Class MmtfStructureReader

  • All Implemented Interfaces:
    Serializable, org.rcsb.mmtf.api.StructureAdapterInterface

    public class MmtfStructureReader
    extends Object
    implements org.rcsb.mmtf.api.StructureAdapterInterface, Serializable
    A biojava specific structure inflator for MMTF. Should be ported to biojava code.
    Anthony Bradley
    See Also:
    Serialized Form
    • Constructor Detail

      • MmtfStructureReader

        public MmtfStructureReader()
        Instantiates a new bio java structure decoder.
    • Method Detail

      • finalizeStructure

        public void finalizeStructure()
        Specified by:
        finalizeStructure in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • initStructure

        public void initStructure​(int totalNumBonds,
                                  int totalNumAtoms,
                                  int totalNumGroups,
                                  int totalNumChains,
                                  int totalNumModels,
                                  String modelId)
        Specified by:
        initStructure in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setModelInfo

        public void setModelInfo​(int inputModelNumber,
                                 int chainCount)
        Specified by:
        setModelInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setChainInfo

        public void setChainInfo​(String chainId,
                                 String chainName,
                                 int groupCount)
        Specified by:
        setChainInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setGroupInfo

        public void setGroupInfo​(String groupName,
                                 int groupNumber,
                                 char insertionCode,
                                 String chemCompType,
                                 int atomCount,
                                 int bondCount,
                                 char singleLetterCode,
                                 int sequenceIndexId,
                                 int secStructType)
        Specified by:
        setGroupInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setAtomInfo

        public void setAtomInfo​(String atomName,
                                int serialNumber,
                                char alternativeLocationId,
                                float x,
                                float y,
                                float z,
                                float occupancy,
                                float temperatureFactor,
                                String element,
                                int charge)
        Specified by:
        setAtomInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setGroupBond

        public void setGroupBond​(int indOne,
                                 int indTwo,
                                 int bondOrder)
        Specified by:
        setGroupBond in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setInterGroupBond

        public void setInterGroupBond​(int indOne,
                                      int indTwo,
                                      int bondOrder)
        Specified by:
        setInterGroupBond in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setXtalInfo

        public void setXtalInfo​(String spaceGroupString,
                                float[] unitCell,
                                double[][] ncsOperMatrixList)
        Specified by:
        setXtalInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setBioAssemblyTrans

        public void setBioAssemblyTrans​(int bioAssemblyId,
                                        int[] inputChainIndices,
                                        double[] inputTransform,
                                        String name)
        Specified by:
        setBioAssemblyTrans in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setEntityInfo

        public void setEntityInfo​(int[] chainIndices,
                                  String sequence,
                                  String description,
                                  String type)
        Specified by:
        setEntityInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setHeaderInfo

        public void setHeaderInfo​(float rFree,
                                  float rWork,
                                  float resolution,
                                  String title,
                                  String depositionDate,
                                  String releaseDate,
                                  String[] experimentalMethods)
        Specified by:
        setHeaderInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface