public class JDXMOLParser extends java.lang.Object implements JmolJDXMOLParser
| Modifier and Type | Field and Description |
|---|---|
private java.lang.String |
baseModel |
private java.lang.String |
lastModel |
private java.lang.String |
line |
private JmolJDXMOLReader |
loader |
private java.lang.String |
modelIdList |
private java.lang.String |
peakFilePath |
private int[] |
peakIndex |
private java.lang.String |
piUnitsX |
private java.lang.String |
piUnitsY |
private java.lang.String |
thisModelID |
private float |
vibScale |
| Constructor and Description |
|---|
JDXMOLParser() |
| Modifier and Type | Method and 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) |
private java.lang.String line
private java.lang.String lastModel
private java.lang.String thisModelID
private java.lang.String baseModel
private float vibScale
private java.lang.String piUnitsX
private java.lang.String piUnitsY
private JmolJDXMOLReader loader
private java.lang.String modelIdList
private int[] peakIndex
private java.lang.String peakFilePath
public JmolJDXMOLParser set(JmolJDXMOLReader loader, java.lang.String filePath, java.util.Map<java.lang.String,java.lang.Object> htParams)
set in interface JmolJDXMOLParserpublic java.lang.String getAttribute(java.lang.String line,
java.lang.String tag)
getAttribute in interface JmolJDXMOLParserpublic java.lang.String getRecord(java.lang.String key)
throws java.lang.Exception
getRecord in interface JmolJDXMOLParserjava.lang.Exceptionpublic boolean readModels()
throws java.lang.Exception
readModels in interface JmolJDXMOLParserjava.lang.Exceptionpublic java.lang.String readACDMolFile()
throws java.lang.Exception
readACDMolFile in interface JmolJDXMOLParserjava.lang.Exceptionpublic javajs.util.Lst<java.lang.String[]> readACDAssignments(int nPoints,
boolean isPeakAssignment)
throws java.lang.Exception
readACDAssignments in interface JmolJDXMOLParserjava.lang.Exceptionpublic 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
setACDAssignments in interface JmolJDXMOLParserjava.lang.Exceptionprivate 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)
public int readPeaks(boolean isSignals,
int peakCount)
throws java.lang.Exception
readPeaks in interface JmolJDXMOLParserjava.lang.Exceptionprivate int setPeakData(javajs.util.Lst<java.lang.Object[]> list,
int offset)
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)
private void getModelData(boolean isFirst)
throws java.lang.Exception
java.lang.Exceptionprivate boolean findRecord(java.lang.String tag)
throws java.lang.Exception
tag - java.lang.Exceptionprivate java.lang.String readLine()
throws java.lang.Exception
java.lang.Exceptionpublic void setLine(java.lang.String s)
setLine in interface JmolJDXMOLParser