Package org.jmol.jsv

Class JDXMOLParser

  • All Implemented Interfaces:
    JmolJDXMOLParser
    public class JDXMOLParser
extends java.lang.Object
implements JmolJDXMOLParser
    Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS. Used in both Jmol and JSpecView. Also gets info from ACD Labs files JCAMP-DX=5.00 $$ ACD/SpecManager v 12.01

    • Constructor Summary

      Constructors 
      Constructor Description
      JDXMOLParser()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private boolean findRecord​(java.lang.String tag)  
      private java.lang.String fixACDAtomList​(java.lang.String atoms, java.util.Map<java.lang.String,​java.lang.String> zzcMap, int nAtoms)  
      private float getACDPeakWidth​(java.lang.String type)  
      java.lang.String getAttribute​(java.lang.String line, java.lang.String tag)  
      private void getModelData​(boolean isFirst)  
      java.lang.String getRecord​(java.lang.String key)  
      private void getStringInfo​(java.lang.String file, java.lang.String title, java.lang.String mytype, java.lang.String model, java.lang.String atoms, java.util.Map<java.lang.String,​java.lang.Object[]> htSets, java.lang.String key, javajs.util.Lst<java.lang.Object[]> list, java.lang.String more)  
      javajs.util.Lst<java.lang.String[]> readACDAssignments​(int nPoints, boolean isPeakAssignment)  
      java.lang.String readACDMolFile()
      MOL file embedded in JDX file
      private java.lang.String readLine()  
      boolean readModels()  
      int readPeaks​(boolean isSignals, int peakCount)  
      JmolJDXMOLParser set​(JmolJDXMOLReader loader, java.lang.String filePath, java.util.Map<java.lang.String,​java.lang.Object> htParams)  
      int setACDAssignments​(java.lang.String model, java.lang.String mytype, int peakCount, javajs.util.Lst<java.lang.String[]> acdlist, java.lang.String molFile)  
      void setLine​(java.lang.String s)  
      private int setPeakData​(javajs.util.Lst<java.lang.Object[]> list, int offset)  

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • line

        private java.lang.String line

      • lastModel

        private java.lang.String lastModel

      • thisModelID

        private java.lang.String thisModelID

      • baseModel

        private java.lang.String baseModel

      • vibScale

        private float vibScale

      • piUnitsX

        private java.lang.String piUnitsX

      • piUnitsY

        private java.lang.String piUnitsY

      • modelIdList

        private java.lang.String modelIdList

      • peakIndex

        private int[] peakIndex

      • peakFilePath

        private java.lang.String peakFilePath

    • Constructor Detail

      • JDXMOLParser

        public JDXMOLParser()

    • Method Detail

      • getAttribute

        public java.lang.String getAttribute​(java.lang.String line,
                                     java.lang.String tag)
        Specified by:
        getAttribute in interface JmolJDXMOLParser

      • getRecord

        public java.lang.String getRecord​(java.lang.String key)
                           throws java.lang.Exception
        Specified by:
        getRecord in interface JmolJDXMOLParser
        Throws:
        java.lang.Exception

      • readModels

        public boolean readModels()
                   throws java.lang.Exception
        Specified by:
        readModels in interface JmolJDXMOLParser
        Throws:
        java.lang.Exception

      • readACDMolFile

        public java.lang.String readACDMolFile()
                                throws java.lang.Exception
        MOL file embedded in JDX file
        Specified by:
        readACDMolFile in interface JmolJDXMOLParser
        Throws:
        java.lang.Exception

      • readACDAssignments

        public javajs.util.Lst<java.lang.String[]> readACDAssignments​(int nPoints,
                                                              boolean isPeakAssignment)
                                                       throws java.lang.Exception
        Specified by:
        readACDAssignments in interface JmolJDXMOLParser
        Throws:
        java.lang.Exception

      • setACDAssignments

        public int setACDAssignments​(java.lang.String model,
                             java.lang.String mytype,
                             int peakCount,
                             javajs.util.Lst<java.lang.String[]> acdlist,
                             java.lang.String molFile)
                      throws java.lang.Exception
        Specified by:
        setACDAssignments in interface JmolJDXMOLParser
        Throws:
        java.lang.Exception

      • fixACDAtomList

        private java.lang.String fixACDAtomList​(java.lang.String atoms,
                                        java.util.Map<java.lang.String,​java.lang.String> zzcMap,
                                        int nAtoms)

      • getACDPeakWidth

        private float getACDPeakWidth​(java.lang.String type)

      • readPeaks

        public int readPeaks​(boolean isSignals,
                     int peakCount)
              throws java.lang.Exception
        Specified by:
        readPeaks in interface JmolJDXMOLParser
        Throws:
        java.lang.Exception

      • setPeakData

        private int setPeakData​(javajs.util.Lst<java.lang.Object[]> list,
                        int offset)

      • getStringInfo

        private void getStringInfo​(java.lang.String file,
                           java.lang.String title,
                           java.lang.String mytype,
                           java.lang.String model,
                           java.lang.String atoms,
                           java.util.Map<java.lang.String,​java.lang.Object[]> htSets,
                           java.lang.String key,
                           javajs.util.Lst<java.lang.Object[]> list,
                           java.lang.String more)

      • getModelData

        private void getModelData​(boolean isFirst)
                   throws java.lang.Exception
        Throws:
        java.lang.Exception

      • findRecord

        private boolean findRecord​(java.lang.String tag)
                    throws java.lang.Exception
        Parameters:
        tag -
        Returns:
        line
        Throws:
        java.lang.Exception

      • readLine

        private java.lang.String readLine()
                           throws java.lang.Exception
        Throws:
        java.lang.Exception