org.jmol.adapter.smarter
Class AtomSetCollectionReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
- Direct Known Subclasses:
- AdfReader, CifReader, CubeReader, FoldingXyzReader, GamessReader, GaussianReader, GhemicalMMReader, HinReader, JaguarReader, JmeReader, Mol2Reader, MolReader, MopacDataReader, MopacReader, NWChemReader, OdysseyReader, OdysseyXMLReader, PdbReader, PsiReader, QchemReader, ShelxReader, SpartanReader, SpartanSmolReader, V3000Reader, XmlReader, XyzReader
public abstract class AtomSetCollectionReader
- extends java.lang.Object
Method Summary |
protected void |
addJmolScript(java.lang.String script)
|
void |
addPrimitiveLatticeVector(int i,
float[] xyz)
|
protected void |
addSites(java.util.Hashtable htSites)
|
void |
applySymmetry()
|
void |
checkLineForScript()
|
protected void |
checkLineForScript(java.lang.String line)
|
private boolean |
checkUnitCell(int n)
|
void |
clearLatticeParameters()
|
protected void |
discardLines(int nLines)
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protected void |
discardLinesUntilBlank()
|
protected java.lang.String |
discardLinesUntilContains(java.lang.String containsMatch)
|
protected java.lang.String |
discardLinesUntilNonBlank()
|
protected java.lang.String |
discardLinesUntilStartsWith(java.lang.String startsWith)
|
protected void |
fillDataBlock(java.lang.String[][] data)
|
boolean |
filterAtom(Atom atom)
|
static java.lang.String |
getElementSymbol(int elementNumber)
|
protected static java.lang.String[] |
getStrings(java.lang.String sinfo,
int nFields,
int width)
|
protected java.lang.String[] |
getTokens()
|
protected static java.lang.String[] |
getTokens(java.lang.String s)
|
protected static java.lang.String[] |
getTokens(java.lang.String s,
int iStart)
|
protected static void |
getTokensFloat(java.lang.String s,
float[] f,
int n)
|
void |
initialize()
|
void |
initialize(java.util.Hashtable htParams)
|
void |
initializeCartesianToFractional()
|
private void |
initializeSymmetry()
|
void |
newAtomSet(java.lang.String name)
|
private SymmetryInterface |
newSymmetry()
|
protected float |
parseFloat()
|
float |
parseFloat(java.lang.String s)
|
protected float |
parseFloat(java.lang.String s,
int iStart,
int iEnd)
|
protected int |
parseInt()
|
int |
parseInt(java.lang.String s)
|
protected int |
parseInt(java.lang.String s,
int iStart)
|
protected int |
parseInt(java.lang.String s,
int iStart,
int iEnd)
|
protected java.lang.String |
parseToken()
|
protected java.lang.String |
parseToken(java.lang.String s)
|
protected java.lang.String |
parseToken(java.lang.String s,
int iStart,
int iEnd)
|
protected java.lang.String |
parseTokenNext(java.lang.String s)
|
protected static java.lang.String |
parseTrimmed(java.lang.String s,
int iStart)
|
protected static java.lang.String |
parseTrimmed(java.lang.String s,
int iStart,
int iEnd)
|
abstract AtomSetCollection |
readAtomSetCollection(java.io.BufferedReader reader)
|
AtomSetCollection |
readAtomSetCollectionFromDOM(java.lang.Object DOMNode)
|
java.lang.String |
readLine()
|
protected java.lang.String |
readLineTrimmed()
|
void |
setAtomCoord(Atom atom)
|
void |
setAtomCoord(Atom atom,
float x,
float y,
float z)
|
AtomSetCollection |
setError(java.lang.Exception e)
|
void |
setFractionalCoordinates(boolean TF)
|
void |
setMOData(java.util.Hashtable moData)
|
void |
setSpaceGroupName(java.lang.String name)
|
void |
setSymmetryOperator(java.lang.String jonesFaithfulOrMatrix)
|
void |
setUnitCell(float a,
float b,
float c,
float alpha,
float beta,
float gamma)
|
void |
setUnitCellItem(int i,
float x)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
atomSetCollection
public AtomSetCollection atomSetCollection
reader
public java.io.BufferedReader reader
line
public java.lang.String line
prevline
public java.lang.String prevline
ptLine
protected long ptLine
ANGSTROMS_PER_BOHR
public static final float ANGSTROMS_PER_BOHR
- See Also:
- Constant Field Values
desiredModelNumber
public int desiredModelNumber
modelNumber
public int modelNumber
iHaveDesiredModel
public boolean iHaveDesiredModel
getHeader
public boolean getHeader
filter
public java.lang.String filter
spaceGroup
public java.lang.String spaceGroup
symmetry
private SymmetryInterface symmetry
notionalUnitCell
public float[] notionalUnitCell
latticeCells
public int[] latticeCells
primitiveLatticeVectors
public float[][] primitiveLatticeVectors
desiredSpaceGroupIndex
public int desiredSpaceGroupIndex
next
public int[] next
readerName
protected java.lang.String readerName
doApplySymmetry
protected boolean doApplySymmetry
doConvertToFractional
boolean doConvertToFractional
fileCoordinatesAreFractional
boolean fileCoordinatesAreFractional
ignoreFileUnitCell
protected boolean ignoreFileUnitCell
ignoreFileSymmetryOperators
protected boolean ignoreFileSymmetryOperators
ignoreFileSpaceGroupName
boolean ignoreFileSpaceGroupName
isTrajectory
boolean isTrajectory
applySymmetryToBonds
protected boolean applySymmetryToBonds
symmetryRange
float symmetryRange
iHaveUnitCell
public boolean iHaveUnitCell
iHaveFractionalCoordinates
private boolean iHaveFractionalCoordinates
iHaveSymmetryOperators
public boolean iHaveSymmetryOperators
needToApplySymmetry
public boolean needToApplySymmetry
nMatrixElements
private int nMatrixElements
AtomSetCollectionReader
public AtomSetCollectionReader()
getTokens
protected java.lang.String[] getTokens()
getTokensFloat
protected static void getTokensFloat(java.lang.String s,
float[] f,
int n)
getTokens
protected static java.lang.String[] getTokens(java.lang.String s)
getTokens
protected static java.lang.String[] getTokens(java.lang.String s,
int iStart)
parseFloat
protected float parseFloat()
parseFloat
public float parseFloat(java.lang.String s)
parseFloat
protected float parseFloat(java.lang.String s,
int iStart,
int iEnd)
parseInt
protected int parseInt()
parseInt
public int parseInt(java.lang.String s)
parseInt
protected int parseInt(java.lang.String s,
int iStart)
parseInt
protected int parseInt(java.lang.String s,
int iStart,
int iEnd)
parseToken
protected java.lang.String parseToken()
parseToken
protected java.lang.String parseToken(java.lang.String s)
parseTokenNext
protected java.lang.String parseTokenNext(java.lang.String s)
parseToken
protected java.lang.String parseToken(java.lang.String s,
int iStart,
int iEnd)
parseTrimmed
protected static java.lang.String parseTrimmed(java.lang.String s,
int iStart)
parseTrimmed
protected static java.lang.String parseTrimmed(java.lang.String s,
int iStart,
int iEnd)
readAtomSetCollection
public abstract AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
readAtomSetCollectionFromDOM
public AtomSetCollection readAtomSetCollectionFromDOM(java.lang.Object DOMNode)
setError
public AtomSetCollection setError(java.lang.Exception e)
initialize
public void initialize()
initialize
public void initialize(java.util.Hashtable htParams)
initializeSymmetry
private void initializeSymmetry()
newAtomSet
public void newAtomSet(java.lang.String name)
setSpaceGroupName
public void setSpaceGroupName(java.lang.String name)
setSymmetryOperator
public void setSymmetryOperator(java.lang.String jonesFaithfulOrMatrix)
initializeCartesianToFractional
public void initializeCartesianToFractional()
clearLatticeParameters
public void clearLatticeParameters()
setUnitCellItem
public void setUnitCellItem(int i,
float x)
setUnitCell
public void setUnitCell(float a,
float b,
float c,
float alpha,
float beta,
float gamma)
addPrimitiveLatticeVector
public void addPrimitiveLatticeVector(int i,
float[] xyz)
checkUnitCell
private boolean checkUnitCell(int n)
newSymmetry
private SymmetryInterface newSymmetry()
setFractionalCoordinates
public void setFractionalCoordinates(boolean TF)
filterAtom
public boolean filterAtom(Atom atom)
setAtomCoord
public void setAtomCoord(Atom atom,
float x,
float y,
float z)
setAtomCoord
public void setAtomCoord(Atom atom)
addSites
protected void addSites(java.util.Hashtable htSites)
applySymmetry
public void applySymmetry()
throws java.lang.Exception
- Throws:
java.lang.Exception
setMOData
public void setMOData(java.util.Hashtable moData)
getElementSymbol
public static java.lang.String getElementSymbol(int elementNumber)
fillDataBlock
protected void fillDataBlock(java.lang.String[][] data)
throws java.lang.Exception
- Throws:
java.lang.Exception
discardLines
protected void discardLines(int nLines)
throws java.lang.Exception
- Throws:
java.lang.Exception
discardLinesUntilStartsWith
protected java.lang.String discardLinesUntilStartsWith(java.lang.String startsWith)
throws java.lang.Exception
- Throws:
java.lang.Exception
discardLinesUntilContains
protected java.lang.String discardLinesUntilContains(java.lang.String containsMatch)
throws java.lang.Exception
- Throws:
java.lang.Exception
discardLinesUntilBlank
protected void discardLinesUntilBlank()
throws java.lang.Exception
- Throws:
java.lang.Exception
discardLinesUntilNonBlank
protected java.lang.String discardLinesUntilNonBlank()
throws java.lang.Exception
- Throws:
java.lang.Exception
checkLineForScript
protected void checkLineForScript(java.lang.String line)
checkLineForScript
public void checkLineForScript()
addJmolScript
protected void addJmolScript(java.lang.String script)
readLine
public java.lang.String readLine()
throws java.lang.Exception
- Throws:
java.lang.Exception
readLineTrimmed
protected java.lang.String readLineTrimmed()
throws java.lang.Exception
- Throws:
java.lang.Exception
getStrings
protected static final java.lang.String[] getStrings(java.lang.String sinfo,
int nFields,
int width)