generate
abstract fun generateChain(nonPolymerMol: Molecule, polymerMol: Polymer, polymerAtoms: List<Atom>): Polymer.Chain
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nonPolymerMol is the input non-polymer molecule to be combined. polymerMol is the combined output molecule, with the polymerAtoms already added. polyerAtoms are the atoms in polymerMol which have already been copied from nonPolymerMol.