Class BiologicalAssemblyBuilder

  • public class BiologicalAssemblyBuilder
    extends Object
    Reconstructs the quaternary structure of a protein from an asymmetric unit
    Peter Rose, Andreas Prlic, Jose Duarte
    • Method Detail

      • rebuildQuaternaryStructure

        public Structure rebuildQuaternaryStructure​(Structure asymUnit,
                                                    List<BiologicalAssemblyTransformation> transformations,
                                                    boolean useAsymIds,
                                                    boolean multiModel)
        Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models. The output Structure will be different depending on the multiModel parameter:
      • the symmetry-expanded chains are added as new models, one per transformId. All original models but the first one are discarded.
      • as original with symmetry-expanded chains added with renamed chain ids and names (in the form originalAsymId_transformId and originalAuthId_transformId)
asymUnit -
transformations -
useAsymIds - if true use Chain.getId() to match the ids in the BiologicalAssemblyTransformation (needed if data read from mmCIF), if false use Chain.getName() for the chain matching (needed if data read from PDB).
multiModel - if true the output Structure will be a multi-model one with one transformId per model, if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).