit atoms.

Parameters:

a - the atom

set - add (true) or remove (false)

add

public void add(MolAtom a)

Adds a new atom to the S-group.

Overrides:

add in class Sgroup

Parameters:

a - the atom

getMultiplier

public final int getMultiplier()

Gets the multiplier.

Returns:

the multiplier

setMultiplier

public final void setMultiplier(int m)

Sets the multiplier.

Parameters:

m - the multiplier

newInstance

public Sgroup newInstance()

Gets a new MultipleSgroup instance.

Returns:

the new object

setAtom

public final void setAtom(int i,
                          MolAtom a)

Sets the specified atom in the S-group graph.

Overrides:

setAtom in class Sgroup

Parameters:

i - the index

a - the atom

removeAtom

protected final void removeAtom(MolAtom a,
                                int opts)

Removes an atom from the S-group.

Overrides:

removeAtom in class Sgroup

Parameters:

a - the atom

opts - 0 or Sgroup.RA_IN_EXPAND

replaceAtom

public final void replaceAtom(MolAtom olda,
                              MolAtom newa,
                              int opts)

Replace an existing atom by a new one.

Overrides:

replaceAtom in class Sgroup

Parameters:

olda - the original atom

newa - the new atom

opts - options

Since:

4.1, 07/25/2006

See Also:

Sgroup.RA_REMOVE_EXCEPT_RU

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 in the case of partial cloning, or null otherwise

Returns:

the new object

Since:

Marvin 5.0.2, 03/07/2008

setSubscript

public void setSubscript(String s)

Sets the subscript.

Overrides:

setSubscript in class Sgroup

Parameters:

s - the multiplier as a string

getSubscript

public String getSubscript()

Gets the subscript.

Overrides:

getSubscript in class Sgroup

Returns:

the subscript in contracted state, empty string in expanded state

expand

public final boolean expand(int opts)

Expands this S-group unless it has expandable child s-group because in that case our calculations' behaviour can not be predicted.

Specified by:

expand in interface Expandable

Overrides:

expand in class Sgroup

Parameters:

opts - expansion options

Returns:

true if the operation was successful, false if already expanded, or has Expandable descendant

Throws:

IllegalArgumentException - if the group is invisible (it has a non-expanded parent)

See Also:

Sgroup.setXState(int)

isExpanded

public final boolean isExpanded()

Is this S-group expanded?

Specified by:

isExpanded in interface Expandable

Returns:

true if expanded, false if contracted

contract

public final boolean contract(int opts)

Contracts this S-group.

Specified by:

contract in interface Expandable

Overrides:

contract in class Sgroup

Parameters:

opts - contraction options

Returns:

true if the operation was successful, false if already contracted

Throws:

IllegalArgumentException - if the group is invisible (it has a non-expanded parent)

See Also:

Sgroup.setXState(int)

isContracted

public final boolean isContracted()

Is this S-group contracted?

Returns:

true if contracted, false if expanded

isBracketVisible

public boolean isBracketVisible()

Tests whether the bracket is visible. Multiple S-group brackets are only visible in expanded state.

Overrides:

isBracketVisible in class Sgroup

Returns:

true in contracted, false in expanded state

Since:

Marvin 3.5.1, 11/12/2004

toString

public String toString(int opts)

Returns a string representation of the group.

Overrides:

toString in class Sgroup

Parameters:

opts - options or 0

Returns:

the string representation

Since:

Marvin 4.1, 07/26/2006

See Also:

Sgroup.PR_ATSYMS