Package 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 Details

    • Sgroup

      public Sgroup()
      Create a new generic Sgroup.

  • Method Details

    • 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