Sgroup (Marvin API documentation (c) 1998-2012 ChemAxon Ltd.)

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chemaxon.struc
Class Sgroup

java.lang.Object
  chemaxon.struc.Sgroup

All Implemented Interfaces:: java.io.Serializable

Direct Known Subclasses:: DataSgroup, MultipleSgroup, RepeatingUnitSgroup, SuperatomSgroup

public class Sgroup
extends java.lang.Object
implements java.io.Serializable
extends java.lang.Object
implements java.io.Serializable

S-group.

Since:: Marvin 3.0
Version:: 5.3, 10/07/2009
Author:: Peter Csizmadia, Szilveszter Juhos, Erika Biro
See Also:: Serialized Form

Field Summary
`protected java.util.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_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
	`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.
`protected`	`Sgroup(Sgroup sg, Molecule m, Sgroup psg, int[] iatoms)` Copy constructor.

Method Summary
`void`	`add(MolAtom a)` Adds a new atom to the S-group.
`void`	`add(MolBond bond)`
`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.
`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`	`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 java.lang.String`	`getAtomSymbolListAsString(MolAtom[] atoms)`
`int`	`getBracketCount()` Gets the number of brackets in this S-group.
`java.util.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.
`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.
`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`	`getTotalCharge()` Calculates the sum of the charge values on the atoms in this S-group.
`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.
`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 wheter 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)` Sets the expanded/contracted state recursively.
`boolean`	`setGUIStateRecursively(boolean v, int opts)` 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.
`void`	`setXState(int state, int opts)` Sets the expanded/contracted state.
`protected void`	`setXState0(int 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.
`java.lang.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

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 java.util.ArrayList<MBracket> brackets

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

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

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:: 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

setXState

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

Sets the expanded/contracted state.

Parameters:: state - the expanded/contracted state; opts - option for updating coordinates
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, Expandable.COORDS_UPDATE

setXState0

protected void setXState0(int state)

setGUIStateRecursively

public boolean setGUIStateRecursively(boolean v)

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:: 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)

setGUIStateRecursively

public boolean setGUIStateRecursively(boolean v,
                                      int opts)
                               throws java.lang.IllegalArgumentException

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; opts - the expansion/contraction options
Returns:: true if at least one S-group's state was changed, false otherwise
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), Expandable.COORDS_UPDATE

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

isOrderedComponentSgroup

public boolean isOrderedComponentSgroup()

Returns if the Sgroup is ordered component Sgroup.

Since:: Marvin 4.1.1, 08/30/2006

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_MIXTURE, ST_FORMULATION, ST_DATA, ST_ANY, ST_GENERIC, ST_MULTICENTER, ST_GRAFT

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 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,
                                        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 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.

Overrides:: toString in class java.lang.Object

Returns:: a string representation of the object
Since:: Marvin 3.4

toString

public java.lang.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 java.lang.String getAtomSymbolListAsString(MolAtom[] atoms)

isDescendantOf

public boolean isDescendantOf(Sgroup psg)

Decides wheter 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 java.util.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()

add

public void add(MolBond bond)

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chemaxon.struc Class Sgroup

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

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

Sgroup

Sgroup

Sgroup

Sgroup

setSgroupGraph

getSgroupGraph

setParentMolecule

getParentMolecule

getChildSgroupCount

getChildSgroup

addChildSgroup

removeChildSgroup

findSmallestSgroupContaining

findSmallestSgroupOf

getParentSgroup

getXState

setXState

setXState

setXState0

setGUIStateRecursively

setGUIStateRecursively

expand

contract

getSuperscript

isOrderedComponentSgroup

getSubscript

setSubscript

getType

getSubType

setSubType

getConnectivity

setConnectivity

hasBrackets

cloneStructure

createMolecule

createMolecule

getAtomArray

getAtom

countAllAtoms

isEmpty

cloneSgroup

chemaxon.struc
Class Sgroup