*
* @param refAtoms
* @param atomSpec
- * @param isNucleotide TODO
- * @param nucleotide - when true, superposition is based on phoshpate backbone, not peptide
+ * @param backbone - superpose based on which kind of atomType
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
- AtomSpecModel atomSpec, boolean isNucleotide);
+ AtomSpecModel atomSpec, AtomSpecType backbone);
/**
* Returns a command to open a file of commands at the given path
*/
StructureCommandI saveSession(String filepath);
+ enum AtomSpecType { RESIDUE_ONLY, ALPHA, PHOSPHATE };
/**
* Returns a representation of the atom set represented by the model, in
* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
* Alpha Carbon (peptide) or Phosphorous (rna) only
*
* @param model
- * @param alphaOnly
+ * @param specType
* @return
*/
- String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+ String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
/**
* Returns the lowest model number used by the structure viewer (likely 0 or