org.jmol.adapter.smarter

Class AtomSetCollectionReader

public abstract class AtomSetCollectionReader extends Object

Field Summary
static floatANGSTROMS_PER_BOHR
protected booleanapplySymmetryToBonds
AtomSetCollectionatomSetCollection
intdesiredModelNumber
intdesiredSpaceGroupIndex
protected booleandoApplySymmetry
booleandoConvertToFractional
booleanfileCoordinatesAreFractional
Stringfilter
booleangetHeader
booleanignoreFileSpaceGroupName
protected booleanignoreFileSymmetryOperators
booleanignoreFileUnitCell
booleaniHaveDesiredModel
booleaniHaveFractionalCoordinates
booleaniHaveSymmetryOperators
booleaniHaveUnitCell
booleanisTrajectory
int[]latticeCells
Stringline
intmodelNumber
booleanneedToApplySymmetry
int[]next
intnMatrixElements
float[]notionalUnitCell
Stringprevline
float[][]primitiveLatticeVectors
protected longptLine
BufferedReaderreader
protected StringreaderName
StringspaceGroup
SymmetryInterfacesymmetry
floatsymmetryRange
Method Summary
protected voidaddJmolScript(String script)
voidaddPrimitiveLatticeVector(int i, float[] xyz)
protected voidaddSites(Hashtable htSites)
voidapplySymmetry()
protected voidcheckLineForScript(String line)
voidcheckLineForScript()
booleancheckUnitCell(int n)
voidclearLatticeParameters()
protected voiddiscardLines(int nLines)
protected voiddiscardLinesUntilBlank()
protected StringdiscardLinesUntilContains(String containsMatch)
protected StringdiscardLinesUntilNonBlank()
protected StringdiscardLinesUntilStartsWith(String startsWith)
protected voidfillDataBlock(String[][] data)
booleanfilterAtom(Atom atom)
static StringgetElementSymbol(int elementNumber)
protected static String[]getStrings(String sinfo, int nFields, int width)
protected String[]getTokens()
protected static String[]getTokens(String s)
protected static String[]getTokens(String s, int iStart)
protected static voidgetTokensFloat(String s, float[] f, int n)
voidinitialize()
voidinitialize(Hashtable htParams)
voidinitializeCartesianToFractional()
voidinitializeSymmetry()
voidnewAtomSet(String name)
SymmetryInterfacenewSymmetry()
protected floatparseFloat()
floatparseFloat(String s)
protected floatparseFloat(String s, int iStart, int iEnd)
protected intparseInt()
intparseInt(String s)
protected intparseInt(String s, int iStart)
protected intparseInt(String s, int iStart, int iEnd)
protected StringparseToken()
protected StringparseToken(String s)
protected StringparseToken(String s, int iStart, int iEnd)
protected StringparseTokenNext(String s)
protected static StringparseTrimmed(String s, int iStart)
protected static StringparseTrimmed(String s, int iStart, int iEnd)
abstract AtomSetCollectionreadAtomSetCollection(BufferedReader reader)
AtomSetCollectionreadAtomSetCollectionFromDOM(Object DOMNode)
StringreadLine()
protected StringreadLineTrimmed()
voidsetAtomCoord(Atom atom, float x, float y, float z)
voidsetAtomCoord(Atom atom)
AtomSetCollectionsetError(Exception e)
voidsetFractionalCoordinates(boolean TF)
voidsetMOData(Hashtable moData)
voidsetSpaceGroupName(String name)
voidsetSymmetryOperator(String jonesFaithfulOrMatrix)
voidsetUnitCell(float a, float b, float c, float alpha, float beta, float gamma)
voidsetUnitCellItem(int i, float x)

Field Detail

ANGSTROMS_PER_BOHR

public static final float ANGSTROMS_PER_BOHR

applySymmetryToBonds

protected boolean applySymmetryToBonds

atomSetCollection

public AtomSetCollection atomSetCollection

desiredModelNumber

public int desiredModelNumber

desiredSpaceGroupIndex

public int desiredSpaceGroupIndex

doApplySymmetry

protected boolean doApplySymmetry

doConvertToFractional

boolean doConvertToFractional

fileCoordinatesAreFractional

boolean fileCoordinatesAreFractional

filter

public String filter

getHeader

public boolean getHeader

ignoreFileSpaceGroupName

boolean ignoreFileSpaceGroupName

ignoreFileSymmetryOperators

protected boolean ignoreFileSymmetryOperators

ignoreFileUnitCell

boolean ignoreFileUnitCell

iHaveDesiredModel

public boolean iHaveDesiredModel

iHaveFractionalCoordinates

private boolean iHaveFractionalCoordinates

iHaveSymmetryOperators

public boolean iHaveSymmetryOperators

iHaveUnitCell

public boolean iHaveUnitCell

isTrajectory

boolean isTrajectory

latticeCells

public int[] latticeCells

line

public String line

modelNumber

public int modelNumber

needToApplySymmetry

public boolean needToApplySymmetry

public int[] next

nMatrixElements

private int nMatrixElements

notionalUnitCell

public float[] notionalUnitCell

prevline

public String prevline

primitiveLatticeVectors

public float[][] primitiveLatticeVectors

ptLine

protected long ptLine

reader

public BufferedReader reader

readerName

protected String readerName

spaceGroup

public String spaceGroup

symmetry

private SymmetryInterface symmetry

symmetryRange

float symmetryRange

Method Detail

addJmolScript

protected void addJmolScript(String script)

addPrimitiveLatticeVector

public void addPrimitiveLatticeVector(int i, float[] xyz)

addSites

protected void addSites(Hashtable htSites)

applySymmetry

public void applySymmetry()

checkLineForScript

protected void checkLineForScript(String line)

checkLineForScript

public void checkLineForScript()

checkUnitCell

private boolean checkUnitCell(int n)

clearLatticeParameters

public void clearLatticeParameters()

discardLines

protected void discardLines(int nLines)

discardLinesUntilBlank

protected void discardLinesUntilBlank()

discardLinesUntilContains

protected String discardLinesUntilContains(String containsMatch)

discardLinesUntilNonBlank

protected String discardLinesUntilNonBlank()

discardLinesUntilStartsWith

protected String discardLinesUntilStartsWith(String startsWith)

fillDataBlock

protected void fillDataBlock(String[][] data)

filterAtom

public boolean filterAtom(Atom atom)

getElementSymbol

public static String getElementSymbol(int elementNumber)

getStrings

protected static final String[] getStrings(String sinfo, int nFields, int width)

getTokens

protected String[] getTokens()

getTokens

protected static String[] getTokens(String s)

getTokens

protected static String[] getTokens(String s, int iStart)

getTokensFloat

protected static void getTokensFloat(String s, float[] f, int n)

initialize

public void initialize()

initialize

public void initialize(Hashtable htParams)

initializeCartesianToFractional

public void initializeCartesianToFractional()

initializeSymmetry

private void initializeSymmetry()

newAtomSet

public void newAtomSet(String name)

newSymmetry

private SymmetryInterface newSymmetry()

parseFloat

protected float parseFloat()

parseFloat

public float parseFloat(String s)

parseFloat

protected float parseFloat(String s, int iStart, int iEnd)

parseInt

protected int parseInt()

parseInt

public int parseInt(String s)

parseInt

protected int parseInt(String s, int iStart)

parseInt

protected int parseInt(String s, int iStart, int iEnd)

parseToken

protected String parseToken()

parseToken

protected String parseToken(String s)

parseToken

protected String parseToken(String s, int iStart, int iEnd)

parseTokenNext

protected String parseTokenNext(String s)

parseTrimmed

protected static String parseTrimmed(String s, int iStart)

parseTrimmed

protected static String parseTrimmed(String s, int iStart, int iEnd)

readAtomSetCollection

public abstract AtomSetCollection readAtomSetCollection(BufferedReader reader)

readAtomSetCollectionFromDOM

public AtomSetCollection readAtomSetCollectionFromDOM(Object DOMNode)

readLine

public String readLine()

readLineTrimmed

protected String readLineTrimmed()

setAtomCoord

public void setAtomCoord(Atom atom, float x, float y, float z)

setAtomCoord

public void setAtomCoord(Atom atom)

setError

public AtomSetCollection setError(Exception e)

setFractionalCoordinates

public void setFractionalCoordinates(boolean TF)

setMOData

public void setMOData(Hashtable moData)

setSpaceGroupName

public void setSpaceGroupName(String name)

setSymmetryOperator

public void setSymmetryOperator(String jonesFaithfulOrMatrix)

setUnitCell

public void setUnitCell(float a, float b, float c, float alpha, float beta, float gamma)

setUnitCellItem

public void setUnitCellItem(int i, float x)