Sgroup (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.struc.Sgroup

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

DataSgroup, MulticenterSgroup, MultipleSgroup, RepeatingUnitSgroup, SuperatomSgroup
```
public class Sgroup
extends Object
implements Serializable
```
Structural group representation in the molecule.
A structural group is an entity in the molecule. Some of these entities has direct subclasses.
Some example use cases:
- It can be an abbreviation of a molecule part represented as SuperatomSgroup.
- A repeating unit in the molecule represented as RepeatingUnitSgroup.
- Data assigned to a part of the molecule represented as DataSgroup .
- A bond which has connection to multiple atom in the molecule is represented as multicenter sgroup type.
- Components in the molecule can be represented as component sgroups.
See also the possible return values of getType() method which describes the possible sgroup types.
Some relevant functions in the molecule to handle these structural elements:
See also example code snippets about Sgroups.
Since:

Marvin 3.0

Version:

5.3, 10/07/2009

Author:

Peter Csizmadia, Szilveszter Juhos, Erika Biro

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`protected Set<MolAtom>`	`atomSet` Set for storing the atoms of the s-group's graph.
`protected ArrayList<MBracket>`	`brackets`
`static int`	`CHARGE_ON_ATOMS` Charge is located on atoms and displayed on atoms.
`static int`	`CHARGE_ON_GROUP` Charge is located on atoms but displayed on the whole group (bracket).
`protected Sgroup`	`parentSgroup`
`static int`	`PR_ATSYMS` Print atom symbols.
`protected static int`	`RA_IN_EXPAND` Atom removal in expand.
`protected static int`	`RA_REMOVE_EXCEPT_RU` Replace without duplicating.
`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.
`static int`	`SGROUP_TYPE_COUNT` Number of S-group types.
`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_AMINOACID` Amino acid s-group type.
`static int`	`ST_ANY` Any polymer S-group type.
`static int`	`ST_COMPONENT` Component 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_GRAFT` Graft 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_MULTICENTER` Multicenter S-group type.
`static int`	`ST_MULTIPLE` Multiple group S-group type.
`static int`	`ST_SRU` SRU (Structural Repeating Unit: polymers and repeating units with repetition ranges) 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

Constructors
Modifier	Constructor and Description
	`Sgroup(Molecule parent, int t)` Deprecated. As of Marvin 5.12, replaced by `SgroupFactory.createSgroup(Molecule, SgroupType)`.
	`Sgroup(Molecule parent, int t, int xstate)` Deprecated. As of Marvin 5.12, replaced by `SgroupFactory.createSgroup(Molecule, SgroupType)` and `setXState(int)`.
`protected`	`Sgroup(Molecule parent, SgroupType type)`
`protected`	`Sgroup(Molecule parent, SgroupType type, int xstate)`
`protected`	`Sgroup(Sgroup sg, Molecule m, Sgroup psg)` Copy constructor.
`protected`	`Sgroup(Sgroup sg, Molecule m, Sgroup psg, int[] iatoms)` Copy constructor.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`add(MolAtom a)` Adds a new atom to the S-group.
`void`	`addBracket(MBracket bracket)` Adds a bracket to this S-group.
`void`	`addChildSgroup(Sgroup sg)` Adds a child S-group.
`boolean`	`areChildSgroupsVisible()` Checks whether the child S-groups are visible.
`protected void`	`checkBondConsistency()`
`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.
`boolean`	`checkConsistencyInEmbeddings()` Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.
`protected boolean`	`checkSgroupGraphConsistency(Sgroup parentSgroup)` Checks whether the parameter s-group contains the atoms of this s-group.
`void`	`clearObjects()` Clears all MObject-s that belong to this S-groups.
`Sgroup`	`cloneSgroup(Molecule m, Sgroup psg)` Gets a new Sgroup instance.
`protected Sgroup`	`cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap)` Gets a new Sgroup instance.
`SelectionMolecule`	`cloneStructure()` Gets the clone of the structure stored.
`boolean`	`contains(MolAtom atom)` Is this atom contained by the s-group?
`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.
`Sgroup`	`createMolecule(Molecule m)` Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
`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.
`protected static String`	`getAtomSymbolListAsString(MolAtom[] atoms)`
`protected static int`	`getAttach(MolAtom atom)` Gets the attachment point information from the ExtraAtomProperties
`MolBond[]`	`getBondArray()` Gets all bonds connecting two atoms that are both in the Sgroup
`int`	`getBracketCount()` Gets the number of brackets in this S-group.
`ArrayList<MBracket>`	`getBrackets()` Gets all graphic brackets from this Sgroup
`int`	`getChargeLocation()` Returns the charge location attribute of the S-group.
`Sgroup`	`getChildSgroup(int i)` Gets a child S-group.
`int`	`getChildSgroupCount()` Gets the number of child S-groups.
`protected Sgroup[]`	`getChildSgroups()` Gets the children of this 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.
`Sgroup`	`getParentSgroup()` Gets the parent S-group.
`SelectionMolecule`	`getSgroupGraph()` Gets a COPY of the molecule graph.
`SgroupType`	`getSgroupType()` Gets the S-group type.
`String`	`getSubscript()` Gets the subscript for non-superatom S-groups.
`int`	`getSubType()` Gets polymer S-group subtype.
`String`	`getSuperscript()` Gets the superscript for non-superatom S-groups.
`int`	`getTotalCharge()` Calculates the sum of the charge values on the atoms in this S-group.
`int`	`getType()` Deprecated. as of Marvin 6.3. use `getSgroupType()` instead. Note that in case of `AminoAcidSgroup`s returned `ST_SUPERATOM` but `getSgroupType()` will return `SgroupType.AMINOACID`.
`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.
`int`	`indexOf(MolBond b)` Gets the bond index in the S-group graph.
`void`	`initBrackets()` Initializes the list of brackets in this S-group.
`boolean`	`isBracketCrossingBond(MolBond bond)`
`boolean`	`isBracketVisible()` Tests whether the bracket is visible.
`boolean`	`isDescendantOf(Sgroup psg)` Decides whether this is a descendant of another sgroup.
`boolean`	`isEmpty()` Is it an empty S-group?
`boolean`	`isOrderedComponentSgroup()` Returns if the Sgroup is ordered component Sgroup.
`boolean`	`isPartSelected(MoleculeGraph sel)` Decides if part of the sgroup is selected or not.
`boolean`	`isRemovable()` Decides whether an S-group should be ungrouped if its structure changes.
`boolean`	`isSelected(MoleculeGraph sel)` Is the sgroup or part of the sgroup selected?
`boolean`	`isTotalSelected(MoleculeGraph sel)` Decides if the whole sgroup is selected or not.
`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`	`removeAtom(MolAtom a, int opts)` Removes an atom and its bonds from the S-group.
`protected static void`	`removeAtom(Sgroup sg, MolAtom a, int opts)` Wrapper method that calls `removeAtom(MolAtom, int)` of sg.
`protected void`	`removeBond(MolBond b)` Removes a bond from the S-group.
`void`	`removeBonds()` Removes the edge references.
`void`	`removeChildSgroup(Sgroup sg)` Removes an S-group from the children list.
`protected static void`	`removeGroupedAtom(MoleculeGraph m, MolAtom a, MolBond[] v, int opts)` Removes an atom from the molecule and remove its specified bonds.
`void`	`removeObject(MObject mo)` Removes the specified MObject from this Sgroup.
`void`	`replaceAtom(MolAtom olda, MolAtom newa)` Replace an existing atom by a new one in this S-group and its parent (recursively).
`void`	`replaceAtom(MolAtom olda, MolAtom newa, int opts)` Replace an existing atom by a new one in this S-group and its parent (recursively).
`void`	`selectAllObjects(boolean s)` Sets the selection state of the MObject-s that belong to this Sgroup.
`void`	`setAtom(int i, MolAtom a)` Sets the specified atom in the S-group graph.
`void`	`setChargeLocation(int location)` Sets the charge location attribute of the S-group.
`void`	`setConnectivity(int c)` Sets S-group connectivity.
`boolean`	`setGUIStateRecursively(boolean v)` Deprecated. as of Marvin 6.2 use `Molecule.setGUIContracted(boolean)`, or `Molecule.setGUIContracted(boolean, int)` methods for such functionality
`boolean`	`setGUIStateRecursively(boolean contract, int opts)` Deprecated. as of Marvin 6.2 use `Molecule.setGUIContracted(boolean)`, or `Molecule.setGUIContracted(boolean, int)` methods for such functionality
`protected void`	`setParentMolecule(Molecule p)` Sets the parent molecule.
`void`	`setSgroupGraph(SelectionMolecule smol)` Sets the molecule graph.
`void`	`setSubscript(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.
`void`	`setXState(int state, int opts)` Deprecated. as of Marvin 6.2, use `setXState(int)` instead
`protected void`	`setXState0(int state)`
`static void`	`sort(Sgroup[] sgroups, int o)` Sorts S-groups in parent-child or child-parent order.
`String`	`toString()` Overrides Object.toString() to ease debugging.
`String`	`toString(int opts)` Gets a string representation of the S-group.
`protected void`	`transformByParent(CTransform3D t, boolean incg)` Applies a transformation matrix to the coordinates.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - SGROUP_TYPE_COUNT
```
public static final int SGROUP_TYPE_COUNT
```
    Number of S-group types. @see #getType()
    
    See Also:
    Constant Field Values
  - 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 (Structural Repeating Unit: polymers and repeating units with repetition ranges) S-group type.
    
    See Also:
    getType(), 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. Mixture S-groups are composed from unordered component S-groups.
    
    See Also:
    ST_COMPONENT, getType(), Constant Field Values
  - ST_FORMULATION
```
public static final int ST_FORMULATION
```
    Formulation S-group type. Formulation S-groups are composed from ordered component S-groups.
    
    See Also:
    ST_COMPONENT, getType(), 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
  - ST_COMPONENT
```
public static final int ST_COMPONENT
```
    Component S-group type. A component here is a set of atoms contained by a component bracket. There are two kind of component S-group: ordered and unordered. The subscript of an unordered S-group contains a simple "c". The subscript of an ordered component S-group contains an additional integer e.g.: "c1" where "1" is the order of the ordered component S-group. Ordered component S-groups can be embedded into formulation S-groups. Unordered component S-groups can be embedded into mixture S-groups.
    
    See Also:
    ST_FORMULATION, ST_MIXTURE, getSubscript(), getType(), Constant Field Values
  - ST_MULTICENTER
```
public static final int ST_MULTICENTER
```
    Multicenter S-group type. @see #getSubType()
    
    See Also:
    Constant Field Values
  - ST_GRAFT
```
public static final int ST_GRAFT
```
    Graft S-group type. @see #getType()
    
    See Also:
    Constant Field Values
  - ST_AMINOACID
```
public static final int ST_AMINOACID
```
    Amino acid 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
  - PR_ATSYMS
```
public static final int PR_ATSYMS
```
    Print atom symbols.
    
    Since:
    
    Marvin 4.1, 07/26/2006
    
    See Also:
    Constant Field Values
  - RA_IN_EXPAND
```
protected static final int RA_IN_EXPAND
```
    Atom removal in expand.
    
    Since:
    
    Marvin 4.1, 07/27/2006
    
    See Also:
    removeAtom(MolAtom, int), Constant Field Values
  - RA_REMOVE_EXCEPT_RU
```
protected static final int RA_REMOVE_EXCEPT_RU
```
    Replace without duplicating.
    
    Since:
    
    Marvin 4.1, 07/27/2006
    
    See Also:
    replaceAtom(MolAtom, MolAtom, int), Constant Field Values
  - CHARGE_ON_ATOMS
```
public static final int CHARGE_ON_ATOMS
```
    Charge is located on atoms and displayed on atoms.
    
    Since:
    
    Marvin 5.2, 01/22/2009
    
    See Also:
    getChargeLocation(), setChargeLocation(int), Constant Field Values
  - CHARGE_ON_GROUP
```
public static final int CHARGE_ON_GROUP
```
    Charge is located on atoms but displayed on the whole group (bracket).
    
    Since:
    
    Marvin 5.2, 01/22/2009
    
    See Also:
    getChargeLocation(), setChargeLocation(int), Constant Field Values
  - parentSgroup
```
protected transient Sgroup parentSgroup
```
  - sgroupType
```
protected transient int sgroupType
```
    The S-group type.
  - sgroupGraph
```
protected transient SelectionMolecule sgroupGraph
```
    The S-group's internal structure.
  - brackets
```
protected transient ArrayList<MBracket> brackets
```
  - atomSet
```
protected Set<MolAtom> atomSet
```
    Set for storing the atoms of the s-group's graph.
- Constructor Detail
  - Sgroup
```
@Deprecated
public Sgroup(Molecule parent,
                 int t)
```
    Deprecated. As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType).
    
    Creates an S-group with the specified parent and type.
    
    Parameters:
    parent - the parent molecule
    t - S-group type
  - Sgroup
```
@Deprecated
public Sgroup(Molecule parent,
                 int t,
                 int xstate)
```
    Deprecated. As of Marvin 5.12, replaced by SgroupFactory.createSgroup(Molecule, SgroupType) and setXState(int).
    
    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(Molecule parent,
      SgroupType type)
```
  - Sgroup
```
protected Sgroup(Molecule parent,
      SgroupType type,
      int xstate)
```
  - 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
  - Sgroup
```
protected Sgroup(Sgroup sg,
      Molecule m,
      Sgroup psg,
      int[] iatoms)
```
    Copy constructor.
    
    Parameters:
    sg - the S-group to copy
    m - the new parent molecule
    psg - the new parent S-group or null
    iatoms - indices of cloned atoms in the original molecule 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 a COPY of the molecule graph. WARNING! If the returned selection molecule is changed then the graph of the S-group remains unchanged!
    
    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
  - removeChildSgroup
```
public final void removeChildSgroup(Sgroup sg)
```
    Removes an S-group from the children list.
    
    Parameters:
    sg - the child to remove
    Since:
    
    Marvin 4.0.4, 01/04/2006
  - 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
  - contains
```
public boolean contains(MolAtom atom)
```
    Is this atom contained by the s-group?
    
    Parameters:
    atom - the atom that's may be part of this s-group
    
    Returns:
    true it the referenced atom is contained by this s-group, false otherwise
  - 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.
    
    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)
```
    Sets the expanded/contracted state.
    
    Parameters:
    state - the expanded/contracted state
    
    Throws:
    
    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
  - setXState
```
@Deprecated
public final void setXState(int state,
                        int opts)
                     throws IllegalArgumentException
```
    Deprecated. as of Marvin 6.2, use setXState(int) instead
    
    Sets the expanded/contracted state.
    
    Parameters:
    state - the expanded/contracted state
    opts - option for updating coordinates
    
    Throws:
    
    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
  - setXState0
```
protected void setXState0(int state)
```
  - setGUIStateRecursively
```
@Deprecated
public boolean setGUIStateRecursively(boolean v)
```
    Deprecated. as of Marvin 6.2 use Molecule.setGUIContracted(boolean), or Molecule.setGUIContracted(boolean, int) methods for such functionality
    
    Sets the expanded/contracted state recursively.
    
    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
    
    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 3.4, 05/04/2004
    
    See Also:
    setXState(int)
  - setGUIStateRecursively
```
@Deprecated
public boolean setGUIStateRecursively(boolean contract,
                                        int opts)
                               throws IllegalArgumentException
```
    Deprecated. as of Marvin 6.2 use Molecule.setGUIContracted(boolean), or Molecule.setGUIContracted(boolean, int) methods for such functionality
    
    Sets the expanded/contracted state recursively.
    
    Parameters:
    contract - 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
    opts - the expansion/contraction options
    
    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 3.4, 05/04/2004
    
    See Also:
    setXState(int), Expandable.COORDS_UPDATE
  - expand
```
protected boolean expand(int f)
                  throws IllegalArgumentException
```
    Sets the state to XSTATE_X or XSTATE_XC.
    
    Parameters:
    f - options, only the Expandable.LEAVE_COORDS_UNCHANGED and the Expandable.MDL_EXPAND flags are taken into account
    
    Returns:
    true
    
    Throws:
    
    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 IllegalArgumentException
```
    Sets the state to XSTATE_C.
    
    Parameters:
    opts - neglected
    
    Returns:
    true
    
    Throws:
    
    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 String getSuperscript()
```
    Gets the superscript for non-superatom S-groups.
    
    Returns:
    the superscript
  - isOrderedComponentSgroup
```
public boolean isOrderedComponentSgroup()
```
    Returns if the Sgroup is ordered component Sgroup.
    
    Since:
    
    Marvin 4.1.1, 08/30/2006
  - getSubscript
```
public String getSubscript()
```
    Gets the subscript for non-superatom S-groups.
    
    Returns:
    the subscript
  - setSubscript
```
public void setSubscript(String s)
```
    Sets the subscript for non-superatom S-groups.
    
    Parameters:
    s - the subscript
  - getType
```
@Deprecated
public int getType()
```
    Deprecated. as of Marvin 6.3. use getSgroupType() instead. Note that in case of AminoAcidSgroups returned ST_SUPERATOM but getSgroupType() will return SgroupType.AMINOACID.
    
    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_MIXTURE, ST_FORMULATION, ST_DATA, ST_ANY, ST_GENERIC, ST_MULTICENTER, ST_GRAFT
  - getSgroupType
```
public SgroupType getSgroupType()
```
    Gets the S-group type.
    
    Returns:
    the type of the S-group
    See Also:
    SgroupType
  - 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
  - createMolecule
```
public Sgroup createMolecule(Molecule m)
```
    Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
    
    Parameters:
    m - the molecule object
    
    Returns:
    the cloned sgroup
    Since:
    
    Marvin 5.0, 09/01/2008
  - 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 final 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
  - cloneSgroup
```
protected Sgroup cloneSgroup(Molecule m,
                 Sgroup psg,
                 int[] atomIndexMap)
```
    Gets a new Sgroup instance.
    
    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:
    
    Marvin 5.0.2, 03/07/2008
  - 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
  - indexOf
```
public int indexOf(MolBond b)
```
    Gets the bond index in the S-group graph.
    
    Parameters:
    b - the bond
    
    Returns:
    the index or -1 if not found
    Since:
    
    Marvin 5.3.2
  - 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
  - removeBonds
```
public void removeBonds()
```
    Removes the edge references.
  - removeAtom
```
public final void removeAtom(MolAtom a)
```
    Removes an atom and its bonds from the S-group.
    
    Parameters:
    a - the atom
  - removeAtom
```
protected void removeAtom(MolAtom a,
              int opts)
```
    Removes an atom and its bonds from the S-group.
    
    Parameters:
    a - the atom
    opts - 0 or RA_IN_EXPAND
    Since:
    
    Marvin 4.1, 07/27/2006
  - removeAtom
```
protected static void removeAtom(Sgroup sg,
              MolAtom a,
              int opts)
```
    Wrapper method that calls removeAtom(MolAtom, int) of sg. Needed by subclasses because they cannot call the protected removeAtom(MolAtom, int) method of another Sgroup.
    
    Parameters:
    sg - the other S-group
    a - the atom
    opts - 0 or RA_IN_EXPAND
    Since:
    
    Marvin 4.1, 07/27/2006
  - removeBond
```
protected void removeBond(MolBond b)
```
    Removes a bond from the S-group.
    
    Parameters:
    b - the bond
  - replaceAtom
```
public final 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
  - replaceAtom
```
public void replaceAtom(MolAtom olda,
               MolAtom newa,
               int opts)
```
    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
    opts - options
    Since:
    
    4.1, 07/25/2006
    
    See Also:
    RA_REMOVE_EXCEPT_RU
  - findCrossingBonds
```
public MolBond[] findCrossingBonds()
```
    Finds the crossing bonds. Use only when the S-group is expanded.
    
    Returns:
    the attachment bonds
    Since:
    
    Marvin 3.3
  - isBracketCrossingBond
```
public boolean isBracketCrossingBond(MolBond bond)
```
  - getCrossingAtoms
```
public MolAtom[] getCrossingAtoms(MolBond[] xbonds)
                           throws IllegalArgumentException
```
    Gets the atoms that have crossing bonds.
    
    Parameters:
    xbonds - the crossing bonds
    
    Returns:
    the attachment atoms
    
    Throws:
    
    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,
                     int opts)
```
    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
    opts - the removal options
    See Also:
    MoleculeGraph.RMCLEANUP_NONE, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS, MoleculeGraph.removeAtom(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
  - transformByParent
```
protected void transformByParent(CTransform3D t,
                     boolean incg)
```
    Applies a transformation matrix to the coordinates. 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).
    
    Parameters:
    t - the transformation matrix
    incg - graph invariants are changed (true) or not (false)
    Since:
    
    Marvin 4.0.2, 10/26/2005
  - 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 final 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.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    a string representation of the object
    Since:
    
    Marvin 3.4
  - toString
```
public String toString(int opts)
```
    Gets a string representation of the S-group. 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.
    
    Parameters:
    opts - options or 0
    
    Returns:
    a string representation of the object
    Since:
    
    Marvin 4.1, 07/26/2006
    
    See Also:
    PR_ATSYMS
  - getAtomSymbolListAsString
```
protected static String getAtomSymbolListAsString(MolAtom[] atoms)
```
  - isDescendantOf
```
public boolean isDescendantOf(Sgroup psg)
```
    Decides whether this is a descendant of another sgroup.
    
    Parameters:
    psg - the other sgroup
    
    Returns:
    true if this is a descendant of the other sgroup, false otherwise.
    Since:
    
    Marvin 5.0
  - isRemovable
```
public boolean isRemovable()
```
    Decides whether an S-group should be ungrouped if its structure changes.
    
    Returns:
    is true if the S-group is removable, false otherwise.
    See Also:
    ST_MULTIPLE, ST_SUPERATOM
  - isSelected
```
public boolean isSelected(MoleculeGraph sel)
```
    Is the sgroup or part of the sgroup selected?
    
    Parameters:
    sel - the molecule that contains the selected atoms
    
    Returns:
    true if the sgroup contains at least one selected atom false otherwise.
    Since:
    
    Marvin 5.0, 04/02/2007
  - isTotalSelected
```
public boolean isTotalSelected(MoleculeGraph sel)
```
    Decides if the whole sgroup is selected or not.
    
    Parameters:
    sel - molecule graph that contains the selection
    
    Returns:
    true if the whole sgroup is selected
    Since:
    
    Marvin 5.3.2, 10/01/2010
  - isPartSelected
```
public boolean isPartSelected(MoleculeGraph sel)
```
    Decides if part of the sgroup is selected or not.
    
    Parameters:
    sel - molecule graph that contains the selection
    
    Returns:
    true if at least one of the sgroup atoms is selected, but the whole group is not
    Since:
    
    Marvin 5.3.2, 10/01/2010
  - clearObjects
```
public void clearObjects()
```
    Clears all MObject-s that belong to this S-groups.
    
    Since:
    
    Marvin 5.3, 11/30/2009
  - removeObject
```
public void removeObject(MObject mo)
```
    Removes the specified MObject from this Sgroup.
    
    Parameters:
    mo - the MObject to remove.
    Since:
    
    Marvin 5.3, 11/30/2009
  - selectAllObjects
```
public void selectAllObjects(boolean s)
```
    Sets the selection state of the MObject-s that belong to this Sgroup.
    
    Parameters:
    s - the state value to set
    Since:
    
    Marvin 5.3, 11/30/2009
  - addBracket
```
public void addBracket(MBracket bracket)
```
    Adds a bracket to this S-group.
    
    Parameters:
    bracket - the bracket to add
    Since:
    
    Marvin 5.3, 11/30/2009
    
    See Also:
    MBracket
  - initBrackets
```
public void initBrackets()
```
    Initializes the list of brackets in this S-group. Creates an empty list of brackets if no brackets were added previously to the S-group, otherwise deletes the brackets from the existing list.
    
    Since:
    
    Marvin 5.3, 11/30/2009
    
    See Also:
    MBracket
  - getBracketCount
```
public int getBracketCount()
```
    Gets the number of brackets in this S-group.
    
    Returns:
    the number of brackets in this S-group.
    Since:
    
    Marvin 5.3, 11/30/2009
    
    See Also:
    MBracket
  - getBrackets
```
public ArrayList<MBracket> getBrackets()
```
    Gets all graphic brackets from this Sgroup
    
    Returns:
    the list of brackets
    Since:
    
    Marvin 5.3, 11/30/2009
    
    See Also:
    MBracket
  - getChargeLocation
```
public int getChargeLocation()
```
    Returns the charge location attribute of the S-group.
    
    Returns:
    charge location type: CHARGE_ON_ATOMS or CHARGE_ON_GROUP.
    Since:
    
    Marvin 5.2, 01/22/2009
    
    See Also:
    CHARGE_ON_ATOMS, CHARGE_ON_GROUP
  - setChargeLocation
```
public void setChargeLocation(int location)
```
    Sets the charge location attribute of the S-group. Possible charge location types: CHARGE_ON_ATOMS or CHARGE_ON_GROUP.
    
    Parameters:
    location - the charge location type to set
    Since:
    
    Marvin 5.2, 01/22/2009
    
    See Also:
    CHARGE_ON_ATOMS, CHARGE_ON_GROUP
  - getTotalCharge
```
public int getTotalCharge()
```
    Calculates the sum of the charge values on the atoms in this S-group.
    
    Returns:
    the sum charge
    Since:
    
    Marvin 5.2, 01/22/2009
    
    See Also:
    MolAtom.getCharge()
  - 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.
    
    Parameters:
    atom - the given atom
  - getAttach
```
protected static int getAttach(MolAtom atom)
```
    Gets the attachment point information from the ExtraAtomProperties
    
    Parameters:
    atom - that attachment point is question.
    
    Returns:
    the attachment point information from ExtraAtomProperties
    Since:
    
    Marvin 6.0, Dec 12, 2012
  - getBondArray
```
public MolBond[] getBondArray()
```
    Gets all bonds connecting two atoms that are both in the Sgroup
    
    Returns:
    sgroup's MolBond object array
    Since:
    
    Marvin 6.1, 04/29/2013
  - checkConsistencyInEmbeddings
```
public boolean checkConsistencyInEmbeddings()
```
    Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.
    
    Returns:
    true if the sgroup is consistent
  - checkBondConsistency
```
protected void checkBondConsistency()
```
  - checkSgroupGraphConsistency
```
protected boolean checkSgroupGraphConsistency(Sgroup parentSgroup)
```
    Checks whether the parameter s-group contains the atoms of this s-group. It checks also that the parent molecule (if exists) contains these atoms as well.
    
    Parameters:
    parentSgroup - parent of Sgroup
    
    Returns:
    true if the s-group is consistent
  - getChildSgroups
```
protected Sgroup[] getChildSgroups()
```
    Gets the children of this S-group.
    
    Returns:
    Child S-groups as an array.

Class Sgroup

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SGROUP_TYPE_COUNT

ST_SUPERATOM

ST_MULTIPLE

ST_SRU

ST_MONOMER

ST_MER

ST_COPOLYMER

ST_CROSSLINK

ST_MODIFICATION

ST_MIXTURE

ST_FORMULATION

ST_DATA

ST_ANY

ST_GENERIC

ST_COMPONENT

ST_MULTICENTER

ST_GRAFT

ST_AMINOACID

SST_ALTERNATING

SST_RANDOM

SST_BLOCK

SCN_EITHER_UNKNOWN

SCN_HEAD_TO_HEAD

SCN_HEAD_TO_TAIL

XSTATE_NONE

XSTATE_X

XSTATE_C

XSTATE_XC

SORT_PARENT_CHILD

SORT_CHILD_PARENT

PR_ATSYMS

RA_IN_EXPAND

RA_REMOVE_EXCEPT_RU

CHARGE_ON_ATOMS

CHARGE_ON_GROUP

parentSgroup

sgroupType

sgroupGraph

brackets

atomSet

Constructor Detail

Sgroup

Sgroup

Sgroup

Sgroup

Sgroup

Sgroup

Method Detail

setSgroupGraph

getSgroupGraph

setParentMolecule

getParentMolecule

getChildSgroupCount

getChildSgroup

addChildSgroup

removeChildSgroup

findSmallestSgroupContaining

contains

findSmallestSgroupOf

getParentSgroup

getXState

setXState

setXState

setXState0

setGUIStateRecursively

setGUIStateRecursively

expand

contract

getSuperscript

isOrderedComponentSgroup

getSubscript

setSubscript

getType

getSgroupType