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:

Marvin 3.0

Version:

3.5.2, 12/15/2004

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	SORT_CHILD_PARENT Parent-child sort order.
static int	SORT_PARENT_CHILD Parent-child sort order.
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.
static int	XSTATE_C S-group is contracted (useful only in GUI!).
static int	XSTATE_NONE S-group is in an undetermined state.
static int	XSTATE_X S-group is expanded.
static int	XSTATE_XC S-group is expanded but its atoms have the same coordinates as in contracted state.

Constructor Summary

	Sgroup(Molecule parent, int t) Creates an S-group with the specified parent and type.
	Sgroup(Molecule parent, int t, int xstate) Creates an S-group with the specified parent and type.
protected	Sgroup(Sgroup sg, Molecule m, Sgroup psg) Copy constructor.

Method Summary

void	add(MolAtom a) Adds a new atom to the S-group.
void	addChildSgroup(Sgroup sg) Adds a child S-group.
boolean	areChildSgroupsVisible() Checks whether the child S-groups are visible.
Sgroup	cloneSgroup(Molecule m, Sgroup psg) Gets a new Sgroup instance.
SelectionMolecule	cloneStructure() Gets the clone of the structure stored.
boolean	containsAllAtomsOf(Sgroup sg) Checks if the S-group contains the atoms of another S-group.
protected boolean	contract(int opts) Sets the state to XSTATE_C.
int	countAllAtoms() Counts the total number of atoms recursively.
Molecule	createMolecule() Creates a molecule object that contains only this group.
protected boolean	expand(int f) Sets the state to XSTATE_X or XSTATE_XC.
MolBond[]	findCrossingBonds() Finds the crossing bonds.
Sgroup	findSmallestSgroupContaining(MolAtom a) Finds the smallest S-group containing the specified node.
Sgroup	findSmallestSgroupOf(MolAtom a) Finds the smallest S-group that has the specified node.
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.
Sgroup	getChildSgroup(int i) Gets a child S-group.
int	getChildSgroupCount() Gets the number of child S-groups.
int	getConnectivity() Gets S-group connectivity.
MolAtom[]	getCrossingAtoms(MolBond[] xbonds) Gets the atoms that have crossing bonds.
Molecule	getParentMolecule() Gets the parent molecule.
Sgroup	getParentSgroup() Gets the parent S-group.
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.
int	getXState() Gets the expanded/contracted state.
boolean	hasAtom(MolAtom a) Is the specified atom an element of this group?
boolean	hasBrackets() Checks if brackets should be painted or not.
int	indexOf(MolAtom a) Gets the atom index in the S-group graph.
boolean	isBracketVisible() Tests whether the bracket is visible.
boolean	isEmpty() Is it an empty S-group?
boolean	isVisible() Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.
void	removeAtom(MolAtom a) Removes an atom and its bonds 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(MoleculeGraph m, MolAtom a, MolBond[] v) Removes an atom from the molecule and remove its specified bonds.
void	replaceAtom(MolAtom olda, MolAtom newa) Replace an existing atom by a new one in this S-group and its parent (recursively).
void	setAtom(int i, MolAtom a) Sets the specified atom in the S-group graph.
void	setConnectivity(int c) Sets S-group connectivity.
void	setGUIStateRecursively(boolean v) Sets the expanded/contracted state recursively.
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.
void	setXState(int state) Sets the expanded/contracted state.
static void	sort(Sgroup[] sgroups, int o) Sorts S-groups in parent-child or child-parent order.
java.lang.String	toString() Overrides Object.toString() to ease debugging.

Methods inherited from class java.lang.Object

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

XSTATE_NONE

public static final int XSTATE_NONE

S-group is in an undetermined state.

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int), Constant Field Values

XSTATE_X

public static final int XSTATE_X

S-group is expanded.

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int), Constant Field Values

XSTATE_C

public static final int XSTATE_C

S-group is contracted (useful only in GUI!).

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int), Constant Field Values

XSTATE_XC

public static final int XSTATE_XC

S-group is expanded but its atoms have the same coordinates as in contracted state.

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int), Constant Field Values

SORT_PARENT_CHILD

public static final int SORT_PARENT_CHILD

Parent-child sort order.

Since:

Marvin 3.4

See Also:

sort(Sgroup[], int), Constant Field Values

SORT_CHILD_PARENT

public static final int SORT_CHILD_PARENT

Parent-child sort order.

Since:

Marvin 3.4

See Also:

sort(Sgroup[], int), 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

Sgroup

public Sgroup(Molecule parent,
              int t,
              int xstate)

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

Parameters:

parent - the parent molecule

t - S-group type

xstate - the expanded state

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int)

Sgroup

protected Sgroup(Sgroup 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

setSgroupGraph

public void setSgroupGraph(SelectionMolecule smol)

Sets the molecule graph.

Parameters:

smol - the molecule graph

Since:

Marvin 3.3, 11/03/2003

getSgroupGraph

public SelectionMolecule getSgroupGraph()

Gets the molecule graph.

Returns:

the molecule graph

Since:

Marvin 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

getChildSgroupCount

public final int getChildSgroupCount()

Gets the number of child S-groups.

Returns:

the number of children

Since:

Marvin 3.4

getChildSgroup

public final Sgroup getChildSgroup(int i)

Gets a child S-group.

Parameters:

i - the child index

Returns:

the child

Since:

Marvin 3.4

addChildSgroup

public final void addChildSgroup(Sgroup sg)

Adds a child S-group.

Parameters:

sg - the child

Since:

Marvin 3.4

findSmallestSgroupContaining

public final Sgroup findSmallestSgroupContaining(MolAtom a)

Finds the smallest S-group containing the specified node. If this parent contains the node, then it searches the children recursively.

Parameters:

a - the node

Returns:

the S-group or null if not found

Since:

Marvin 3.4, 05/05/2004

findSmallestSgroupOf

public final Sgroup findSmallestSgroupOf(MolAtom a)

Finds the smallest S-group that has the specified node. If this parent has the node, then it searches the children recursively.

Parameters:

a - the node

Returns:

the S-group or null if not found

Since:

Marvin 3.4, 05/05/2004

getParentSgroup

public final Sgroup getParentSgroup()

Gets the parent S-group.

Returns:

the parent S-group

Since:

Marvin 3.4

getXState

public final int getXState()

Gets the expanded/contracted state. WARNING! This method is under development, do not use it yet!

Returns:

the expanded/contracted state

Since:

Marvin 3.4, 05/04/2004

See Also:

XSTATE_X, XSTATE_C, XSTATE_XC

setXState

public final void setXState(int state)
                     throws java.lang.IllegalArgumentException

Sets the expanded/contracted state. WARNING! This method is under development, do not use it yet!

Parameters:

state - the expanded/contracted state

Throws:

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

Since:

Marvin 3.4, 05/04/2004

See Also:

XSTATE_X, XSTATE_C, XSTATE_XC

setGUIStateRecursively

public final void setGUIStateRecursively(boolean v)
                                  throws java.lang.IllegalArgumentException

Sets the expanded/contracted state recursively. WARNING! This method is under development, do not use it yet!

Parameters:

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

Throws:

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

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int)

expand

protected boolean expand(int f)
                  throws java.lang.IllegalArgumentException

Sets the state to XSTATE_X or XSTATE_XC.

Parameters:

f - options, only the Expandable.REVERSIBLE_EXPAND and the Expandable.MDL_EXPAND flags are taken into account

Returns:

true

Throws:

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

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int)

contract

protected boolean contract(int opts)
                    throws java.lang.IllegalArgumentException

Sets the state to XSTATE_C.

Parameters:

opts - neglected

Returns:

true

Throws:

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

Since:

Marvin 3.4, 05/04/2004

See Also:

setXState(int)

getSuperscript

public java.lang.String getSuperscript()

Gets the superscript for non-superatom S-groups.

Returns:

the superscript

getSubscript

public java.lang.String getSubscript()

Gets the subscript for non-superatom S-groups.

Returns:

the subscript

setSubscript

public void setSubscript(java.lang.String s)

Sets the subscript for non-superatom S-groups.

Parameters:

s - 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:

Marvin 3.3

cloneStructure

public final SelectionMolecule cloneStructure()

Gets the clone of the structure stored.

Returns:

the clone

createMolecule

public 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

cloneSgroup

public Sgroup cloneSgroup(Molecule m,
                          Sgroup psg)

Gets a new Sgroup instance.

Parameters:

m - the new parent molecule

psg - the new parent S-group

Returns:

the new object

Since:

Marvin 3.4

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

hasAtom

public boolean hasAtom(MolAtom a)

Is the specified atom an element of this group?

Parameters:

a - the atom

Returns:

true if it contains the atom, false otherwise

Since:

Marvin 3.4

containsAllAtomsOf

public boolean containsAllAtomsOf(Sgroup sg)

Checks if the S-group contains the atoms of another S-group.

Returns:

true if this S-group contains the specified one

Since:

Marvin 3.4

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 and its bonds 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

replaceAtom

public void replaceAtom(MolAtom olda,
                        MolAtom newa)

Replace an existing atom by a new one in this S-group and its parent (recursively).

Parameters:

olda - the original atom

newa - the new atom

Since:

3.5.2, 12/15/2004

findCrossingBonds

public MolBond[] findCrossingBonds()

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

Returns:

the attachment bonds

Since:

Marvin 3.3

getCrossingAtoms

public MolAtom[] getCrossingAtoms(MolBond[] xbonds)
                           throws java.lang.IllegalArgumentException

Gets the atoms that have crossing bonds.

Parameters:

xbonds - the crossing bonds

Returns:

the attachment atoms

Throws:

java.lang.IllegalArgumentException - if a bond in the specified array is not a crossing bond

Since:

Marvin 3.3

removeGroupedAtom

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

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

Parameters:

m - the molecule graph

a - the atom

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

See Also:

CGraph.removeNode(int, int)

areChildSgroupsVisible

public boolean areChildSgroupsVisible()

Checks whether the child S-groups are visible.

Returns:

true if children are visible, false otherwise

Since:

Marvin 3.4

isVisible

public final boolean isVisible()

Checks whether this group is 'visible' (all parents are expanded in case of superatom S-groups) or not.

Returns:

true if the group is visible, false otherwise

Since:

Marvin 3.4

isBracketVisible

public boolean isBracketVisible()

Tests whether the bracket is visible.

Returns:

true if visible, false otherwise

Since:

Marvin 3.5.1, 11/12/2004

sort

public static void sort(Sgroup[] sgroups,
                        int o)

Sorts S-groups in parent-child or child-parent order.

Parameters:

sgroups - the array to sort

o - the sort order

Since:

Marvin 3.4

See Also:

SORT_PARENT_CHILD, SORT_CHILD_PARENT

toString

public java.lang.String toString()

Overrides Object.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object.

Returns:

a string representation of the object

Since:

Marvin 3.4