chemaxon.struc.sgroup
Class SuperatomSgroup

java.lang.Object
  chemaxon.struc.Sgroup
      chemaxon.struc.sgroup.SuperatomSgroup

All Implemented Interfaces:

Expandable, java.io.Serializable

public class SuperatomSgroup

extends Sgroup

implements Expandable

Superatom S-group.

Since:

Marvin 3.0, 11/05/2002

Version:

3.5.5, 03/08/2005

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.Sgroup

SCN_EITHER_UNKNOWN, SCN_HEAD_TO_HEAD, SCN_HEAD_TO_TAIL, sgroupGraph, sgroupType, SORT_CHILD_PARENT, SORT_PARENT_CHILD, SST_ALTERNATING, SST_BLOCK, SST_RANDOM, ST_ANY, ST_COPOLYMER, ST_CROSSLINK, ST_DATA, ST_FORMULATION, ST_GENERIC, ST_MER, ST_MIXTURE, ST_MODIFICATION, ST_MONOMER, ST_MULTIPLE, ST_SRU, ST_SUPERATOM, XSTATE_C, XSTATE_NONE, XSTATE_X, XSTATE_XC

Fields inherited from interface chemaxon.struc.sgroup.Expandable

DEFAULT_OPTIONS, MDL_EXPAND, NONRECURSIVE_EXPAND, REVERSIBLE_EXPAND

Constructor Summary

	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) Copy constructor.

Method Summary

protected void	addAttachAtom(MolAtom a) Adds an atom to the list of attachments.
boolean	areChildSgroupsVisible() Checks whether the child S-groups are visible.
Sgroup	cloneSgroup(Molecule m, Sgroup psg) Gets a new Sgroup instance.
boolean	contract(int opts) Contracts this S-group.
Molecule	createMolecule() Creates a molecule object that contains only this group.
boolean	expand(int opts) Expands this S-group.
MolBond[]	findCrossingBonds() Finds the crossing bonds.
MolAtom	getAttachAtom(int i) Gets an attachment point.
MolAtom[]	getCrossingAtoms(MolBond[] xbonds) Gets the atoms that have crossing bonds.
MolAtom[]	getFreeLegalAttachAtoms() Gets the unused legal attachment points.
MolAtom[]	getLegalAttachAtoms() Gets the legal attachment points.
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	isBracketVisible() Tests whether the bracket is visible.
boolean	isContracted() Is this S-group contracted?
boolean	isExpanded() Is this S-group expanded?
boolean	isLegalAttachment(MolAtom a) Checks if the specified atom is attached to a legal attachment point.
void	removeAtom(MolAtom a) Removes an atom from the S-group.
void	removeBond(MolBond b) Removes a bond from the S-group.
void	replaceAtom(MolAtom olda, MolAtom newa) Replace an existing atom by a new one.
void	setAtom(int i, MolAtom a) Sets the specified atom in the S-group graph.
void	setSgroupGraph(SelectionMolecule smol) Sets the molecule graph.
MolBond[]	updateSgroupCrossings() Deprecated. as of Marvin 3.3, replaced by Sgroup.findCrossingBonds()

Methods inherited from class chemaxon.struc.Sgroup

add, addChildSgroup, cloneStructure, containsAllAtomsOf, countAllAtoms, findSmallestSgroupContaining, findSmallestSgroupOf, getAtom, getAtomArray, getAtomCount, getChildSgroup, getChildSgroupCount, getConnectivity, getParentMolecule, getParentSgroup, getSubscript, getSubType, getSuperscript, getType, getXState, indexOf, isEmpty, isVisible, removeEdges, removeGroupedAtom, setConnectivity, setGUIStateRecursively, setParentMolecule, setSubscript, setSubType, setXState, sort, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SuperatomSgroup

public SuperatomSgroup(Molecule parent)

Constructs a superatom S-group in expanded state.

Parameters:

parent - the parent molecule

Since:

Marvin 3.5.3, 01/18/2005

SuperatomSgroup

public SuperatomSgroup(Molecule parent,
                       boolean expanded)

Constructs a superatom S-group.

Parameters:

parent - the parent molecule

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

SuperatomSgroup

protected SuperatomSgroup(SuperatomSgroup 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 3.4

Method Detail

getSuperAtom

public final SgroupAtom getSuperAtom()

Gets the superatom.

Returns:

the superatom

getAttachAtom

public final MolAtom getAttachAtom(int i)

Gets an attachment point. This method should only be called when the residue is in contracted state.

Parameters:

i - the attachment point index

Returns:

the attachment atom

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

setSgroupGraph

public void setSgroupGraph(SelectionMolecule smol)

Sets the molecule graph. The first n nodes are supposed to be the attachment points if the S-group is in contracted state.

Overrides:

setSgroupGraph in class Sgroup

Parameters:

smol - the molecule graph

Since:

Marvin 3.3, 11/04/2003

cloneSgroup

public Sgroup cloneSgroup(Molecule m,
                          Sgroup psg)

Gets a new Sgroup instance.

Overrides:

cloneSgroup in class Sgroup

Parameters:

m - the new parent molecule

psg - the new parent S-group

Returns:

the new object

Since:

Marvin 3.4

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

public final void removeAtom(MolAtom a)

Removes an atom from the S-group.

Overrides:

removeAtom in class Sgroup

Parameters:

a - the atom

removeBond

public final void removeBond(MolBond b)

Removes a bond from the S-group.

Overrides:

removeBond in class Sgroup

Parameters:

b - 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 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()

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 java.lang.IllegalArgumentException

Expands this S-group. Atom indexes are preserved during expansion.

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:

java.lang.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)
                       throws java.lang.IllegalArgumentException

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:

java.lang.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.

Overrides:

isBracketVisible in class Sgroup

Returns:

false, superatom S-group brackets are not visible

Since:

Marvin 3.5.1, 11/12/2004

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

getLegalAttachAtoms

public final MolAtom[] getLegalAttachAtoms()

Gets the legal attachment points.

Returns:

array of attachment points

isLegalAttachment

public final boolean isLegalAttachment(MolAtom a)

Checks if the specified atom is attached to a legal attachment point.

Returns:

true if it is attached to a legal attachment point, false otherwise

Since:

3.5, 11/04/2004

getFreeLegalAttachAtoms

public final MolAtom[] getFreeLegalAttachAtoms()

Gets the unused legal attachment points.

Returns:

array of attachment points

createMolecule

public Molecule createMolecule()

Creates a molecule object that contains only this group.

Overrides:

createMolecule in class Sgroup

Returns:

the molecule

Since:

Marvin 3.4

addAttachAtom

protected void addAttachAtom(MolAtom a)

Adds an atom to the list of attachments.

Parameters:

a - the atom

replaceAtom

public final void replaceAtom(MolAtom olda,
                              MolAtom newa)

Replace an existing atom by a new one.

Overrides:

replaceAtom in class Sgroup

Parameters:

olda - the original atom

newa - the new atom

Since:

3.5.2, 12/15/2004

updateSgroupCrossings

public final MolBond[] updateSgroupCrossings()

Deprecated. as of Marvin 3.3, replaced by Sgroup.findCrossingBonds()

Generates the attachment atoms. Use only when the S-group is expanded.

Returns:

the attachment bonds