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.
        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.
        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.
        unmodifiable bond set
      • getParents

        public final Set<Sgroup> getParents()
        Access the parents of this Sgroup.
      • addAtom

        public final void addAtom​(IAtom atom)
        Add an atom to this Sgroup.
        atom - the atom
      • removeAtom

        public final void removeAtom​(IAtom atom)
        Remove an atom from this Sgroup.
        atom - the atom
      • addBond

        public final void addBond​(IBond bond)
        Add a bond to this Sgroup. The bond list
        bond - bond to add
      • removeBond

        public final void removeBond​(IBond bond)
        Remove a bond from this Sgroup.
        bond - the bond
      • addParent

        public final void addParent​(Sgroup parent)
        Add a parent Sgroup.
        parent - parent sgroup
      • removeParents

        public final void removeParents​(Collection<Sgroup> parents)
        Remove the specified parent associations from this Sgroup.
        parents - parent associations
      • putValue

        public void putValue​(SgroupKey key,
                             Object val)
        Store an attribute for the Sgroup.
        key - attribute key
        val - attribute value
      • getValue

        public <T> T getValue​(SgroupKey key)
        Access an attribute for the Sgroup.
        key - attribute key
      • getSubscript

        public final String getSubscript()
        Access the subscript value.
        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.
        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
        downcast instance