Package org.jmol.jsv
Class JDXMOLParser
java.lang.Object
org.jmol.jsv.JDXMOLParser
- All Implemented Interfaces:
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 -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate boolean
findRecord
(String tag) private String
fixACDAtomList
(String atoms, Map<String, String> zzcMap, int nAtoms) private float
getACDPeakWidth
(String type) getAttribute
(String line, String tag) private void
getModelData
(boolean isFirst) 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) MOL file embedded in JDX fileprivate String
readLine()
boolean
int
readPeaks
(boolean isSignals, int peakCount) int
setACDAssignments
(String model, String mytype, int peakCount, javajs.util.Lst<String[]> acdlist, String molFile) void
private int
setPeakData
(javajs.util.Lst<Object[]> list, int offset)
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Field Details
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line
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lastModel
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thisModelID
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baseModel
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vibScale
private float vibScale -
piUnitsX
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piUnitsY
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loader
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modelIdList
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peakIndex
private int[] peakIndex -
peakFilePath
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Constructor Details
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JDXMOLParser
public JDXMOLParser()
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Method Details
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set
- Specified by:
set
in interfaceJmolJDXMOLParser
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getAttribute
- Specified by:
getAttribute
in interfaceJmolJDXMOLParser
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getRecord
- Specified by:
getRecord
in interfaceJmolJDXMOLParser
- Throws:
Exception
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readModels
- Specified by:
readModels
in interfaceJmolJDXMOLParser
- Throws:
Exception
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readACDMolFile
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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fixACDAtomList
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getACDPeakWidth
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readPeaks
- Specified by:
readPeaks
in interfaceJmolJDXMOLParser
- Throws:
Exception
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setPeakData
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getStringInfo
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getModelData
- Throws:
Exception
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findRecord
- Parameters:
tag
-- Returns:
- line
- Throws:
Exception
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readLine
- Throws:
Exception
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setLine
- Specified by:
setLine
in interfaceJmolJDXMOLParser
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