Class MmtfStructureReader

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

    public class MmtfStructureReader
    extends java.lang.Object
    implements org.rcsb.mmtf.api.StructureAdapterInterface, java.io.Serializable
    A biojava specific structure inflator for MMTF. Should be ported to biojava code.
    Since:
    5.0
    Author:
    Anthony Bradley
    See Also:
    Serialized Form
    • Constructor Summary

      Constructors 
      Constructor Description
      MmtfStructureReader()
      Instantiates a new bio java structure decoder.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void finalizeStructure()  
      Structure getStructure()
      Gets the structure.
      void initStructure​(int totalNumBonds, int totalNumAtoms, int totalNumGroups, int totalNumChains, int totalNumModels, java.lang.String modelId)  
      void setAtomInfo​(java.lang.String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, java.lang.String element, int charge)  
      void setBioAssemblyTrans​(int bioAssemblyId, int[] inputChainIndices, double[] inputTransform, java.lang.String name)  
      void setChainInfo​(java.lang.String chainId, java.lang.String chainName, int groupCount)  
      void setEntityInfo​(int[] chainIndices, java.lang.String sequence, java.lang.String description, java.lang.String type)  
      void setGroupBond​(int indOne, int indTwo, int bondOrder)  
      void setGroupInfo​(java.lang.String groupName, int groupNumber, char insertionCode, java.lang.String chemCompType, int atomCount, int bondCount, char singleLetterCode, int sequenceIndexId, int secStructType)  
      void setHeaderInfo​(float rFree, float rWork, float resolution, java.lang.String title, java.lang.String depositionDate, java.lang.String releaseDate, java.lang.String[] experimentalMethods)  
      void setInterGroupBond​(int indOne, int indTwo, int bondOrder)  
      void setModelInfo​(int inputModelNumber, int chainCount)  
      void setXtalInfo​(java.lang.String spaceGroupString, float[] unitCell, double[][] ncsOperMatrixList)  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • MmtfStructureReader

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

      • getStructure

        public Structure getStructure()
        Gets the structure.
        Returns:
        the structure
      • 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,
                                  java.lang.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​(java.lang.String chainId,
                                 java.lang.String chainName,
                                 int groupCount)
        Specified by:
        setChainInfo in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setGroupInfo

        public void setGroupInfo​(java.lang.String groupName,
                                 int groupNumber,
                                 char insertionCode,
                                 java.lang.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​(java.lang.String atomName,
                                int serialNumber,
                                char alternativeLocationId,
                                float x,
                                float y,
                                float z,
                                float occupancy,
                                float temperatureFactor,
                                java.lang.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​(java.lang.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,
                                        java.lang.String name)
        Specified by:
        setBioAssemblyTrans in interface org.rcsb.mmtf.api.StructureAdapterInterface
      • setEntityInfo

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

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