org.jmol.adapter.smarter
public abstract class AtomSetCollectionReader extends Object
Field Summary | |
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static float | ANGSTROMS_PER_BOHR |
protected boolean | applySymmetryToBonds |
AtomSetCollection | atomSetCollection |
int | desiredModelNumber |
int | desiredSpaceGroupIndex |
protected boolean | doApplySymmetry |
boolean | doConvertToFractional |
boolean | fileCoordinatesAreFractional |
String | filter |
boolean | getHeader |
boolean | ignoreFileSpaceGroupName |
protected boolean | ignoreFileSymmetryOperators |
boolean | ignoreFileUnitCell |
boolean | iHaveDesiredModel |
boolean | iHaveFractionalCoordinates |
boolean | iHaveSymmetryOperators |
boolean | iHaveUnitCell |
boolean | isTrajectory |
int[] | latticeCells |
String | line |
int | modelNumber |
boolean | needToApplySymmetry |
int[] | next |
int | nMatrixElements |
float[] | notionalUnitCell |
String | prevline |
float[][] | primitiveLatticeVectors |
protected long | ptLine |
BufferedReader | reader |
protected String | readerName |
String | spaceGroup |
SymmetryInterface | symmetry |
float | symmetryRange |
Method Summary | |
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protected void | addJmolScript(String script) |
void | addPrimitiveLatticeVector(int i, float[] xyz) |
protected void | addSites(Hashtable htSites) |
void | applySymmetry() |
protected void | checkLineForScript(String line) |
void | checkLineForScript() |
boolean | checkUnitCell(int n) |
void | clearLatticeParameters() |
protected void | discardLines(int nLines) |
protected void | discardLinesUntilBlank() |
protected String | discardLinesUntilContains(String containsMatch) |
protected String | discardLinesUntilNonBlank() |
protected String | discardLinesUntilStartsWith(String startsWith) |
protected void | fillDataBlock(String[][] data) |
boolean | filterAtom(Atom atom) |
static String | getElementSymbol(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 void | getTokensFloat(String s, float[] f, int n) |
void | initialize() |
void | initialize(Hashtable htParams) |
void | initializeCartesianToFractional() |
void | initializeSymmetry() |
void | newAtomSet(String name) |
SymmetryInterface | newSymmetry() |
protected float | parseFloat() |
float | parseFloat(String s) |
protected float | parseFloat(String s, int iStart, int iEnd) |
protected int | parseInt() |
int | parseInt(String s) |
protected int | parseInt(String s, int iStart) |
protected int | parseInt(String s, int iStart, int iEnd) |
protected String | parseToken() |
protected String | parseToken(String s) |
protected String | parseToken(String s, int iStart, int iEnd) |
protected String | parseTokenNext(String s) |
protected static String | parseTrimmed(String s, int iStart) |
protected static String | parseTrimmed(String s, int iStart, int iEnd) |
abstract AtomSetCollection | readAtomSetCollection(BufferedReader reader) |
AtomSetCollection | readAtomSetCollectionFromDOM(Object DOMNode) |
String | readLine() |
protected String | readLineTrimmed() |
void | setAtomCoord(Atom atom, float x, float y, float z) |
void | setAtomCoord(Atom atom) |
AtomSetCollection | setError(Exception e) |
void | setFractionalCoordinates(boolean TF) |
void | setMOData(Hashtable moData) |
void | setSpaceGroupName(String name) |
void | setSymmetryOperator(String jonesFaithfulOrMatrix) |
void | setUnitCell(float a, float b, float c, float alpha, float beta, float gamma) |
void | setUnitCellItem(int i, float x) |