org.jmol.adapter.smarter
Class AtomSetCollectionReader

java.lang.Object
  extended by 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


Field Summary
static float ANGSTROMS_PER_BOHR
           
protected  boolean applySymmetryToBonds
           
 AtomSetCollection atomSetCollection
           
 int desiredModelNumber
           
 int desiredSpaceGroupIndex
           
protected  boolean doApplySymmetry
           
(package private)  boolean doConvertToFractional
           
(package private)  boolean fileCoordinatesAreFractional
           
 java.lang.String filter
           
 boolean getHeader
           
(package private)  boolean ignoreFileSpaceGroupName
           
protected  boolean ignoreFileSymmetryOperators
           
protected  boolean ignoreFileUnitCell
           
 boolean iHaveDesiredModel
           
private  boolean iHaveFractionalCoordinates
           
 boolean iHaveSymmetryOperators
           
 boolean iHaveUnitCell
           
(package private)  boolean isTrajectory
           
 int[] latticeCells
           
 java.lang.String line
           
 int modelNumber
           
 boolean needToApplySymmetry
           
 int[] next
           
private  int nMatrixElements
           
 float[] notionalUnitCell
           
 java.lang.String prevline
           
 float[][] primitiveLatticeVectors
           
protected  long ptLine
           
 java.io.BufferedReader reader
           
protected  java.lang.String readerName
           
 java.lang.String spaceGroup
           
private  SymmetryInterface symmetry
           
(package private)  float symmetryRange
           
 
Constructor Summary
AtomSetCollectionReader()
           
 
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)
           
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
 

Field Detail

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
Constructor Detail

AtomSetCollectionReader

public AtomSetCollectionReader()
Method Detail

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)