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