Package org.openscience.cdk.sgroup

Class 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 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