Field Detail

• line

  private String line

• lastModel

  private String lastModel

• thisModelID

  private String thisModelID

• baseModel

  private String baseModel

• vibScale

  private float vibScale

• piUnitsX

  private String piUnitsX

• piUnitsY

  private String piUnitsY

• loader

  private JmolJDXMOLReader loader

• modelIdList

  private String modelIdList

• peakIndex

  private int[] peakIndex

• peakFilePath

  private String peakFilePath

Constructor Detail

• JDXMOLParser

  public JDXMOLParser()

Method Detail

• set

  public JmolJDXMOLParser set(JmolJDXMOLReader loader,
                              String filePath,
                              Map<String,Object> htParams)

  Specified by:

  set in interface JmolJDXMOLParser

• getAttribute

  public String getAttribute(String line,
                             String tag)

  Specified by:

  getAttribute in interface JmolJDXMOLParser

• getRecord

  public String getRecord(String key)
                   throws Exception

  Specified by:

  getRecord in interface JmolJDXMOLParser

  Throws:

  Exception

• readModels

  public boolean readModels()
                     throws Exception

  Specified by:

  readModels in interface JmolJDXMOLParser

  Throws:

  Exception

• readACDMolFile

  public String readACDMolFile()
                        throws Exception

  MOL file embedded in JDX file

  Specified by:

  readACDMolFile in interface JmolJDXMOLParser

  Throws:

  Exception

• readACDAssignments

  public javajs.util.Lst<String[]> readACDAssignments(int nPoints,
                                                      boolean isPeakAssignment)
                                               throws Exception

  Specified by:

  readACDAssignments in interface JmolJDXMOLParser

  Throws:

  Exception

• setACDAssignments

  public int setACDAssignments(String model,
                               String mytype,
                               int peakCount,
                               javajs.util.Lst<String[]> acdlist,
                               String molFile)
                        throws Exception

  Specified by:

  setACDAssignments in interface JmolJDXMOLParser

  Throws:

  Exception

• fixACDAtomList

  private String fixACDAtomList(String atoms,
                                Map<String,String> zzcMap,
                                int nAtoms)

• getACDPeakWidth

  private float getACDPeakWidth(String type)

• readPeaks

  public int readPeaks(boolean isSignals,
                       int peakCount)
                throws Exception

  Specified by:

  readPeaks in interface JmolJDXMOLParser

  Throws:

  Exception

• setPeakData

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

• getStringInfo

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

• getModelData

  private void getModelData(boolean isFirst)
                     throws Exception

  Throws:

  Exception

• findRecord

  private boolean findRecord(String tag)
                      throws Exception

  Parameters:

  tag -

  Returns:

  line

  Throws:

  Exception

• readLine

  private String readLine()
                   throws Exception

  Throws:

  Exception

• setLine

  public void setLine(String s)

  Specified by:

  setLine in interface JmolJDXMOLParser