chemaxon.struc.sgroup
Class SuperatomSgroup

java.lang.Object
  chemaxon.struc.Sgroup
      chemaxon.struc.sgroup.SuperatomSgroup

All Implemented Interfaces:

chemaxon.struc.AbbreviationForBuilder<java.lang.Integer>, chemaxon.struc.MoleculeForBuilder, Expandable, java.io.Serializable

public class SuperatomSgroup
extends Sgroup
implements Expandable, chemaxon.struc.AbbreviationForBuilder<java.lang.Integer>

Superatom S-group.

Since:

Marvin 3.0, 11/05/2002

Version:

5.3, 09/13/2009

Author:

Peter Csizmadia

See Also:

Serialized Form

Field Summary

Fields inherited from class chemaxon.struc.Sgroup

brackets, CHARGE_ON_ATOMS, CHARGE_ON_GROUP, parentSgroup, PR_ATSYMS, RA_IN_EXPAND, RA_REMOVE_EXCEPT_RU, SCN_EITHER_UNKNOWN, SCN_HEAD_TO_HEAD, SCN_HEAD_TO_TAIL, SGROUP_TYPE_COUNT, sgroupGraph, sgroupType, SORT_CHILD_PARENT, SORT_PARENT_CHILD, SST_ALTERNATING, SST_BLOCK, SST_RANDOM, ST_ANY, ST_COMPONENT, ST_COPOLYMER, ST_CROSSLINK, ST_DATA, ST_FORMULATION, ST_GENERIC, ST_GRAFT, ST_MER, ST_MIXTURE, ST_MODIFICATION, ST_MONOMER, ST_MULTICENTER, ST_MULTIPLE, ST_SRU, ST_SUPERATOM, XSTATE_C, XSTATE_NONE, XSTATE_X, XSTATE_XC

Fields inherited from interface chemaxon.struc.sgroup.Expandable

COORDS_UPDATE, DEFAULT_OPTIONS, FAST_COORDS, MDL_EXPAND, NONRECURSIVE_EXPAND, REVERSIBLE_EXPAND

Constructor Summary

	SuperatomSgroup(Molecule parent) Constructs a superatom S-group in expanded state.
	SuperatomSgroup(Molecule parent, boolean expanded) Constructs a superatom S-group.
protected	SuperatomSgroup(SuperatomSgroup sg, Molecule m, Sgroup psg, int[] atomIndexMap) Copy constructor.

Method Summary

protected void	addAttachAtom(MolAtom a) Adds an atom to the list of attachments.
boolean	areChildSgroupsVisible() Checks whether the child S-groups are visible.
void	calculateAttachmentPoints() Sets the attachment points on an S-group where the S-group has crossing bonds.
protected Sgroup	cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap) Gets a new Sgroup instance.
boolean	contract(int opts) Contracts this S-group.
Molecule	createMolecule() Creates a molecule object that contains only this group.
boolean	expand(int opts) Expands this S-group.
boolean	expandOther(int opts, Molecule moltoexpand) Expands sgtoexpand S-group the same way as it would be this.
MolAtom	findAttachAtom() Gets the most likely attachment point.
MolBond[]	findCrossingBonds() Finds the crossing bonds.
MolAtom[]	getAttachAtoms() Gets the attachment points.
java.lang.Integer	getConnectionAtom(int connectionIndex)
MolAtom[]	getCrossingAtoms(MolBond[] xbonds) Gets the atoms from the S-group that have crossing bonds.
int	getExternalConnections(MolAtom a) Gets the number of bonds of a specified atom where the neighbor doesn't belong to the S-group.
MolAtom[]	getFreeLegalAttachAtoms() Gets the unused legal attachment points.
MolAtom[]	getLegalAttachAtoms() Gets the legal attachment points.
SelectionMolecule	getParentSgroupGraph() Gets the parent exact sgroupgraph.
SelectionMolecule	getSgroupGraph() Gets the molecule graph as a selection.
SgroupAtom	getSuperAtom() Gets the superatom.
boolean	hasAtom(MolAtom a) Is the specified atom an element of this group?
boolean	hasBrackets() Checks if brackets should be painted or not.
boolean	isBracketVisible() Tests whether the bracket is visible.
boolean	isContracted() Decides whether this S-group is contracted or not.
boolean	isExpanded() Is this S-group expanded?
boolean	isFreeLegalAttachAtom(MolAtom a) Tests whether the specified atom is a legal attachment point with a free valence.
boolean	isLegalAttachment(MolAtom a) Tests whether the specified atom is attached to a legal attachment point.
boolean	isTotalSelected(MoleculeGraph sel) Decides if the whole superatom sgroup is selected or not.
protected void	removeAtom(MolAtom a, int opts) Removes an atom from the S-group.
void	removeBond(MolBond b) Removes a bond from the S-group.
void	replaceAtom(MolAtom olda, MolAtom newa, int opts) Replace an existing atom by a new one.
void	setAtom(int i, MolAtom a) Sets the specified atom in the S-group graph.
boolean	setGUIStateRecursively(boolean v) Sets the expanded/contracted state recursively.
void	setNextConnectionAtom(int atomIndex)
void	setSgroupGraph(SelectionMolecule smol) Sets the molecule graph.
void	sortXBonds() Sorts the crossing bonds in the parent molecule in attachment point number order.
java.lang.String	toString(int opts) Returns a string representation of the group.
protected void	transformByParent(CTransform3D t, boolean incg) Applies a transformation matrix to the Sgroup coordinates.
void	updateAttachmentPoints() Adjusts attachment point information to current bonding.
MolBond[]	updateSgroupCrossings() Deprecated. as of Marvin 3.3, replaced by Sgroup.findCrossingBonds()

Methods inherited from class chemaxon.struc.Sgroup

add, add, addBracket, addChildSgroup, clearObjects, cloneSgroup, cloneStructure, containsAllAtomsOf, countAllAtoms, createMolecule, findSmallestSgroupContaining, findSmallestSgroupOf, getAtom, getAtomArray, getAtomCount, getAtomSymbolListAsString, getBracketCount, getBrackets, getChargeLocation, getChildSgroup, getChildSgroupCount, getConnectivity, getParentMolecule, getParentSgroup, getSubscript, getSubType, getSuperscript, getTotalCharge, getType, getXState, indexOf, indexOf, initBrackets, isBracketCrossingBond, isDescendantOf, isEmpty, isOrderedComponentSgroup, isPartSelected, isRemovable, isSelected, isVisible, removeAtom, removeAtom, removeBonds, removeChildSgroup, removeGroupedAtom, removeObject, replaceAtom, selectAllObjects, setChargeLocation, setConnectivity, setGUIStateRecursively, setParentMolecule, setSubscript, setSubType, setXState, setXState, setXState0, sort, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SuperatomSgroup

public SuperatomSgroup(Molecule parent)

Constructs a superatom S-group in expanded state. Its superatom is automatically created.

Parameters:

parent - the parent molecule

Since:

Marvin 3.5.3, 01/18/2005

See Also:

Sgroup.ST_SUPERATOM, MolAtom.SGROUP, getSuperAtom()

SuperatomSgroup

public SuperatomSgroup(Molecule parent,
                       boolean expanded)

Constructs a superatom S-group. Its superatom is automatically created.

Parameters:

parent - the parent molecule

expanded - whether the S-group is created in expanded state or not

See Also:

Sgroup.ST_SUPERATOM, MolAtom.SGROUP, getSuperAtom()

SuperatomSgroup

protected SuperatomSgroup(SuperatomSgroup sg,
                          Molecule m,
                          Sgroup psg,
                          int[] atomIndexMap)

Copy constructor.

Parameters:

sg - the S-group to copy

m - the new parent molecule

psg - the new parent S-group or null

atomIndexMap - indices of cloned atoms in the original molecule or null

Since:

Marvin 5.0.2, 03/07/2008

Method Detail

getSuperAtom

public final SgroupAtom getSuperAtom()

Gets the superatom.

Returns:

the superatom

getAttachAtoms

public final MolAtom[] getAttachAtoms()

Gets the attachment points. This method should only be called when the residue is in contracted state.

Returns:

the attachment atoms

Since:

Marvin 4.0.4, 01/09/2006

updateAttachmentPoints

public void updateAttachmentPoints()

Adjusts attachment point information to current bonding.

getSgroupGraph

public SelectionMolecule getSgroupGraph()

Gets the molecule graph as a selection. The nodes are ordered, the first n are the attachment atoms.

Overrides:

getSgroupGraph in class Sgroup

Returns:

the molecule graph

Since:

Marvin 3.3, 11/04/2003

getParentSgroupGraph

public SelectionMolecule getParentSgroupGraph()

Gets the parent exact sgroupgraph. Internal use only.

Returns:

the sgroupGraph

setSgroupGraph

public void setSgroupGraph(SelectionMolecule smol)

Sets the molecule graph. If the S-group is in contracted state then:

• In case of single attachment points the first n nodes are supposed to be the attachment points.
• In case of double attachment point the graph is searched for the attachment point.

Overrides:

setSgroupGraph in class Sgroup

Parameters:

smol - the molecule graph

Since:

Marvin 3.3, 11/04/2003

cloneSgroup

protected Sgroup cloneSgroup(Molecule m,
                             Sgroup psg,
                             int[] atomIndexMap)

Gets a new Sgroup instance.

Overrides:

cloneSgroup in class Sgroup

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:

5.0.2, 03/07/2008

setAtom

public final void setAtom(int i,
                          MolAtom a)

Sets the specified atom in the S-group graph.

Overrides:

setAtom in class Sgroup

Parameters:

i - the index

a - the atom

removeAtom

protected final void removeAtom(MolAtom a,
                                int opts)

Removes an atom from the S-group.

Overrides:

removeAtom in class Sgroup

Parameters:

a - the atom

opts - unused argument

removeBond

public final void removeBond(MolBond b)

Removes a bond from the S-group.

Overrides:

removeBond in class Sgroup

Parameters:

b - the bond

findCrossingBonds

public MolBond[] findCrossingBonds()

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

Overrides:

findCrossingBonds in class Sgroup

Returns:

the attachment bonds

Since:

Marvin 3.3

getCrossingAtoms

public MolAtom[] getCrossingAtoms(MolBond[] xbonds)

Gets the atoms from the S-group that have crossing bonds.

Overrides:

getCrossingAtoms in class Sgroup

Parameters:

xbonds - the crossing bonds

Returns:

the attachment atoms

Since:

Marvin 3.3

See Also:

findCrossingBonds()

findAttachAtom

public MolAtom findAttachAtom()

Gets the most likely attachment point.

Returns:

the most likely attachment point

Since:

Marvin 4.1, 03/08/2006

transformByParent

protected void transformByParent(CTransform3D t,
                                 boolean incg)

Applies a transformation matrix to the Sgroup coordinates. (Only absolute placement.) 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).

Overrides:

transformByParent in class Sgroup

Parameters:

t - the transformation matrix

incg - graph invariants are changed (true) or not (false)

Since:

Marvin 5.0, 08/18/2007

hasBrackets

public boolean hasBrackets()

Checks if brackets should be painted or not.

Overrides:

hasBrackets in class Sgroup

Returns:

true if the group is in expanded state

Since:

Marvin 3.3

hasAtom

public boolean hasAtom(MolAtom a)

Is the specified atom an element of this group?

Overrides:

hasAtom in class Sgroup

Parameters:

a - the atom

Returns:

true if it contains the atom, false otherwise

Since:

Marvin 3.4

expand

public final boolean expand(int opts)
                     throws java.lang.IllegalArgumentException

Expands this S-group. Atom indexes are preserved during expansion.

Specified by:

expand in interface Expandable

Overrides:

expand in class Sgroup

Parameters:

opts - expansion options

Returns:

true if the operation was successful, false if already expanded

Throws:

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

See Also:

Expandable.DEFAULT_OPTIONS, Expandable.COORDS_UPDATE, Expandable.REVERSIBLE_EXPAND, Expandable.MDL_EXPAND, Expandable.FAST_COORDS, Expandable.NONRECURSIVE_EXPAND

expandOther

public final boolean expandOther(int opts,
                                 Molecule moltoexpand)
                          throws java.lang.IllegalArgumentException

Expands sgtoexpand S-group the same way as it would be this. Atom indexes are preserved during expansion.

Parameters:

opts - expansion options

moltoexpand - molecule containing an Sgroup that has to be expanded

Returns:

true if the operation was successful, false if already expanded

Throws:

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

isExpanded

public final boolean isExpanded()

Is this S-group expanded?

Specified by:

isExpanded in interface Expandable

Returns:

true if expanded, false if contracted

contract

public final boolean contract(int opts)
                       throws java.lang.IllegalArgumentException

Contracts this S-group.

Specified by:

contract in interface Expandable

Overrides:

contract in class Sgroup

Parameters:

opts - contraction options

Returns:

true if the operation was successful, false if already contracted

Throws:

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

See Also:

Expandable.NONRECURSIVE_EXPAND, Sgroup.RA_REMOVE_EXCEPT_RU, Expandable.REVERSIBLE_EXPAND

isContracted

public final boolean isContracted()

Decides whether this S-group is contracted or not.

Returns:

true if contracted false otherwise

isBracketVisible

public boolean isBracketVisible()

Tests whether the bracket is visible.

Overrides:

isBracketVisible in class Sgroup

Returns:

false, superatom S-group brackets are not visible

Since:

Marvin 3.5.1, 11/12/2004

isTotalSelected

public boolean isTotalSelected(MoleculeGraph sel)

Decides if the whole superatom sgroup is selected or not. Overrides method in parent class.

Overrides:

isTotalSelected in class Sgroup

Parameters:

sel - molecule graph that contains the selection

Returns:

true if the whole superatom group is selected

areChildSgroupsVisible

public boolean areChildSgroupsVisible()

Checks whether the child S-groups are visible.

Overrides:

areChildSgroupsVisible in class Sgroup

Returns:

true if children are visible, false otherwise

Since:

Marvin 3.4

getLegalAttachAtoms

public final MolAtom[] getLegalAttachAtoms()

Gets the legal attachment points.

Returns:

array of attachment points

sortXBonds

public void sortXBonds()

Sorts the crossing bonds in the parent molecule in attachment point number order.

Since:

Marvin 5.0, 12/07/2007

isLegalAttachment

public final boolean isLegalAttachment(MolAtom a)

Tests whether the specified atom is attached to a legal attachment point.

Parameters:

a - the atom

Returns:

true if it is attached to a legal attachment point, false otherwise

Since:

3.5, 11/04/2004

isFreeLegalAttachAtom

public final boolean isFreeLegalAttachAtom(MolAtom a)

Tests whether the specified atom is a legal attachment point with a free valence.

Parameters:

a - the atom

Returns:

true if there is a free valence, false otherwise

Since:

5.0, 09/23/2007

getExternalConnections

public int getExternalConnections(MolAtom a)

Gets the number of bonds of a specified atom where the neighbor doesn't belong to the S-group.

Parameters:

a - the atom whose connections to be checked

Returns:

the number of external connection or 0 if the specified atom doesn't belong to the S-group.

getFreeLegalAttachAtoms

public final MolAtom[] getFreeLegalAttachAtoms()

Gets the unused legal attachment points.

Returns:

array of attachment points

createMolecule

public Molecule createMolecule()

Creates a molecule object that contains only this group.

Overrides:

createMolecule in class Sgroup

Returns:

the molecule

Since:

Marvin 3.4

addAttachAtom

protected void addAttachAtom(MolAtom a)

Adds an atom to the list of attachments.

Parameters:

a - the atom

replaceAtom

public final void replaceAtom(MolAtom olda,
                              MolAtom newa,
                              int opts)

Replace an existing atom by a new one.

Overrides:

replaceAtom in class Sgroup

Parameters:

olda - the original atom

newa - the new atom

opts - options

Since:

4.1, 07/25/2006

See Also:

Sgroup.RA_REMOVE_EXCEPT_RU

updateSgroupCrossings

public final MolBond[] updateSgroupCrossings()

Deprecated. as of Marvin 3.3, replaced by Sgroup.findCrossingBonds()

Generates the attachment atoms. Use only when the S-group is expanded.

Returns:

the attachment bonds

toString

public java.lang.String toString(int opts)

Returns a string representation of the group.

Overrides:

toString in class Sgroup

Parameters:

opts - options or 0

Returns:

the string representation

Since:

Marvin 4.1, 07/26/2006

See Also:

Sgroup.PR_ATSYMS

setGUIStateRecursively

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

Sets the expanded/contracted state recursively.

Overrides:

setGUIStateRecursively in class Sgroup

Parameters:

v - true sets Sgroup.XSTATE_C if previous state was Sgroup.XSTATE_XC, false sets Sgroup.XSTATE_XC if previous state was Sgroup.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 5.1

See Also:

Sgroup.setXState(int)

calculateAttachmentPoints

public void calculateAttachmentPoints()

Sets the attachment points on an S-group where the S-group has crossing bonds.

Throws:

java.lang.UnsupportedOperationException - for S-groups with more than 2 crossing bonds

setNextConnectionAtom

public void setNextConnectionAtom(int atomIndex)

getConnectionAtom

public java.lang.Integer getConnectionAtom(int connectionIndex)

Specified by:

getConnectionAtom in interface chemaxon.struc.AbbreviationForBuilder<java.lang.Integer>