chemaxon.struc
Class Sgroup

java.lang.Object
  chemaxon.struc.Sgroup

All Implemented Interfaces:

java.io.Serializable

Direct Known Subclasses:

MultipleSgroup, SuperatomSgroup

public class Sgroup

extends java.lang.Object

implements java.io.Serializable

S-group.

Since:

3.0

Version:

3.3, 12/07/2003

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

static int	SCN_EITHER_UNKNOWN Either unknown S-group connectivity.
static int	SCN_HEAD_TO_HEAD Head-to-head S-group connectivity.
static int	SCN_HEAD_TO_TAIL Head-to-tail S-group connectivity.
protected SelectionMolecule	sgroupGraph The S-group's internal structure.
protected int	sgroupType The S-group type.
static int	SST_ALTERNATING Alternating polymer S-group subtype.
static int	SST_BLOCK Block polymer S-group subtype.
static int	SST_RANDOM Random polymer S-group subtype.
static int	ST_ANY Any polymer S-group type.
static int	ST_COPOLYMER Copolymer S-group type.
static int	ST_CROSSLINK Crosslink S-group type.
static int	ST_DATA Data S-group type.
static int	ST_FORMULATION Formulation S-group type.
static int	ST_GENERIC Generic S-group type.
static int	ST_MER Mer S-group type.
static int	ST_MIXTURE Mixture S-group type.
static int	ST_MODIFICATION Modification S-group type.
static int	ST_MONOMER Monomer S-group type.
static int	ST_MULTIPLE Multiple group S-group type.
static int	ST_SRU SRU S-group type.
static int	ST_SUPERATOM Superatom S-group type.

Constructor Summary

Sgroup(Molecule parent, int t)
Creates an S-group with the specified parent and type.

Method Summary

void	add(MolAtom a) Adds a new atom to the S-group.
SelectionMolecule	cloneStructure() Gets the clone of the structure stored.
protected void	copy(Sgroup sg2, Molecule m) Make a copy of this S-group.
int	countAllAtoms() Counts the total number of atoms recursively.
Molecule	createMolecule() Creates a molecule object that contains only this group.
MolBond[]	findCrossingBonds() Finds the crossing bonds.
MolAtom	getAtom(int i) Gets an atom in the S-group.
MolAtom[]	getAtomArray() Gets the array of atoms in the S-group.
int	getAtomCount() Gets the number of atoms in the S-group.
int	getConnectivity() Gets S-group connectivity.
MolAtom[]	getCrossingAtoms(MolBond[] xbonds) Gets the atoms that have crossing bonds.
Molecule	getParentMolecule() Gets the parent molecule.
SelectionMolecule	getSgroupGraph() Gets the molecule graph.
java.lang.String	getSubscript() Gets the subscript for non-superatom S-groups.
int	getSubType() Gets polymer S-group subtype.
java.lang.String	getSuperscript() Gets the superscript for non-superatom S-groups.
int	getType() Gets S-group type.
boolean	hasBrackets() Checks if brackets should be painted or not.
int	indexOf(MolAtom a) Gets the atom index in the S-group graph.
boolean	isEmpty() Is it an empty S-group?
Sgroup	newInstance() Gets a new Sgroup instance.
void	removeAtom(MolAtom a) Removes an atom from the S-group.
protected void	removeBond(MolBond b) Removes a bond from the S-group.
void	removeEdges() Removes the edge references.
protected static void	removeGroupedAtom(Molecule m, MolAtom a, MolBond[] v) Removes an atom from the molecule and remove its specified bonds.
void	setAtom(int i, MolAtom a) Sets the specified atom in the S-group graph.
void	setConnectivity(int c) Sets S-group connectivity.
protected void	setParentMolecule(Molecule p) Sets the parent molecule.
void	setSgroupGraph(SelectionMolecule smol) Sets the molecule graph.
void	setSubscript(java.lang.String s) Sets the subscript for non-superatom S-groups.
void	setSubType(int t) Sets polymer S-group subtype.

Methods inherited from class java.lang.Object

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

Field Detail

ST_SUPERATOM

public static final int ST_SUPERATOM

Superatom S-group type. @see #getType

See Also:

Constant Field Values

ST_MULTIPLE

public static final int ST_MULTIPLE

Multiple group S-group type. @see #getType

See Also:

Constant Field Values

ST_SRU

public static final int ST_SRU

SRU S-group type. @see #getType

See Also:

Constant Field Values

ST_MONOMER

public static final int ST_MONOMER

Monomer S-group type. @see #getType

See Also:

Constant Field Values

ST_MER

public static final int ST_MER

Mer S-group type. @see #getType

See Also:

Constant Field Values

ST_COPOLYMER

public static final int ST_COPOLYMER

Copolymer S-group type. @see #getType

See Also:

Constant Field Values

ST_CROSSLINK

public static final int ST_CROSSLINK

Crosslink S-group type. @see #getType

See Also:

Constant Field Values

ST_MODIFICATION

public static final int ST_MODIFICATION

Modification S-group type. @see #getType

See Also:

Constant Field Values

ST_MIXTURE

public static final int ST_MIXTURE

Mixture S-group type. @see #getType

See Also:

Constant Field Values

ST_FORMULATION

public static final int ST_FORMULATION

Formulation S-group type. @see #getType

See Also:

Constant Field Values

ST_DATA

public static final int ST_DATA

Data S-group type. @see #getType

See Also:

Constant Field Values

ST_ANY

public static final int ST_ANY

Any polymer S-group type. @see #getType

See Also:

Constant Field Values

ST_GENERIC

public static final int ST_GENERIC

Generic S-group type. @see #getType

See Also:

Constant Field Values

SST_ALTERNATING

public static final int SST_ALTERNATING

Alternating polymer S-group subtype. @see #getSubType

See Also:

Constant Field Values

SST_RANDOM

public static final int SST_RANDOM

Random polymer S-group subtype. @see #getSubType

See Also:

Constant Field Values

SST_BLOCK

public static final int SST_BLOCK

Block polymer S-group subtype. @see #getSubType

See Also:

Constant Field Values

SCN_EITHER_UNKNOWN

public static final int SCN_EITHER_UNKNOWN

Either unknown S-group connectivity. @see #getConnectivity

See Also:

Constant Field Values

SCN_HEAD_TO_HEAD

public static final int SCN_HEAD_TO_HEAD

Head-to-head S-group connectivity. @see #getConnectivity

See Also:

Constant Field Values

SCN_HEAD_TO_TAIL

public static final int SCN_HEAD_TO_TAIL

Head-to-tail S-group connectivity. @see #getConnectivity

See Also:

Constant Field Values

sgroupType

protected transient int sgroupType

The S-group type.

sgroupGraph

protected transient SelectionMolecule sgroupGraph

The S-group's internal structure.

Constructor Detail

Sgroup

public Sgroup(Molecule parent,
              int t)

Creates an S-group with the specified parent and type.

Parameters:

parent - the parent molecule

t - S-group type

Method Detail

setSgroupGraph

public void setSgroupGraph(SelectionMolecule smol)

Sets the molecule graph.

Parameters:

smol - the molecule graph

Since:

3.3, 11/03/2003

getSgroupGraph

public SelectionMolecule getSgroupGraph()

Gets the molecule graph.

Returns:

the molecule graph

Since:

3.3, 11/03/2003

setParentMolecule

protected final void setParentMolecule(Molecule p)

Sets the parent molecule.

Parameters:

p - the parent molecule

getParentMolecule

public final Molecule getParentMolecule()

Gets the parent molecule.

Returns:

the parent molecule

getSuperscript

public java.lang.String getSuperscript()

Gets the superscript for non-superatom S-groups.

Returns:

the superscript

setSubscript

public void setSubscript(java.lang.String s)

Sets the subscript for non-superatom S-groups.

Parameters:

s - the subscript

getSubscript

public java.lang.String getSubscript()

Gets the subscript for non-superatom S-groups.

Returns:

the subscript

getType

public int getType()

Gets S-group type.

Returns:

the type

See Also:

ST_SUPERATOM, ST_MULTIPLE, ST_SRU, ST_MONOMER, ST_MER, ST_COPOLYMER, ST_CROSSLINK, ST_MODIFICATION, ST_MODIFICATION, ST_MIXTURE, ST_FORMULATION, ST_DATA, ST_ANY, ST_GENERIC

getSubType

public int getSubType()

Gets polymer S-group subtype.

Returns:

the type

See Also:

SST_ALTERNATING, SST_RANDOM, SST_BLOCK

setSubType

public void setSubType(int t)

Sets polymer S-group subtype.

Parameters:

t - the type

See Also:

getSubType()

getConnectivity

public int getConnectivity()

Gets S-group connectivity.

Returns:

the connectivity

See Also:

SCN_EITHER_UNKNOWN, SCN_HEAD_TO_HEAD, SCN_HEAD_TO_TAIL

setConnectivity

public void setConnectivity(int c)

Sets S-group connectivity.

Parameters:

c - the connectivity

See Also:

getConnectivity()

hasBrackets

public boolean hasBrackets()

Checks if brackets should be painted or not.

Returns:

always true in the default implementation

Since:

3.3

cloneStructure

public final SelectionMolecule cloneStructure()

Gets the clone of the structure stored.

Returns:

the clone

createMolecule

public final Molecule createMolecule()

Creates a molecule object that contains only this group.

Returns:

the molecule

getAtomArray

public final MolAtom[] getAtomArray()

Gets the array of atoms in the S-group.

Returns:

the atom array

getAtom

public final MolAtom getAtom(int i)

Gets an atom in the S-group.

Parameters:

i - the atom index

Returns:

the atom

countAllAtoms

public final int countAllAtoms()

Counts the total number of atoms recursively.

Returns:

the number of atoms

isEmpty

public final boolean isEmpty()

Is it an empty S-group?

Returns:

true if the S-group does not contain any atoms, false otherwise

newInstance

public Sgroup newInstance()

Gets a new Sgroup instance.

Returns:

the new object

getAtomCount

public final int getAtomCount()

Gets the number of atoms in the S-group.

Returns:

the number of atoms

indexOf

public int indexOf(MolAtom a)

Gets the atom index in the S-group graph.

Parameters:

a - the atom

Returns:

the index or -1 if not found

add

public void add(MolAtom a)

Adds a new atom to the S-group.

Parameters:

a - the atom

setAtom

public void setAtom(int i,
                    MolAtom a)

Sets the specified atom in the S-group graph.

Parameters:

i - the index

a - the atom

removeEdges

public void removeEdges()

Removes the edge references.

removeAtom

public void removeAtom(MolAtom a)

Removes an atom from the S-group.

Parameters:

a - the atom

removeBond

protected void removeBond(MolBond b)

Removes a bond from the S-group.

Parameters:

b - the bond

findCrossingBonds

public MolBond[] findCrossingBonds()

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

Returns:

the attachment bonds

Since:

3.3

getCrossingAtoms

public MolAtom[] getCrossingAtoms(MolBond[] xbonds)

Gets the atoms that have crossing bonds.

Parameters:

xbonds - the crossing bonds

Returns:

the attachment atoms

Since:

3.3

copy

protected void copy(Sgroup sg2,
                    Molecule m)

Make a copy of this S-group.

Parameters:

sg2 - the target S-group

m - the target molecule or null

removeGroupedAtom

protected static void removeGroupedAtom(Molecule m,
                                        MolAtom a,
                                        MolBond[] v)

Removes an atom from the molecule and remove its specified bonds.

Parameters:

m - the molecule

a - the atom

v - bonds to remove from the atom, remove all bonds if null

See Also:

CGraph.removeNode(int, int)