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

S-group.

Since:

3.0, 11/05/2002

Version:

3.3, 12/11/2003

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, 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

Fields inherited from interface chemaxon.struc.sgroup.Expandable

DEFAULT_OPTIONS, MDL_EXPAND

Constructor Summary

SuperatomSgroup(Molecule parent, boolean expanded)
Constructs a superatom S-group.

Method Summary

protected void	addAttachAtom(MolAtom a) Adds an atom to the list of attachments.
boolean	contract(int opts) Contracts this S-group.
protected void	copy(Sgroup sg2, Molecule m) Make a copy of this S-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	hasBrackets() Checks if brackets should be painted or not.
boolean	isContracted() Is this S-group contracted?
boolean	isExpanded() Is this S-group expanded?
Sgroup	newInstance() Gets a new SuperatomSgroup instance.
void	removeAtom(MolAtom a) Removes an atom from the S-group.
void	removeBond(MolBond b) Removes a bond from the S-group.
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, cloneStructure, countAllAtoms, createMolecule, getAtom, getAtomArray, getAtomCount, getConnectivity, getParentMolecule, getSubscript, getSubType, getSuperscript, getType, indexOf, isEmpty, removeEdges, removeGroupedAtom, setConnectivity, setParentMolecule, setSubscript, setSubType

Methods inherited from class java.lang.Object

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

Constructor Detail

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

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:

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:

3.3, 11/04/2003

newInstance

public Sgroup newInstance()

Gets a new SuperatomSgroup instance.

Overrides:

newInstance in class Sgroup

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

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:

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:

3.3

copy

protected final void copy(Sgroup sg2,
                          Molecule m)

Make a copy of this S-group.

Overrides:

copy in class Sgroup

Parameters:

sg2 - the target S-group

m - the target molecule or null

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:

3.3

expand

public final boolean expand(int opts)

Expands this S-group.

Specified by:

expand in interface Expandable

Parameters:

opts - expansion options

Returns:

true if the operation was successful, false if already expanded

See Also:

Expandable.DEFAULT_OPTIONS, Expandable.MDL_EXPAND

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

Parameters:

opts - contraction options

Returns:

true if the operation was successful, false if already contracted

See Also:

Expandable.DEFAULT_OPTIONS

isContracted

public final boolean isContracted()

Is this S-group contracted?

Returns:

true if contracted, false if expanded

getLegalAttachAtoms

public final MolAtom[] getLegalAttachAtoms()

Gets the legal attachment points.

Returns:

array of attachment points

getFreeLegalAttachAtoms

public final MolAtom[] getFreeLegalAttachAtoms()

Gets the unused legal attachment points.

Returns:

array of attachment points

addAttachAtom

protected void addAttachAtom(MolAtom a)

Adds an atom to the list of attachments.

Parameters:

a - the atom

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