Interface IPolymer

    • Method Detail

      • addAtom

        void addAtom​(IAtom oAtom)
        Adds the atom oAtom without specifying a Monomer. Therefore the atom to this AtomContainer, but not to a certain Monomer (intended e.g. for HETATMs).
        Specified by:
        addAtom in interface IAtomContainer
        Parameters:
        oAtom - The atom to add
      • addAtom

        void addAtom​(IAtom oAtom,
                     IMonomer oMonomer)
        Adds the atom oAtom to a specified Monomer.
        Parameters:
        oAtom - The atom to add
        oMonomer - The monomer the atom belongs to
      • getMonomerCount

        int getMonomerCount()
        Return the number of monomers present in the Polymer.
        Returns:
        number of monomers
      • getMonomer

        IMonomer getMonomer​(String cName)
        Retrieve a Monomer object by specifying its name.
        Parameters:
        cName - The name of the monomer to look for
        Returns:
        The Monomer object which was asked for
      • getMonomerNames

        Collection<String> getMonomerNames()
        Returns a collection of the names of all Monomers in this polymer.
        Returns:
        a Collection of all the monomer names.
      • removeMonomer

        void removeMonomer​(String name)
        Removes a particular monomer, specified by its name.
        Parameters:
        name - The name of the monomer to be removed