org.openscience.cdk.sgroup

Class Sgroup

java.lang.Object

org.openscience.cdk.sgroup.Sgroup

public class Sgroup
extends Object

Generic CTab Sgroup (substructure group) that stores all other types of group. This representation is allows reading from CTfiles (e.g. Molfile, SDfile). The class uses a key-value store for Sgroup attributes simplifying both input and output.

Constructor Summary

Constructors

Constructor and Description
Sgroup() Create a new generic Sgroup.

Method Summary

Modifier and Type	Method and Description
void	addAtom(IAtom atom) Add an atom to this Sgroup.
void	addBond(IBond bond) Add a bond to this Sgroup.
void	addBracket(SgroupBracket bracket) Add a bracket for this Sgroup.
void	addParent(Sgroup parent) Add a parent Sgroup.
<T> T	downcast() Downcast this, maybe generic, Sgroup to a specific concrete implementation.
Set<IAtom>	getAtoms() Access the atoms of this substructure group.
Set<SgroupKey>	getAttributeKeys() Access all the attribute keys of this Sgroup.
Set<IBond>	getBonds() Access the bonds that belong to this substructure group.
Set<Sgroup>	getParents() Access the parents of this Sgroup.
String	getSubscript() Access the subscript value.
SgroupType	getType() Access the type of the Sgroup.
<T> T	getValue(SgroupKey key) Access an attribute for the Sgroup.
void	putValue(SgroupKey key, Object val) Store an attribute for the Sgroup.
void	removeAtom(IAtom atom) Remove an atom from this Sgroup.
void	removeBond(IBond bond) Remove a bond from this Sgroup.
void	removeParents(Collection<Sgroup> parents) Remove the specified parent associations from this Sgroup.
void	setSubscript(String label) Set the subscript value.
void	setType(SgroupType type) Set the type of the Sgroup.

Methods inherited from class java.lang.Object

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

Constructor Detail

Sgroup

public Sgroup()

Create a new generic Sgroup.

Method Detail

getAttributeKeys

public final Set<SgroupKey> getAttributeKeys()

Access all the attribute keys of this Sgroup.

Returns:

attribute keys

setType

public final void setType(SgroupType type)

Set the type of the Sgroup.

getType

public final SgroupType getType()

Access the type of the Sgroup.

getAtoms

public final Set<IAtom> getAtoms()

Access the atoms of this substructure group.

Returns:

unmodifiable atom set

getBonds

public final Set<IBond> getBonds()

Access the bonds that belong to this substructure group. For data Sgroups, the bonds are the containment bonds, for all other Sgroup types, they are crossing bonds.

Returns:

unmodifiable bond set

getParents

public final Set<Sgroup> getParents()

Access the parents of this Sgroup.

Returns:

parents

addAtom

public final void addAtom(IAtom atom)

Add an atom to this Sgroup.

Parameters:

atom - the atom

removeAtom

public final void removeAtom(IAtom atom)

Remove an atom from this Sgroup.

Parameters:

atom - the atom

addBond

public final void addBond(IBond bond)

Add a bond to this Sgroup. The bond list

Parameters:

bond - bond to add

removeBond

public final void removeBond(IBond bond)

Remove a bond from this Sgroup.

Parameters:

bond - the bond

addParent

public final void addParent(Sgroup parent)

Add a parent Sgroup.

Parameters:

parent - parent sgroup

removeParents

public final void removeParents(Collection<Sgroup> parents)

Remove the specified parent associations from this Sgroup.

Parameters:

parents - parent associations

putValue

public void putValue(SgroupKey key,
                     Object val)

Store an attribute for the Sgroup.

Parameters:

key - attribute key

val - attribute value

getValue

public <T> T getValue(SgroupKey key)

Access an attribute for the Sgroup.

Parameters:

key - attribute key

getSubscript

public final String getSubscript()

Access the subscript value.

Returns:

subscript value (or null if not present)

setSubscript

public final void setSubscript(String label)

Set the subscript value.

addBracket

public final void addBracket(SgroupBracket bracket)

Add a bracket for this Sgroup.

Parameters:

bracket - sgroup bracket

downcast

public <T> T downcast()

Downcast this, maybe generic, Sgroup to a specific concrete implementation. This method should be called on load by a reader once all data has been added to the sgroup.

Type Parameters:

T - return type

Returns:

downcast instance