org.jmol.adapter.smarter
Class AtomSetCollectionReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
- Direct Known Subclasses:
- AdfReader, AimsReader, AlchemyReader, CastepReader, CifReader, CubeReader, FFReader, FoldingXyzReader, GaussianWfnReader, GhemicalMMReader, GromacsReader, HinReader, JmeReader, MdCrdReader, MolReader, MopacDataReader, MopacReader, MOReader, OdysseyXMLReader, PdbReader, ShelxReader, SpartanInputReader, SpartanReader, V3000Reader, Wien2kReader, 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 |
applySymmetryAndSetTrajectory()
|
void |
checkLineForScript()
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protected void |
checkLineForScript(java.lang.String line)
|
private boolean |
checkUnitCell(int n)
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void |
clearLatticeParameters()
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protected static java.lang.String |
deducePdbElementSymbol(boolean isHetero,
java.lang.String XX,
java.lang.String group3)
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protected void |
discardLines(int nLines)
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protected void |
discardLinesUntilBlank()
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protected java.lang.String |
discardLinesUntilContains(java.lang.String containsMatch)
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protected java.lang.String |
discardLinesUntilNonBlank()
|
protected java.lang.String |
discardLinesUntilStartsWith(java.lang.String startsWith)
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protected boolean |
doGetModel(int modelNumber)
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protected void |
fillDataBlock(java.lang.String[][] data)
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protected boolean |
filterAtom(Atom atom)
|
protected boolean |
filterAtom(Atom atom,
int iAtom)
filter can contain [XXX] or ![XXX], .XXX; or !.XXX;, :X, !:X |
private java.lang.Object |
finalize(java.util.Hashtable htParams,
java.lang.String filename)
|
static java.lang.String |
getElementSymbol(int elementNumber)
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protected static java.lang.String[] |
getStrings(java.lang.String sinfo,
int nFields,
int width)
|
protected java.lang.String[] |
getTokens()
|
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)
|
(package private) void |
initialize(java.util.Hashtable htParams)
|
private void |
initializeCartesianToFractional()
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private void |
initializeSymmetry()
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protected boolean |
isLastModel(int modelNumber)
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protected void |
newAtomSet(java.lang.String name)
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private SymmetryInterface |
newSymmetry()
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protected float |
parseFloat()
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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)
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protected java.lang.String |
parseToken(java.lang.String s,
int iStart,
int iEnd)
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protected java.lang.String |
parseTokenNext(java.lang.String s)
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protected static java.lang.String |
parseTrimmed(java.lang.String s,
int iStart)
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protected static java.lang.String |
parseTrimmed(java.lang.String s,
int iStart,
int iEnd)
|
abstract void |
readAtomSetCollection(java.io.BufferedReader reader)
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void |
readAtomSetCollectionFromDOM(java.lang.Object DOMNode)
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java.lang.Object |
readData(java.lang.String filename,
java.util.Hashtable htParams,
java.io.BufferedReader reader)
|
protected java.lang.Object |
readData(java.lang.String filename,
java.util.Hashtable htParams,
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)
|
protected void |
setError(java.lang.Exception e)
|
void |
setFractionalCoordinates(boolean TF)
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void |
setMOData(java.util.Hashtable moData)
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void |
setSpaceGroupName(java.lang.String name)
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void |
setSymmetryOperator(java.lang.String xyz)
|
void |
setTransform(float x1,
float y1,
float z1,
float x2,
float y2,
float z2,
float x3,
float y3,
float z3)
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protected void |
setUnitCell(float a,
float b,
float c,
float alpha,
float beta,
float gamma)
|
void |
setUnitCellItem(int i,
float x)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ANGSTROMS_PER_BOHR
public static final float ANGSTROMS_PER_BOHR
- See Also:
- Constant Field Values
atomSetCollection
protected AtomSetCollection atomSetCollection
reader
protected java.io.BufferedReader reader
readerName
protected java.lang.String readerName
htParams
public java.util.Hashtable htParams
line
public java.lang.String line
prevline
public java.lang.String prevline
next
protected int[] next
ptLine
private long ptLine
latticeCells
public int[] latticeCells
iHaveUnitCell
public boolean iHaveUnitCell
iHaveSymmetryOperators
public boolean iHaveSymmetryOperators
doApplySymmetry
protected boolean doApplySymmetry
ignoreFileSymmetryOperators
protected boolean ignoreFileSymmetryOperators
isTrajectory
protected boolean isTrajectory
applySymmetryToBonds
protected boolean applySymmetryToBonds
needToApplySymmetry
protected boolean needToApplySymmetry
getHeader
protected boolean getHeader
templateAtomCount
protected int templateAtomCount
modelNumber
protected int modelNumber
bsModels
protected java.util.BitSet bsModels
bsFilter
protected java.util.BitSet bsFilter
filter
protected java.lang.String filter
haveAtomFilter
protected boolean haveAtomFilter
spaceGroup
protected java.lang.String spaceGroup
havePartialChargeFilter
protected boolean havePartialChargeFilter
calculationType
public java.lang.String calculationType
iHaveFractionalCoordinates
private boolean iHaveFractionalCoordinates
doPackUnitCell
private boolean doPackUnitCell
doConvertToFractional
private boolean doConvertToFractional
fileCoordinatesAreFractional
private boolean fileCoordinatesAreFractional
ignoreFileUnitCell
protected boolean ignoreFileUnitCell
ignoreFileSpaceGroupName
private boolean ignoreFileSpaceGroupName
symmetryRange
private float symmetryRange
notionalUnitCell
private float[] notionalUnitCell
firstLastStep
private int[] firstLastStep
desiredModelNumber
private int desiredModelNumber
lastModelNumber
private int lastModelNumber
desiredSpaceGroupIndex
private int desiredSpaceGroupIndex
symmetry
private SymmetryInterface symmetry
haveModel
private boolean haveModel
nMatrixElements
private int nMatrixElements
matrixRotate
private javax.vecmath.Matrix3f matrixRotate
previousScript
private java.lang.String previousScript
AtomSetCollectionReader
public AtomSetCollectionReader()
readData
public java.lang.Object readData(java.lang.String filename,
java.util.Hashtable htParams,
java.io.BufferedReader reader)
throws java.lang.Exception
- Throws:
java.lang.Exception
readData
protected java.lang.Object readData(java.lang.String filename,
java.util.Hashtable htParams,
java.lang.Object DOMNode)
readAtomSetCollection
public abstract void readAtomSetCollection(java.io.BufferedReader reader)
readAtomSetCollectionFromDOM
public void readAtomSetCollectionFromDOM(java.lang.Object DOMNode)
finalize
private java.lang.Object finalize(java.util.Hashtable htParams,
java.lang.String filename)
setError
protected void setError(java.lang.Exception e)
initialize
void initialize(java.util.Hashtable htParams)
doGetModel
protected boolean doGetModel(int modelNumber)
isLastModel
protected boolean isLastModel(int modelNumber)
initializeSymmetry
private void initializeSymmetry()
newAtomSet
protected void newAtomSet(java.lang.String name)
setSpaceGroupName
public void setSpaceGroupName(java.lang.String name)
setSymmetryOperator
public void setSymmetryOperator(java.lang.String xyz)
initializeCartesianToFractional
private void initializeCartesianToFractional()
clearLatticeParameters
public void clearLatticeParameters()
setUnitCellItem
public void setUnitCellItem(int i,
float x)
setUnitCell
protected 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
protected boolean filterAtom(Atom atom)
filterAtom
protected boolean filterAtom(Atom atom,
int iAtom)
- filter can contain [XXX] or ![XXX], .XXX; or !.XXX;, :X, !:X
- Parameters:
atom
- iAtom
-
- Returns:
- true if we want this 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)
applySymmetryAndSetTrajectory
public void applySymmetryAndSetTrajectory()
throws java.lang.Exception
- Throws:
java.lang.Exception
setMOData
public void setMOData(java.util.Hashtable moData)
setTransform
public void setTransform(float x1,
float y1,
float z1,
float x2,
float y2,
float z2,
float x3,
float y3,
float z3)
getElementSymbol
public static java.lang.String getElementSymbol(int elementNumber)
deducePdbElementSymbol
protected static java.lang.String deducePdbElementSymbol(boolean isHetero,
java.lang.String XX,
java.lang.String group3)
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)
getTokens
protected java.lang.String[] getTokens()
getTokensFloat
protected static void getTokensFloat(java.lang.String s,
float[] f,
int n)
getTokens
public 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)