java.lang.Object

org.jmol.jsv.JDXMOLParser

All Implemented Interfaces:: JmolJDXMOLParser

public class JDXMOLParser extends 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

Field Summary

Fields

Modifier and Type

Field

Description

private String

baseModel

private String

lastModel

private String

line

private JmolJDXMOLReader

loader

private String

modelIdList

private String

peakFilePath

private int[]

peakIndex

private String

piUnitsX

private String

piUnitsY

private String

thisModelID

private float

vibScale
Constructor Summary

Constructors

Constructor

Description

JDXMOLParser()
Method Summary

Modifier and Type

Method

Description

private boolean

findRecord(String tag)

private String

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

private float

getACDPeakWidth(String type)

String

getAttribute(String line, String tag)

private void

getModelData(boolean isFirst)

String

getRecord(String key)

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)

javajs.util.Lst<String[]>

readACDAssignments(int nPoints, boolean isPeakAssignment)

String

readACDMolFile()

MOL file embedded in JDX file

private String

readLine()

boolean

readModels()

int

readPeaks(boolean isSignals, int peakCount)

JmolJDXMOLParser

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

int

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

void

setLine(String s)

private int

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- 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 Details
- JDXMOLParser
  
  public JDXMOLParser()
Method Details
- 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

Class JDXMOLParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

line

lastModel

thisModelID

baseModel

vibScale

piUnitsX

piUnitsY

loader

modelIdList

peakIndex

peakFilePath

Constructor Details

JDXMOLParser

Method Details

set

getAttribute

getRecord

readModels

readACDMolFile

readACDAssignments

setACDAssignments

fixACDAtomList

getACDPeakWidth

readPeaks

setPeakData

getStringInfo

getModelData

findRecord

readLine

setLine