Class AtomSetCollectionReader

Method Details

• getPackingRangeValue

  public float getPackingRangeValue(float def)

• setup

  protected void setup(String fullPath, Map<String,Object> htParams, Object readerOrDocument)

• setupASCR

  protected void setupASCR(String fullPath, Map<String,Object> htParams, Object readerOrDocument)

• readDataObject

  protected Object readDataObject(Object node) throws Exception

  Throws:

  Exception

• processDOM

  protected void processDOM(Object DOMNode)

  Parameters:

  DOMNode -

• processBinaryDocument

  protected void processBinaryDocument() throws Exception

  Throws:

  Exception

• initializeReader

  protected void initializeReader() throws Exception

  Throws:

  Exception

• checkLine

  protected boolean checkLine() throws Exception

  Returns:

  true if need to read new line

  Throws:

  Exception

• checkLastModel

  public boolean checkLastModel()

  sets continuing and doProcessLines

  Returns:

  TRUE if continuing, FALSE if not

• isLastModel

  public boolean isLastModel(int modelNumber)

  after reading a model, Q: Is this the last model?

  Parameters:

  modelNumber -

  Returns:

  Yes/No

• appendLoadNote

  public void appendLoadNote(String info)

• initializeTrajectoryFile

  protected void initializeTrajectoryFile()

• finalizeSubclassReader

  protected void finalizeSubclassReader() throws Exception

  Throws:

  Exception

• finalizeReaderASCR

  protected void finalizeReaderASCR() throws Exception

  Throws:

  Exception

• setLoadNote

  protected String setLoadNote()

  //////////////////////////////////////////////////////////////////////////////////

• setIsPDB

  public void setIsPDB()

• setModelPDB

  protected void setModelPDB(boolean isPDB)

• parsePrecision

  protected float parsePrecision(String s)

  Track the precision (count of y digits in "xx.yyyy") for setting cellSlop. We assume that with the numbers 0.25 0.33333 that the precision is really 5, not 2. Note that in the end, the precision will never be set lower than 4.

  Parameters:

  s -

  Returns:

  parsed number

• setPrecision

  protected void setPrecision()

  Called by PWMAT ALWAYS and CIFReader as well if a double-precision value for alpha is found.

• initializeSymmetryOptions

  protected void initializeSymmetryOptions()

• doGetModel

  public boolean doGetModel(int modelNumber, String title)

• discardPreviousAtoms

  protected void discardPreviousAtoms()

• initializeSymmetry

  protected final void initializeSymmetry()

• newAtomSet

  protected void newAtomSet(String name)

• cloneLastAtomSet

  protected int cloneLastAtomSet(int ac, P3[] pts) throws Exception

  Throws:

  Exception

• setSpaceGroupName

  public void setSpaceGroupName(String name)

• setSymmetryOperator

  public int setSymmetryOperator(String xyz)

• warnSkippingOperation

  protected void warnSkippingOperation(String xyz)

• clearUnitCell

  public void clearUnitCell()

• setUnitCellItem

  public void setUnitCellItem(int i, float x)

• setUnitCell

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

• addExplicitLatticeVector

  public void addExplicitLatticeVector(int i, float[] xyz, int i0)

• getSymmetry

  public XtalSymmetry.FileSymmetry getSymmetry()

• fractionalizeCoordinates

  protected void fractionalizeCoordinates(boolean toFrac)

• setFractionalCoordinates

  public void setFractionalCoordinates(boolean TF)

• setFilterAtomTypeStr

  protected void setFilterAtomTypeStr(String s)

• setFilter

  protected void setFilter(String filter0)

• getFilterWithCase

  public String getFilterWithCase(String key)

• getFilter

  public String getFilter(String key)

• checkFilterKey

  public boolean checkFilterKey(String key)

• checkAndRemoveFilterKey

  public boolean checkAndRemoveFilterKey(String key)

  Parameters:

  key -

  Returns:

  true if the key existed; filter is set null if this is the only key

• filterAtom

  protected boolean filterAtom(Atom atom, int iAtom)

  Parameters:

  atom -

  iAtom -

  Returns:

  true if we want this atom

• rejectAtomName

  public boolean rejectAtomName(String name)

• filterReject

  protected boolean filterReject(String f, String code, String atomCode)

• set2D

  protected void set2D()

• doGetVibration

  public boolean doGetVibration(int vibrationNumber)

• setTransform

  public void setTransform(float x1, float y1, float z1, float x2, float y2, float z2, float x3, float y3, float z3)

• setAtomCoordXYZ

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

  //////////////////////////

• setAtomCoordScaled

  public Atom setAtomCoordScaled(Atom atom, String[] tokens, int i, float f)

• setAtomCoordTokens

  protected void setAtomCoordTokens(Atom atom, String[] tokens, int i)

• addAtomXYZSymName

  public Atom addAtomXYZSymName(String[] tokens, int i, String sym, String name)

• setAtomCoord

  public void setAtomCoord(Atom atom)

• addSites

  public void addSites(Map<String, Map<String,Object>> htSites)

• applySymmetryAndSetTrajectory

  public void applySymmetryAndSetTrajectory() throws Exception

  Throws:

  Exception

• applySymTrajASCR

  public XtalSymmetry.FileSymmetry applySymTrajASCR() throws Exception

  Throws:

  Exception

• finalizeSubclassSymmetry

  protected void finalizeSubclassSymmetry(boolean haveSymmetry) throws Exception

  Parameters:

  haveSymmetry -

  Throws:

  Exception

• doPreSymmetry

  protected void doPreSymmetry(boolean doApplySymmetry) throws Exception

  Throws:

  Exception

• finalizeMOData

  public void finalizeMOData(Map<String,Object> moData)

• getElementSymbol

  public static String getElementSymbol(int elementNumber)

• fillDataBlock

  protected void fillDataBlock(String[][] data, int minLineLen) throws Exception

  fills an array with a pre-defined number of lines of token data, skipping blank lines in the process

  Parameters:

  data -

  minLineLen -

  Throws:

  Exception

• fill3x3

  protected double[][] fill3x3(String[] tokens, int pt) throws Exception

  fills a double[3][3]

  Parameters:

  tokens - or null if to read each line for three values (as last 3 on line)

  pt - initial index; if tokens == null, then negative index is from end of each line

  Returns:

  double[3][3]

  Throws:

  Exception

• fillFloatArray

  protected float[] fillFloatArray(String s, int width, float[] data) throws Exception

  fills a float array with string data from a file

  Parameters:

  s - string data containing floats

  width - column width or 0 to read tokens

  data - result data to be filled

  Returns:

  data

  Throws:

  Exception

• fillFrequencyData

  protected void fillFrequencyData(int iAtom0, int ac, int modelAtomCount, boolean[] ignore, boolean isWide, int col0, int colWidth, int[] atomIndexes, int minLineLen, String[][] data) throws Exception

  Extracts a block of frequency data from a file. This block may be of two types -- either X Y Z across a row or each of X Y Z on a separate line. Data is presumed to be in fixed FORTRAN-like column format, not space-separated columns.

  Parameters:

  iAtom0 - the first atom to be assigned a frequency

  ac - the number of atoms to be assigned

  modelAtomCount - the number of atoms in each model

  ignore - the frequencies to ignore because the user has selected only certain vibrations to be read or for whatever reason; length serves to set the number of frequencies to be read

  isWide - when TRUE, this is a table that has X Y Z for each mode within the same row; when FALSE, this is a table that has X Y Z for each mode on a separate line.

  col0 - the column in which data starts

  colWidth - the width of the data columns

  atomIndexes - an array either null or indicating exactly which atoms get the frequencies (used by CrystalReader)

  minLineLen -

  data -

  Throws:

  Exception

• fillDataBlockFixed

  protected void fillDataBlockFixed(String[][] data, int col0, int colWidth, int minLineLen) throws Exception

  Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format. Used exclusively for frequency data

  Parameters:

  data -

  col0 -

  colWidth -

  minLineLen - or -ptNonblank

  Throws:

  Exception

• readLines

  protected String readLines(int nLines) throws Exception

  Throws:

  Exception

• discardLinesUntilStartsWith

  public String discardLinesUntilStartsWith(String startsWith) throws Exception

  Throws:

  Exception

• discardLinesUntilContains

  public String discardLinesUntilContains(String containsMatch) throws Exception

  Throws:

  Exception

• discardLinesUntilContains2

  public String discardLinesUntilContains2(String s1, String s2) throws Exception

  Throws:

  Exception

• discardLinesUntilBlank

  public String discardLinesUntilBlank() throws Exception

  Throws:

  Exception

• discardLinesUntilNonBlank

  public String discardLinesUntilNonBlank() throws Exception

  Throws:

  Exception

• checkLineForScript

  protected void checkLineForScript(String line)

• checkCurrentLineForScript

  public void checkCurrentLineForScript()

• addJmolScript

  public void addJmolScript(String script)

• addSiteScript

  protected void addSiteScript(String script)

• rd

  public String rd() throws Exception

  Throws:

  Exception

• RL

  public String RL() throws Exception

  Throws:

  Exception

• getStrings

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

• getTokens

  public String[] getTokens()

• getTokensFloat

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

• parseFloat

  protected float parseFloat()

• parseFloatStr

  public float parseFloatStr(String s)

• parseFloatRange

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

• parseInt

  protected int parseInt()

• parseIntStr

  public int parseIntStr(String s)

• parseIntAt

  public int parseIntAt(String s, int iStart)

• parseIntRange

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

• parseToken

  protected String parseToken()

• parseTokenStr

  protected String parseTokenStr(String s)

• parseTokenNext

  protected String parseTokenNext(String s)

• parseTokenRange

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

• getFortranFormatLengths

  protected static Lst<Integer> getFortranFormatLengths(String s)

  get all integers after letters negative entries are spaces (1Xn)

  Parameters:

  s -

  Returns:

  Vector of integers

• read3Vectors

  protected V3[] read3Vectors(boolean isBohr) throws Exception

  read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block

  Parameters:

  isBohr -

  Returns:

  three vectors

  Throws:

  Exception

• setElementAndIsotope

  protected void setElementAndIsotope(Atom atom, String str)

  allow 13C, 15N, 2H, etc. for isotopes

  Parameters:

  atom -

  str -

• finalizeModelSet

  public void finalizeModelSet()

• setChainID

  public void setChainID(Atom atom, String label)

• readNextLine

  public String readNextLine() throws Exception

  Specified by:

  readNextLine in interface GenericLineReader

  Throws:

  Exception

• addMoreUnitCellInfo

  public void addMoreUnitCellInfo(String info)

• getInterface

  public Object getInterface(String className)

• forceSymmetry

  public void forceSymmetry(boolean andPack)

• fixFloatA

  public void fixFloatA(float[] pts)

• fixDoubleA

  public void fixDoubleA(double[] pts)

• fixFloatPt

  public void fixFloatPt(P3 pt, float prec)