org.jmol.adapter.smarter
public abstract class AtomSetCollectionReader extends Object
| Field Summary | |
|---|---|
| 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 | |
|---|---|
| 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) |