chemaxon.struc.sgroup

Class SuperatomSgroup

java.lang.Object

chemaxon.struc.Sgroup

chemaxon.struc.sgroup.SuperatomSgroup

All Implemented Interfaces:

chemaxon.core.structure.AbbreviationForBuilder<Integer>, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.RootStructureForBuilder, chemaxon.core.structure.StructureForBuilder, Expandable, Serializable

public class SuperatomSgroup
extends Sgroup
implements Expandable, chemaxon.core.structure.AbbreviationForBuilder<Integer>

Superatom S-group.

Since:

Marvin 3.0, 11/05/2002

Version:

6.0, Dec. 5, 2012

Author:

Peter Csizmadia, Janos Kendi, Domonkos Kiss, Mate Steiner, Peter Szakacs

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 and Description
	SuperatomSgroup(Molecule parent) Constructs a superatom S-group in expanded state.
	SuperatomSgroup(Molecule parent, boolean expanded) Constructs a superatom S-group.
protected	SuperatomSgroup(SuperatomSgroup sg, Molecule m, Sgroup psg, int[] atomIndexMap) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(MolAtom atom) Adds a new atom to the S-group.
int	addAttachmentPoint(MolAtom atom) Adds a new free attachment point for an atom.
int	addAttachmentPoint(MolAtom atom, int order) Adds a new free attachment point of the given attachment atom and order.
int	addAttachmentPoint(MolAtom atom, int order, MolBond bond) Adds a new free attachment point.
boolean	areChildSgroupsVisible() Checks whether the child S-groups are visible.
void	calculateAttachmentPoints() Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.
protected void	calculateCoordinates(Molecule parentMol, MolBond[] xbonds, MoleculeGraph g, int opts, boolean isContract, SelectionMolecule otherSgroup, List<Double> xBondLength) Calculates the coordinates during expand and contract.
protected void	checkBonds(MolAtom atom) Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
protected boolean	checkSgroupGraphConsistency(Sgroup parent) Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup.
SuperatomSgroup	clone() Clones the SuperatomSgroup (and not the Molecule).
protected void	cloneLeavingGroups(SuperatomSgroup sasg) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
protected Sgroup	cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap) Gets a new Sgroup instance.
boolean	contract(int opts) Contracts this S-group.
protected SuperatomSgroup	createGroup()
Molecule	createMolecule() Creates a molecule object that contains only one SuperatomSgroup identical to this one.
boolean	expand(int opts) Expands this S-group.
boolean	expandOther(int opts, Molecule moltoexpand) Deprecated. as of Marvin 6.2. use expand(int) instead on the s-groups desired to be expanded
MolAtom	findAttachAtom() Gets the attachment atom of attachment point with the smallest order.
MolBond[]	findCrossingBonds() Finds the crossing bonds.
MolAtom[]	getAllAttachAtoms() Gets the attachment atoms (atoms having attachment point).
MolAtom[]	getAttachAtoms() Deprecated. As of Marvin 6.0, replaced by getBoundAttachAtoms().
chemaxon.struc.sgroup.AttachmentPoint	getAttachmentPoint(int order) Gets the attachment point that's order is given as parameter
int	getAttachmentPointCount() Gets the number of the attachment points.
List<Integer>	getAttachmentPointOrders() Gets the orders with which attachment point exists
List<Integer>	getAttachmentPointOrders(MolAtom atom) Gets the attachment orders of the given attachment atom.
List<chemaxon.struc.sgroup.AttachmentPoint>	getAttachmentPoints() Gets the sorted copy of the attachment point list.
MolAtom[]	getBoundAttachAtoms() Gets atoms with attachment point having crossing bond and the related leaving group is not visible.
MolAtom[]	getCrossingAtoms(MolBond[] xbonds) Gets the atoms from the S-group that have crossing bonds.
int	getExternalConnections(MolAtom a) Gets the number of bonds of a specified atom where the neighbor atom doesn't belong to the S-group.
MolAtom[]	getFreeAttachAtoms() Gets the atoms with free attachment points.
int	getFreeAttachmentPointCount() Gets the number of free attachment points.
List<Integer>	getFreeAttachmentPointOrders() Gets the increasingly sorted orders of the free attachment points.
List<Integer>	getFreeAttachmentPointOrders(MolAtom atom) Gets the sorted free attachment orders of the given attachment atom.
MolAtom[]	getFreeLegalAttachAtoms() Deprecated. As of Marvin 6.0, replaced by getFreeAttachAtoms().
MolAtom[]	getLegalAttachAtoms() Deprecated. As of Marvin 6.0, replaced by getAllAttachAtoms().
SelectionMolecule	getParentSgroupGraph() Deprecated. as of Marvin 6.2, intended for internal use, similar functionality can be reached by getSgroupGraph()
SelectionMolecule	getSgroupGraph() Gets the molecule graph as a selection.
SgroupAtom	getSuperAtom() Gets the superatom.
boolean	hasAtom(MolAtom a) Is the specified atom an element of this group?
boolean	hasBrackets() Checks if brackets should be painted or not.
boolean	isAttachmentAtom(MolAtom a) Checks whether the given atom is an attachment atom or not.
boolean	isBracketVisible() Tests whether the bracket is visible.
boolean	isContracted() Decides whether this S-group is contracted or not.
boolean	isExpanded() Is this S-group expanded?
boolean	isFreeAttachAtom(MolAtom a) Checks whether the specified atom has free attachment point.
boolean	isFreeLegalAttachAtom(MolAtom a) Deprecated. As of Marvin 6.0, replaced by isFreeAttachAtom(MolAtom a).
boolean	isLegalAttachment(MolAtom atom) Deprecated. As of Marvin 6.0, replaced by isAttachmentAtom(MolAtom).
boolean	isTotalSelected(MoleculeGraph sel) Decides if the whole superatom sgroup is selected or not.
void	removeAllAttachmentPoints() Removes all of the attachment points of the Superatom s-group.
protected void	removeAtom(MolAtom atom, int opts) Removes an atom from the S-group.
void	removeAttachmentPoint(int order) Removes the attachment point with the given order.
void	removeAttachmentPoints(MolAtom atom) Removes all attachment points of the given attachment atom.
void	removeBond(MolBond bond) Removes a the given bond from the S-group.
void	removeLeavingGroup(int order) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
void	replaceAtom(MolAtom oldAtom, MolAtom newAtom, 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	setAttachmentPointOrder(MolAtom atom, int oldOrder, int newOrder) Sets a new order for the given attachment point.
void	setCrossingBond(int order, MolBond bond) Change the crossing bond of an attachment point.
void	setCrossingBondType(int order, chemaxon.struc.BondType newType) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
boolean	setGUIStateRecursively(boolean v) Sets the expanded/contracted state recursively.
void	setLeavingGroup(int order, int atNo) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
void	setLeavingGroup(int order, int atNo, String alternativeName) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
void	setLeavingGroup(int order, int atNo, String alternativeName, chemaxon.struc.BondType crossingBondType) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
void	setLeavingGroupAlternativeName(int order, String alternativeName) Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
void	setSgroupGraph(SelectionMolecule smol) Sets the molecule graph.
void	sortXBonds() Deprecated. As of Marvin 5.12, no replacement. 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.
String	toString(int opts) Returns a string representation of the group.
protected void	transformByParent(CTransform3D t, boolean incg) Applies a transformation matrix to the Sgroup coordinates.
void	updateAttachmentPoints() Deprecated. as of Marvin 6.2, use calculateAttachmentPoints() instead

Methods inherited from class chemaxon.struc.Sgroup

addBracket, addChildSgroup, checkBondConsistency, checkConsistencyInEmbeddings, clearObjects, cloneSgroup, cloneStructure, contains, containsAllAtomsOf, countAllAtoms, createMolecule, findSmallestSgroupContaining, findSmallestSgroupOf, getAtom, getAtomArray, getAtomCount, getAtomSymbolListAsString, getAttach, getBondArray, getBracketCount, getBrackets, getChargeLocation, getChildSgroup, getChildSgroupCount, getChildSgroups, getConnectivity, getParentMolecule, getParentSgroup, getSgroupType, getSubscript, getSubType, getSuperscript, getTotalCharge, getType, getXState, indexOf, indexOf, initBrackets, isBracketCrossingBond, isDescendantOf, isEmpty, isOrderedComponentSgroup, isPartSelected, isRemovable, isSelected, isVisible, removeAtom, removeAtom, removeBonds, removeChildSgroup, removeGroupedAtom, removeObject, replaceAtom, selectAllObjects, setChargeLocation, setConnectivity, setGUIStateRecursively, setParentMolecule, setSubscript, setSubType, setXState, setXState, setXState0, sort, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface chemaxon.core.structure.StructureForBuilder

getAtomCount

Constructor Detail

SuperatomSgroup

public SuperatomSgroup(Molecule parent)

Constructs a superatom S-group in expanded state. Its superatom is automatically created.

Parameters:

parent - the parent molecule

Since:

Marvin 3.5.3, 01/18/2005

See Also:

Sgroup.ST_SUPERATOM, MolAtom.SGROUP, getSuperAtom()

SuperatomSgroup

public SuperatomSgroup(Molecule parent,
               boolean expanded)

Constructs a superatom S-group. Its superatom is automatically created.

Parameters:

parent - the parent molecule

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

See Also:

Sgroup.ST_SUPERATOM, MolAtom.SGROUP, getSuperAtom()

SuperatomSgroup

protected SuperatomSgroup(SuperatomSgroup 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 5.0.2, 03/07/2008

Method Detail

getSuperAtom

public final SgroupAtom getSuperAtom()

Gets the superatom.

Returns:

the superatom

getAttachAtoms

@Deprecated
public final MolAtom[] getAttachAtoms()

Deprecated. As of Marvin 6.0, replaced by getBoundAttachAtoms().

Gets atoms with attachment point having crossing bond. This method should only be called when the residue is in contracted state.

Returns:

the attachment atoms

Since:

Marvin 4.0.4, 01/09/2006

getBoundAttachAtoms

public final MolAtom[] getBoundAttachAtoms()

Gets atoms with attachment point having crossing bond and the related leaving group is not visible. This method should only be called when the residue is in contracted state.

Returns:

the attachment atoms having crossing bond and not visible leaving group

Since:

Marvin 6.0, Dec 11, 2012

getFreeLegalAttachAtoms

@Deprecated
public final MolAtom[] getFreeLegalAttachAtoms()

Deprecated. As of Marvin 6.0, replaced by getFreeAttachAtoms().

Gets the atoms with free attachment points. Free if the corresponding attachment point is free.

Returns:

array of MolAtoms having free attachment point.

See Also:

AttachmentPoint.isFree()

getFreeAttachAtoms

public final MolAtom[] getFreeAttachAtoms()

Gets the atoms with free attachment points. Free if the corresponding attachment point is free.

Returns:

array of MolAtoms having free attachment point.

Since:

Marvin 6.0, Dec 11, 2012

See Also:

AttachmentPoint.isFree()

isFreeLegalAttachAtom

@Deprecated
public final boolean isFreeLegalAttachAtom(MolAtom a)

Deprecated. As of Marvin 6.0, replaced by isFreeAttachAtom(MolAtom a).

Tests whether the specified atom has a free attachment point.

Parameters:

a - the atom

Returns:

true if it has free attachment point, false otherwise

Since:

5.0, 09/23/2007

isFreeAttachAtom

public final boolean isFreeAttachAtom(MolAtom a)

Checks whether the specified atom has free attachment point.

Parameters:

a - the atom

Returns:

true if it has free attachment point, false otherwise

Since:

Marvin 6.0, Dec 11, 2012

See Also:

AttachmentPoint.isFree(), getFreeAttachAtoms()

getLegalAttachAtoms

@Deprecated
public final MolAtom[] getLegalAttachAtoms()

Deprecated. As of Marvin 6.0, replaced by getAllAttachAtoms().

Gets all attachment atoms (from free and bound attachment points).

Returns:

array of attachment atoms

getAllAttachAtoms

public final MolAtom[] getAllAttachAtoms()

Gets the attachment atoms (atoms having attachment point).

Returns:

array of attach atoms

Since:

Marvin 6.0, Dec 11, 2012

isLegalAttachment

@Deprecated
public final boolean isLegalAttachment(MolAtom atom)

Deprecated. As of Marvin 6.0, replaced by isAttachmentAtom(MolAtom).

Checks whether the given atom is an attachment atom or not.

Parameters:

atom - the atom

Returns:

true if the given atom is an attachment atom false otherwise

Since:

3.5, 11/04/2004

isAttachmentAtom

public final boolean isAttachmentAtom(MolAtom a)

Checks whether the given atom is an attachment atom or not.

Parameters:

a - the atom

Returns:

true if the given atom is an attachment atom false otherwise

Since:

Marvin 6.0, Dec 11, 2012

See Also:

getAllAttachAtoms()

updateAttachmentPoints

@Deprecated
public void updateAttachmentPoints()

Deprecated. as of Marvin 6.2, use calculateAttachmentPoints() instead

Adjusts attachment point information to current bonding.

Throws:

NoFreeAttachmentPointException - if there are not enough free attachment point

getSgroupGraph

public SelectionMolecule getSgroupGraph()

Gets the molecule graph as a selection. The nodes are ordered, the first n are the attachment atoms.

Overrides:

getSgroupGraph in class Sgroup

Returns:

the molecule graph

Since:

Marvin 3.3, 11/04/2003

getParentSgroupGraph

@Deprecated
public SelectionMolecule getParentSgroupGraph()

Deprecated. as of Marvin 6.2, intended for internal use, similar functionality can be reached by getSgroupGraph()

Gets the parent exact sgroupgraph. Internal use only.

Returns:

the sgroupGraph

setSgroupGraph

public void setSgroupGraph(SelectionMolecule smol)

Sets the molecule graph. If the S-group is in contracted state then:

• In case of single attachment points the first n nodes are supposed to be the attachment points.
• In case of double attachment point the graph is searched for the attachment point.

Overrides:

setSgroupGraph in class Sgroup

Parameters:

smol - the molecule graph

Since:

Marvin 3.3, 11/04/2003

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:

5.0.2, 03/07/2008

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 atom,
              int opts)

Removes an atom from the S-group.

Overrides:

removeAtom in class Sgroup

Parameters:

atom - the atom

opts - unused argument

removeBond

public final void removeBond(MolBond bond)

Removes a the given bond from the S-group.

Overrides:

removeBond in class Sgroup

Parameters:

bond - the bond

findCrossingBonds

public MolBond[] findCrossingBonds()

Finds the crossing bonds. Use only when the S-group is expanded.

Overrides:

findCrossingBonds in class Sgroup

Returns:

the attachment bonds

Since:

Marvin 3.3

getCrossingAtoms

public MolAtom[] getCrossingAtoms(MolBond[] xbonds)

Gets the atoms from the S-group that have crossing bonds.

Overrides:

getCrossingAtoms in class Sgroup

Parameters:

xbonds - the crossing bonds

Returns:

the attachment atoms

Since:

Marvin 3.3

See Also:

findCrossingBonds()

findAttachAtom

public MolAtom findAttachAtom()

Gets the attachment atom of attachment point with the smallest order.

Returns:

the attachment point with the smallest order or null if there is not any attachment point

Since:

Marvin 4.1, 03/08/2006

transformByParent

protected void transformByParent(CTransform3D t,
                     boolean incg)

Applies a transformation matrix to the Sgroup coordinates. (Only absolute placement.) This method is called by the parent molecule's Molecule.transform(CTransform3D, boolean) method, thus only those atom coordinates are transformed here that are not handled in MoleculeGraph.transform(CTransform3D, boolean).

Overrides:

transformByParent in class Sgroup

Parameters:

t - the transformation matrix

incg - graph invariants are changed (true) or not (false)

Since:

Marvin 5.0, 08/18/2007

hasBrackets

public boolean hasBrackets()

Checks if brackets should be painted or not.

Overrides:

hasBrackets in class Sgroup

Returns:

true if the group is in expanded state

Since:

Marvin 3.3

hasAtom

public boolean hasAtom(MolAtom a)

Is the specified atom an element of this group?

Overrides:

hasAtom in class Sgroup

Parameters:

a - the atom

Returns:

true if it contains the atom, false otherwise

Since:

Marvin 3.4

expand

public final boolean expand(int opts)
                     throws IllegalArgumentException

Expands this S-group. Atom indexes are preserved during expansion. During the expand, the atoms of the superatom s-group get into MoleculeGraph.

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

Throws:

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

See Also:

Expandable.DEFAULT_OPTIONS, Expandable.COORDS_UPDATE, Expandable.LEAVE_COORDS_UNCHANGED, Expandable.MDL_EXPAND, Expandable.FAST_COORDS, Expandable.NONRECURSIVE_EXPAND

expandOther

@Deprecated
public final boolean expandOther(int opts,
                             Molecule moltoexpand)
                          throws IllegalArgumentException

Deprecated. as of Marvin 6.2. use expand(int) instead on the s-groups desired to be expanded

Expands other S-group the same way as it would be this. The other Sgroup is the first S-group of the other molecule (moltoexpand). Atom indices are preserved during expansion.

Parameters:

opts - expansion options

moltoexpand - molecule containing an Sgroup that has to be expanded

Returns:

true if the operation was successful, false if already expanded

Throws:

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

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)
                       throws IllegalArgumentException

Contracts this S-group. During the contraction, atoms of this superatom s-group vanish from the molecule graph and substituded with one superatom.

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:

Expandable.NONRECURSIVE_EXPAND, Sgroup.RA_REMOVE_EXCEPT_RU, Expandable.LEAVE_COORDS_UNCHANGED

calculateCoordinates

protected void calculateCoordinates(Molecule parentMol,
                        MolBond[] xbonds,
                        MoleculeGraph g,
                        int opts,
                        boolean isContract,
                        SelectionMolecule otherSgroup,
                        List<Double> xBondLength)

Calculates the coordinates during expand and contract.

Parameters:

parentMol - the parent molecule of the superatomSgroup

xbonds - array of the crossing bonds

g - graph of the sgroup

opts - expand option

isContract - true if it is called from contract, false if do so from expand

otherSgroup - graph of the other sgroup in expandOther

Since:

Marvin 6.2, Aug 8, 2013

isContracted

public final boolean isContracted()

Decides whether this S-group is contracted or not.

Returns:

true if contracted false otherwise

isBracketVisible

public boolean isBracketVisible()

Tests whether the bracket is visible.

Overrides:

isBracketVisible in class Sgroup

Returns:

false, superatom S-group brackets are not visible

Since:

Marvin 3.5.1, 11/12/2004

isTotalSelected

public boolean isTotalSelected(MoleculeGraph sel)

Decides if the whole superatom sgroup is selected or not. Overrides method in parent class.

Overrides:

isTotalSelected in class Sgroup

Parameters:

sel - molecule graph that contains the selection

Returns:

true if the whole superatom group is selected

areChildSgroupsVisible

public boolean areChildSgroupsVisible()

Checks whether the child S-groups are visible.

Overrides:

areChildSgroupsVisible in class Sgroup

Returns:

true if children are visible, false otherwise

Since:

Marvin 3.4

sortXBonds

@Deprecated
public void sortXBonds()

Deprecated. As of Marvin 5.12, no replacement.
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.

Sorts the crossing bonds in the parent molecule in attachment point number order.

Since:

Marvin 5.0, 12/07/2007

getExternalConnections

public int getExternalConnections(MolAtom a)

Gets the number of bonds of a specified atom where the neighbor atom doesn't belong to the S-group.

Parameters:

a - the atom whose connections to be checked

Returns:

the number of external connection or 0 if the specified atom doesn't belong to the S-group.

createMolecule

public Molecule createMolecule()

Creates a molecule object that contains only one SuperatomSgroup identical to this one.

Overrides:

createMolecule in class Sgroup

Returns:

the molecule containing one SuperatomSgroup

Since:

Marvin 3.4

createGroup

protected SuperatomSgroup createGroup()

replaceAtom

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

Replace an existing atom by a new one.

Overrides:

replaceAtom in class Sgroup

Parameters:

oldAtom - the original atom

newAtom - the new atom

opts - options

Since:

4.1, 07/25/2006

See Also:

Sgroup.RA_REMOVE_EXCEPT_RU

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

setGUIStateRecursively

public final boolean setGUIStateRecursively(boolean v)
                                     throws IllegalArgumentException

Sets the expanded/contracted state recursively.

Overrides:

setGUIStateRecursively in class Sgroup

Parameters:

v - true sets Sgroup.XSTATE_C if previous state was Sgroup.XSTATE_XC, false sets Sgroup.XSTATE_XC if previous state was Sgroup.XSTATE_C, no operation in other cases

Returns:

true if at least one S-group's state was changed, false otherwise

Throws:

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

Since:

Marvin 5.1

See Also:

Sgroup.setXState(int)

calculateAttachmentPoints

public void calculateAttachmentPoints()

Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.

1. The properly set crossing bond are kept
2. Those attachment points that's bond is not-crossing bond will be removed
3. For those crossing bonds that have no attachment point connected will be calculated one from the free ones or will be given a new one

removeAttachmentPoints

public void removeAttachmentPoints(MolAtom atom)

Removes all attachment points of the given attachment atom.

Parameters:

atom - the attachment atom

Throws:

IllegalArgumentException - if the given atom is not part of the superatom s-group

setAttachmentPointOrder

public void setAttachmentPointOrder(MolAtom atom,
                           int oldOrder,
                           int newOrder)

Sets a new order for the given attachment point. The order must be a positive number.

Parameters:

atom - the attachment atom of the attachment point

oldOrder - the old attachment order of the attachment point

newOrder - the new attachment order of the attachment point

Throws:

IllegalArgumentException - if the given atom is not part of the superatom S-group or the given new order is negativ or zero

Since:

Marvin 6.0, Dec 5, 2012

getAttachmentPointOrders

public List<Integer> getAttachmentPointOrders(MolAtom atom)

Gets the attachment orders of the given attachment atom.

Parameters:

atom - the attachment atom

Returns:

the list of the attachment orders

Since:

Marvin 6.0, Dec 5, 2012

getFreeAttachmentPointOrders

public List<Integer> getFreeAttachmentPointOrders(MolAtom atom)

Gets the sorted free attachment orders of the given attachment atom.

Parameters:

atom - the attachment atom

Returns:

the sorted list of the free attachment orders

Since:

Marvin 6.0, Dec 5, 2012

See Also:

AttachmentPoint.isFree()

add

public void add(MolAtom atom)

Adds a new atom to the S-group.

Overrides:

add in class Sgroup

Parameters:

atom - the atom

Since:

Marvin 6.0 Dec 5, 2012.

getAttachmentPointCount

public int getAttachmentPointCount()

Gets the number of the attachment points.

Specified by:

getAttachmentPointCount in interface chemaxon.core.structure.AbbreviationForBuilder<Integer>

Returns:

the number of the attachment points

Since:

Marvin 6.0, Dec 4, 2012

checkBonds

protected void checkBonds(MolAtom atom)

Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup. If the newly added bond was crossing bond then the attachment point connected to this bond will be removed.

Overrides:

checkBonds in class Sgroup

Parameters:

atom - the atom

getAttachmentPoints

public List<chemaxon.struc.sgroup.AttachmentPoint> getAttachmentPoints()

Gets the sorted copy of the attachment point list.

Returns:

the list of the attachment points

Since:

Marvin 6.0, Dec 5, 2012

setCrossingBond

public void setCrossingBond(int order,
                   MolBond bond)

Change the crossing bond of an attachment point.

Parameters:

order - the order of the attachment point

bond - the crossing bond to be set

Throws:

IllegalArgumentException -

if no attachment point exists with the given order

if the attachment atom for the given order is not the same as the original attachment atom in expanded state

if the given bond is not a crossing bond for this superatom s-group

IllegalStateException

NoFreeAttachmentPointException - if the attachment point for the given order is not free

addAttachmentPoint

public int addAttachmentPoint(MolAtom atom)

Adds a new free attachment point for an atom. The order will be the smallest non used order.

Parameters:

atom - the attachment atom of the new attachment point

Returns:

the attachment order of the new attachment point

Throws:

IllegalArgumentException - if the given atom is not part of the superatom S-group

Since:

Marvin 6.0, Dec 5, 2012

addAttachmentPoint

public int addAttachmentPoint(MolAtom atom,
                     int order)

Adds a new free attachment point of the given attachment atom and order. The order must be a positive number.

Parameters:

atom - the attachment atom of the new attachment point

order - the attachment order of the new attachment point

Returns:

the attachment order of the new attachment point

Throws:

IllegalArgumentException - if the order is a non positive number

Since:

Marvin 6.0, Dec 5, 2012

addAttachmentPoint

public int addAttachmentPoint(MolAtom atom,
                     int order,
                     MolBond bond)

Adds a new free attachment point.

Parameters:

atom - the attachment atom of the new attachment point

bond - the crossing bond of the new attachment point

order - the attachment order of the new attachment point

Returns:

the attachment order of the new attachment point

Throws:

IllegalArgumentException - if the given atom is not part of the superatom S-group

Since:

Marvin 6.0, Dec 5, 2012

setLeavingGroup

@Deprecated
public void setLeavingGroup(int order,
                              int atNo)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Defines the leaving group for an attachment point.

Parameters:

order - the order of the attachment point to which the leaving group information is added

atNo - the atomic number of the leaving atom

Throws:

IllegalArgumentException - if the given order does not exist in the superatom sgroup

Since:

Marvin 6.0, 2013.02.11.

setLeavingGroup

@Deprecated
public void setLeavingGroup(int order,
                              int atNo,
                              String alternativeName)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Defines the leaving group for an attachment point.

Parameters:

order - the order of the attachment point to which the leaving group information is added

atNo - the atomic number of the leaving atom

alternativeName - the alternative name of the leaving group. P.e.: in case of dna it can be 3', 5', etc.

Throws:

IllegalArgumentException - if the given order does not exist in the superatom sgroup

Since:

Marvin 6.0, 2013.02.11.

setLeavingGroup

@Deprecated
public void setLeavingGroup(int order,
                              int atNo,
                              String alternativeName,
                              chemaxon.struc.BondType crossingBondType)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Defines the leaving group for an attachment point.

Parameters:

order - the order of the attachment point to which the leaving group information is added

atNo - the atomic number of the leaving atom

alternativeName - the alternative name of the leaving group. P.e.: in case of DNA it can be 3', 5', etc.

crossingBondType - the type of the bond connecting the superatom sgroup and the leaving group

Throws:

IllegalArgumentException -

if the given order does not exist in the superatom sgroup, or the type of the given bond is not single, double or triple

if the given order is not free and the type of the current crossing bond is not the same as the given type of the leaving group bond

Since:

Marvin 6.0, Feb 12, 2013

See Also:

BondType, AttachmentPoint.isFree()

setLeavingGroupAlternativeName

@Deprecated
public void setLeavingGroupAlternativeName(int order,
                                             String alternativeName)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Sets the alternative name of the given ordered attachment point's leaving group.

Parameters:

order - the order of the attachment point to which the leaving group information is added

alternativeName - the alternative name of the leaving group. P.e.: in case of DNA it can be 3', 5', etc.

Throws:

IllegalArgumentException - if attachment point with the given attachment order does not exist, or the attachment point does not have leaving group

Since:

Marvin 6.0, 2013.02.11.

removeLeavingGroup

@Deprecated
public void removeLeavingGroup(int order)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Removes the leaving group of an attachment point and the leaving group atom as well.

Parameters:

order - the attachment order

Since:

Marvin 6.0, Feb 13, 2013

removeAllAttachmentPoints

public void removeAllAttachmentPoints()

Removes all of the attachment points of the Superatom s-group.

Since:

Marvin 6.0, Dec 17, 2012

removeAttachmentPoint

public void removeAttachmentPoint(int order)

Removes the attachment point with the given order.

Parameters:

order - the order which's attachment point will be removed

getFreeAttachmentPointOrders

public List<Integer> getFreeAttachmentPointOrders()

Gets the increasingly sorted orders of the free attachment points.

Returns:

the list of the increasingly sorted orders of the free attachment points

getAttachmentPoint

public chemaxon.struc.sgroup.AttachmentPoint getAttachmentPoint(int order)

Gets the attachment point that's order is given as parameter

Parameters:

order - the required attachment point's order

Returns:

the attachment point that's order equals to the parameter

setCrossingBondType

@Deprecated
public void setCrossingBondType(int order,
                                  chemaxon.struc.BondType newType)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Sets the type of the crossing bond.

Parameters:

order - the attachment order

newType - new type of the crossing bond

Throws:

IllegalStateException -

if the attachment point does not have a leaving group

if the attachment point is not free

Since:

Marvin 6.0, Feb 15, 2013

getFreeAttachmentPointCount

public int getFreeAttachmentPointCount()

Gets the number of free attachment points.

Returns:

the number of free attachment points.

clone

public SuperatomSgroup clone()

Clones the SuperatomSgroup (and not the Molecule).

Overrides:

clone in class Object

Returns:

the cloned superatom s-group

Since:

Marvin 6.0, 2013.02.21.

cloneLeavingGroups

@Deprecated
protected void cloneLeavingGroups(SuperatomSgroup sasg)

Deprecated. As of Marvin 6.2, no replacement.
Not supported feature.

Clones the leaving groups of the given superatom s-group.

Parameters:

sasg - the superatom s-group

Since:

Marvin 6.1, 2013.05.27.

getAttachmentPointOrders

public List<Integer> getAttachmentPointOrders()

Gets the orders with which attachment point exists

Returns:

the list of the orders of the attachment points

checkSgroupGraphConsistency

protected boolean checkSgroupGraphConsistency(Sgroup parent)

Checks whether the parameter s-group contain the proper atoms of this SuperatomSgroup. That means the SgroupAtom of this s-group if it is contracted state or all of it's atoms if it is in expanded state.

Overrides:

checkSgroupGraphConsistency in class Sgroup

Parameters:

parent - parent of Sgroup

Returns:

true if the s-group is consistent