Package org.biojava.nbio.structure.quaternary

Class BiologicalAssemblyBuilder

  • public class BiologicalAssemblyBuilder
extends java.lang.Object
    Reconstructs the quaternary structure of a protein from an asymmetric unit
    Author:
    Peter Rose, Andreas Prlic, Jose Duarte

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String COMPOSED_OPERATOR_SEPARATOR
      The character separating operator ids that are composed.
      static java.lang.String SYM_CHAIN_ID_SEPARATOR
      The character separating the original chain identifier from the operator id.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<BiologicalAssemblyTransformation> getBioUnitTransformationList​(org.rcsb.cif.schema.mm.PdbxStructAssembly pdbxStructAssembly, int assemblyIndex, org.rcsb.cif.schema.mm.PdbxStructAssemblyGen pdbxStructAssemblyGen, org.rcsb.cif.schema.mm.PdbxStructOperList pdbxStructOperList)
      Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
      Structure rebuildQuaternaryStructure​(Structure asymUnit, java.util.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.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • SYM_CHAIN_ID_SEPARATOR

        public static final java.lang.String SYM_CHAIN_ID_SEPARATOR
        The character separating the original chain identifier from the operator id.
        See Also:
        Constant Field Values

      • COMPOSED_OPERATOR_SEPARATOR

        public static final java.lang.String COMPOSED_OPERATOR_SEPARATOR
        The character separating operator ids that are composed.
        See Also:
        Constant Field Values

    • Constructor Detail

      • BiologicalAssemblyBuilder

        public BiologicalAssemblyBuilder()

    • Method Detail

      • rebuildQuaternaryStructure

        public Structure rebuildQuaternaryStructure​(Structure asymUnit,
                                            java.util.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)
Parameters:
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).
Returns: