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 JmolJDXMOLParser
public java.lang.String getAttribute(java.lang.String line, java.lang.String tag)
getAttribute
in interface JmolJDXMOLParser
public java.lang.String getRecord(java.lang.String key) throws java.lang.Exception
getRecord
in interface JmolJDXMOLParser
java.lang.Exception
public boolean readModels() throws java.lang.Exception
readModels
in interface JmolJDXMOLParser
java.lang.Exception
public java.lang.String readACDMolFile() throws java.lang.Exception
readACDMolFile
in interface JmolJDXMOLParser
java.lang.Exception
public javajs.util.Lst<java.lang.String[]> readACDAssignments(int nPoints, boolean isPeakAssignment) throws java.lang.Exception
readACDAssignments
in interface JmolJDXMOLParser
java.lang.Exception
public 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 JmolJDXMOLParser
java.lang.Exception
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)
public int readPeaks(boolean isSignals, int peakCount) throws java.lang.Exception
readPeaks
in interface JmolJDXMOLParser
java.lang.Exception
private 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.Exception
private boolean findRecord(java.lang.String tag) throws java.lang.Exception
tag
- java.lang.Exception
private java.lang.String readLine() throws java.lang.Exception
java.lang.Exception
public void setLine(java.lang.String s)
setLine
in interface JmolJDXMOLParser