Package org.jmol.jsv
Class JDXMOLParser
- java.lang.Object
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- org.jmol.jsv.JDXMOLParser
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- 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
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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
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Constructor Summary
Constructors Constructor Description JDXMOLParser()
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Method Summary
All Methods Instance Methods Concrete Methods 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 fileprivate 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)
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Field Detail
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line
private String line
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lastModel
private String lastModel
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thisModelID
private String thisModelID
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baseModel
private String baseModel
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vibScale
private float vibScale
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piUnitsX
private String piUnitsX
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piUnitsY
private String piUnitsY
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loader
private JmolJDXMOLReader loader
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modelIdList
private String modelIdList
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peakIndex
private int[] peakIndex
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peakFilePath
private String peakFilePath
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Method Detail
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set
public JmolJDXMOLParser set(JmolJDXMOLReader loader, String filePath, Map<String,Object> htParams)
- Specified by:
set
in interfaceJmolJDXMOLParser
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getAttribute
public String getAttribute(String line, String tag)
- Specified by:
getAttribute
in interfaceJmolJDXMOLParser
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getRecord
public String getRecord(String key) throws Exception
- Specified by:
getRecord
in interfaceJmolJDXMOLParser
- Throws:
Exception
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readModels
public boolean readModels() throws Exception
- Specified by:
readModels
in interfaceJmolJDXMOLParser
- Throws:
Exception
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readACDMolFile
public String readACDMolFile() throws Exception
MOL file embedded in JDX file- Specified by:
readACDMolFile
in interfaceJmolJDXMOLParser
- Throws:
Exception
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readACDAssignments
public javajs.util.Lst<String[]> readACDAssignments(int nPoints, boolean isPeakAssignment) throws Exception
- Specified by:
readACDAssignments
in interfaceJmolJDXMOLParser
- Throws:
Exception
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setACDAssignments
public int setACDAssignments(String model, String mytype, int peakCount, javajs.util.Lst<String[]> acdlist, String molFile) throws Exception
- Specified by:
setACDAssignments
in interfaceJmolJDXMOLParser
- Throws:
Exception
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getACDPeakWidth
private float getACDPeakWidth(String type)
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readPeaks
public int readPeaks(boolean isSignals, int peakCount) throws Exception
- Specified by:
readPeaks
in interfaceJmolJDXMOLParser
- Throws:
Exception
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setPeakData
private int setPeakData(javajs.util.Lst<Object[]> list, int offset)
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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)
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findRecord
private boolean findRecord(String tag) throws Exception
- Parameters:
tag
-- Returns:
- line
- Throws:
Exception
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setLine
public void setLine(String s)
- Specified by:
setLine
in interfaceJmolJDXMOLParser
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