Field Detail

• ANGSTROMS_PER_BOHR

  public static final float ANGSTROMS_PER_BOHR

  See Also:

  Constant Field Values

• isBinary

  public boolean isBinary

• debugging

  public boolean debugging

• requiresBSFilter

  protected boolean requiresBSFilter

• primitiveToCrystal

  public javajs.util.M3 primitiveToCrystal

• asc

  public AtomSetCollection asc

• reader

  protected java.io.BufferedReader reader

• binaryDoc

  protected javajs.api.GenericBinaryDocument binaryDoc

• readerName

  protected java.lang.String readerName

• htParams

  public java.util.Map<java.lang.String,​java.lang.Object> htParams

• trajectorySteps

  public javajs.util.Lst<javajs.util.P3[]> trajectorySteps

• domains

  private java.lang.Object domains

• validation

  public java.lang.Object validation

• dssr

  public java.lang.Object dssr

• isConcatenated

  protected boolean isConcatenated

• addedData

  public java.lang.String addedData

• addedDataKey

  public java.lang.String addedDataKey

• fixJavaFloat

  public boolean fixJavaFloat

• thisBiomolecule

  public java.util.Map<java.lang.String,​java.lang.Object> thisBiomolecule

• lstNCS

  public javajs.util.Lst<javajs.util.M4> lstNCS

• line

  public java.lang.String line

• prevline

  public java.lang.String prevline

• next

  protected int[] next

• ptLine

  protected int ptLine

• latticeType

  protected java.lang.String latticeType

• latticeCells

  public int[] latticeCells

• fillRange

  public java.lang.Object fillRange

• doProcessLines

  public boolean doProcessLines

• iHaveUnitCell

  public boolean iHaveUnitCell

• iHaveSymmetryOperators

  public boolean iHaveSymmetryOperators

• continuing

  public boolean continuing

• vwr

  public Viewer vwr

• doApplySymmetry

  public boolean doApplySymmetry

• ignoreFileSymmetryOperators

  protected boolean ignoreFileSymmetryOperators

• isTrajectory

  protected boolean isTrajectory

• applySymmetryToBonds

  public boolean applySymmetryToBonds

• doCheckUnitCell

  protected boolean doCheckUnitCell

• getHeader

  protected boolean getHeader

• isSequential

  protected boolean isSequential

• isMolecular

  public boolean isMolecular

• templateAtomCount

  protected int templateAtomCount

• modelNumber

  public int modelNumber

• vibrationNumber

  public int vibrationNumber

• desiredVibrationNumber

  public int desiredVibrationNumber

• bsModels

  protected javajs.util.BS bsModels

• useFileModelNumbers

  protected boolean useFileModelNumbers

• havePartialChargeFilter

  protected boolean havePartialChargeFilter

• calculationType

  public java.lang.String calculationType

• sgName

  protected java.lang.String sgName

• ignoreFileUnitCell

  protected boolean ignoreFileUnitCell

• ignoreFileSpaceGroupName

  protected boolean ignoreFileSpaceGroupName

• unitCellParams

  public float[] unitCellParams

• desiredModelNumber

  protected int desiredModelNumber

• symmetry

  public SymmetryInterface symmetry

• out

  protected javajs.util.OC out

• iHaveFractionalCoordinates

  protected boolean iHaveFractionalCoordinates

• doPackUnitCell

  public boolean doPackUnitCell

• ptSupercell

  protected javajs.util.P3 ptSupercell

• mustFinalizeModelSet

  protected boolean mustFinalizeModelSet

• forcePacked

  protected boolean forcePacked

• packingError

  public float packingError

• rotateHexCell

  protected boolean rotateHexCell

• isPrimitive

  protected boolean isPrimitive

• modDim

  public int modDim

• loadNote

  private javajs.util.SB loadNote

• doConvertToFractional

  public boolean doConvertToFractional

• fileCoordinatesAreFractional

  boolean fileCoordinatesAreFractional

• merging

  boolean merging

• symmetryRange

  float symmetryRange

• firstLastStep

  private int[] firstLastStep

• lastModelNumber

  private int lastModelNumber

• desiredSpaceGroupIndex

  public int desiredSpaceGroupIndex

• fileScaling

  protected javajs.util.P3 fileScaling

• latticeScaling

  protected float latticeScaling

• fileOffset

  protected javajs.util.P3 fileOffset

• fileOffsetFractional

  private javajs.util.P3 fileOffsetFractional

• unitCellOffset

  protected javajs.util.P3 unitCellOffset

• unitCellOffsetFractional

  private boolean unitCellOffsetFractional

• moreUnitCellInfo

  private javajs.util.Lst<java.lang.String> moreUnitCellInfo

• paramsLattice

  public javajs.util.T3 paramsLattice

• paramsCentroid

  public boolean paramsCentroid

• paramsPacked

  private boolean paramsPacked

• filePath

  protected java.lang.String filePath

• fileName

  protected java.lang.String fileName

• baseAtomIndex

  public int baseAtomIndex

  first atom index for this collection, current modelset.ac

• baseBondIndex

  public int baseBondIndex

• stateScriptVersionInt

  protected int stateScriptVersionInt

• isFinalized

  protected boolean isFinalized

• haveModel

  protected boolean haveModel

• previousSpaceGroup

  private java.lang.String previousSpaceGroup

• previousUnitCell

  private float[] previousUnitCell

• nMatrixElements

  private int nMatrixElements

• ucItems

  public float[] ucItems

• matUnitCellOrientation

  protected javajs.util.M3 matUnitCellOrientation

• bsFilter

  protected javajs.util.BS bsFilter

• filter

  public java.lang.String filter

• haveAtomFilter

  public boolean haveAtomFilter

• filterAltLoc

  private boolean filterAltLoc

• filterGroup3

  private boolean filterGroup3

• filterChain

  private boolean filterChain

• filterAtomName

  private boolean filterAtomName

• filterAtomType

  private boolean filterAtomType

• filterAtomTypeStr

  private java.lang.String filterAtomTypeStr

• filterAtomNameTerminator

  private java.lang.String filterAtomNameTerminator

• filterElement

  private boolean filterElement

• filterHetero

  protected boolean filterHetero

• filterEveryNth

  private boolean filterEveryNth

• filterSymop

  java.lang.String filterSymop

• filterN

  private int filterN

• nFiltered

  private int nFiltered

• doSetOrientation

  private boolean doSetOrientation

• doCentralize

  protected boolean doCentralize

• addVibrations

  protected boolean addVibrations

• useAltNames

  protected boolean useAltNames

• ignoreStructure

  protected boolean ignoreStructure

• isDSSP1

  protected boolean isDSSP1

• allowPDBFilter

  protected boolean allowPDBFilter

• doReadMolecularOrbitals

  public boolean doReadMolecularOrbitals

• reverseModels

  protected boolean reverseModels

• nameRequired

  private java.lang.String nameRequired

• doCentroidUnitCell

  public boolean doCentroidUnitCell

• centroidPacked

  public boolean centroidPacked

• strSupercell

  public java.lang.String strSupercell

• allow_a_len_1

  public boolean allow_a_len_1

• filter1

  private java.lang.String filter1

• filter2

  private java.lang.String filter2

• matRot

  private javajs.util.M3 matRot

• ms

  public MSInterface ms

• vibsFractional

  public boolean vibsFractional

• previousScript

  private java.lang.String previousScript

• siteScript

  private java.lang.String siteScript

Constructor Detail

• AtomSetCollectionReader

  public AtomSetCollectionReader()

Method Detail

• setup

  protected void setup​(java.lang.String fullPath,
                       java.util.Map<java.lang.String,​java.lang.Object> htParams,
                       java.lang.Object readerOrDocument)

• setupASCR

  protected void setupASCR​(java.lang.String fullPath,
                           java.util.Map<java.lang.String,​java.lang.Object> htParams,
                           java.lang.Object readerOrDocument)

• readData

  java.lang.Object readData()
                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• fixBaseIndices

  private void fixBaseIndices()

• readDataObject

  protected java.lang.Object readDataObject​(java.lang.Object node)
                                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• processDOM

  protected void processDOM​(java.lang.Object DOMNode)

  Parameters:

  DOMNode -

• processBinaryDocument

  protected void processBinaryDocument()
                                throws java.lang.Exception

  Throws:

  java.lang.Exception

• initializeReader

  protected void initializeReader()
                           throws java.lang.Exception

  Throws:

  java.lang.Exception

• checkLine

  protected boolean checkLine()
                       throws java.lang.Exception

  Returns:

  true if need to read new line

  Throws:

  java.lang.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​(java.lang.String info)

• initializeTrajectoryFile

  protected void initializeTrajectoryFile()

• finalizeSubclassReader

  protected void finalizeSubclassReader()
                                 throws java.lang.Exception

  optional reader-specific method run first.

  Throws:

  java.lang.Exception

• finalizeReaderASCR

  protected void finalizeReaderASCR()
                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• setLoadNote

  protected java.lang.String setLoadNote()

• setIsPDB

  public void setIsPDB()

• setModelPDB

  protected void setModelPDB​(boolean isPDB)

• finish

  private java.lang.Object finish()

• setError

  private void setError​(java.lang.Throwable e)

  Parameters:

  e -

• initialize

  private void initialize()

• initializeSymmetryOptions

  protected void initializeSymmetryOptions()

• doGetModel

  public boolean doGetModel​(int modelNumber,
                            java.lang.String title)

• discardPreviousAtoms

  protected void discardPreviousAtoms()

• initializeSymmetry

  protected final void initializeSymmetry()

• newAtomSet

  protected void newAtomSet​(java.lang.String name)

• cloneLastAtomSet

  protected int cloneLastAtomSet​(int ac,
                                 javajs.util.P3[] pts)
                          throws java.lang.Exception

  Throws:

  java.lang.Exception

• setSpaceGroupName

  public void setSpaceGroupName​(java.lang.String name)

• setSymmetryOperator

  public int setSymmetryOperator​(java.lang.String xyz)

• initializeCartesianToFractional

  private void initializeCartesianToFractional()

• 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)

• checkUnitCell

  private boolean checkUnitCell​(int n)

• getSymmetry

  public SymmetryInterface getSymmetry()

• checkUnitCellOffset

  private void checkUnitCellOffset()

• fractionalizeCoordinates

  protected void fractionalizeCoordinates​(boolean toFrac)

• getNewSymmetry

  protected SymmetryInterface getNewSymmetry()

• setFractionalCoordinates

  public void setFractionalCoordinates​(boolean TF)

• setFilterAtomTypeStr

  protected void setFilterAtomTypeStr​(java.lang.String s)

• setFilter

  protected void setFilter​(java.lang.String filter0)

• getFilter

  public java.lang.String getFilter​(java.lang.String key)

• checkFilterKey

  public boolean checkFilterKey​(java.lang.String key)

• checkAndRemoveFilterKey

  public boolean checkAndRemoveFilterKey​(java.lang.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

• checkFilter

  private boolean checkFilter​(Atom atom,
                              java.lang.String f)

  Parameters:

  atom -

  f -

  Returns:

  true if a filter is found

• rejectAtomName

  public boolean rejectAtomName​(java.lang.String name)

• allowAtomName

  private boolean allowAtomName​(java.lang.String atomName,
                                java.lang.String f)

• filterReject

  protected boolean filterReject​(java.lang.String f,
                                 java.lang.String code,
                                 java.lang.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,
                                 java.lang.String[] tokens,
                                 int i,
                                 float f)

• setAtomCoordTokens

  protected void setAtomCoordTokens​(Atom atom,
                                    java.lang.String[] tokens,
                                    int i)

• addAtomXYZSymName

  public Atom addAtomXYZSymName​(java.lang.String[] tokens,
                                int i,
                                java.lang.String sym,
                                java.lang.String name)

• setAtomCoord

  public void setAtomCoord​(Atom atom)

• addSites

  public void addSites​(java.util.Map<java.lang.String,​java.util.Map<java.lang.String,​java.lang.Object>> htSites)

• applySymmetryAndSetTrajectory

  public void applySymmetryAndSetTrajectory()
                                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• applySymTrajASCR

  public SymmetryInterface applySymTrajASCR()
                                     throws java.lang.Exception

  Throws:

  java.lang.Exception

• finalizeSubclassSymmetry

  protected void finalizeSubclassSymmetry​(boolean haveSymmetry)
                                   throws java.lang.Exception

  Parameters:

  haveSymmetry -

  Throws:

  java.lang.Exception

• doPreSymmetry

  protected void doPreSymmetry()
                        throws java.lang.Exception

  Throws:

  java.lang.Exception

• finalizeMOData

  public void finalizeMOData​(java.util.Map<java.lang.String,​java.lang.Object> moData)

• getElementSymbol

  public static java.lang.String getElementSymbol​(int elementNumber)

• fillDataBlock

  protected void fillDataBlock​(java.lang.String[][] data,
                               int minLineLen)
                        throws java.lang.Exception

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

  Parameters:

  data -

  minLineLen - TODO

  Throws:

  java.lang.Exception

• fill3x3

  protected double[][] fill3x3​(java.lang.String[] tokens,
                               int pt)
                        throws java.lang.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:

  java.lang.Exception

• fillFloatArray

  protected float[] fillFloatArray​(java.lang.String s,
                                   int width,
                                   float[] data)
                            throws java.lang.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:

  java.lang.Exception

• fillFrequencyData

  protected void fillFrequencyData​(int iAtom0,
                                   int ac,
                                   int modelAtomCount,
                                   boolean[] ignore,
                                   boolean isWide,
                                   int col0,
                                   int colWidth,
                                   int[] atomIndexes,
                                   int minLineLen,
                                   java.lang.String[][] data)
                            throws java.lang.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 - TODO

  data - TODO

  Throws:

  java.lang.Exception

• fillDataBlockFixed

  protected void fillDataBlockFixed​(java.lang.String[][] data,
                                    int col0,
                                    int colWidth,
                                    int minLineLen)
                             throws java.lang.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:

  java.lang.Exception

• readLines

  protected java.lang.String readLines​(int nLines)
                                throws java.lang.Exception

  Throws:

  java.lang.Exception

• discardLinesUntilStartsWith

  public java.lang.String discardLinesUntilStartsWith​(java.lang.String startsWith)
                                               throws java.lang.Exception

  Throws:

  java.lang.Exception

• discardLinesUntilContains

  public java.lang.String discardLinesUntilContains​(java.lang.String containsMatch)
                                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• discardLinesUntilContains2

  public java.lang.String discardLinesUntilContains2​(java.lang.String s1,
                                                     java.lang.String s2)
                                              throws java.lang.Exception

  Throws:

  java.lang.Exception

• discardLinesUntilBlank

  public java.lang.String discardLinesUntilBlank()
                                          throws java.lang.Exception

  Throws:

  java.lang.Exception

• discardLinesUntilNonBlank

  public java.lang.String discardLinesUntilNonBlank()
                                             throws java.lang.Exception

  Throws:

  java.lang.Exception

• checkLineForScript

  protected void checkLineForScript​(java.lang.String line)

• checkCurrentLineForScript

  public void checkCurrentLineForScript()

• addJmolScript

  public void addJmolScript​(java.lang.String script)

• addSiteScript

  protected void addSiteScript​(java.lang.String script)

• rd

  public java.lang.String rd()
                      throws java.lang.Exception

  Throws:

  java.lang.Exception

• RL

  public java.lang.String RL()
                      throws java.lang.Exception

  Throws:

  java.lang.Exception

• getStrings

  protected static final java.lang.String[] getStrings​(java.lang.String sinfo,
                                                       int nFields,
                                                       int width)

• getTokens

  public java.lang.String[] getTokens()

• getTokensFloat

  public static float[] getTokensFloat​(java.lang.String s,
                                       float[] f,
                                       int n)

• parseFloat

  protected float parseFloat()

• parseFloatStr

  public float parseFloatStr​(java.lang.String s)

• parseFloatRange

  protected float parseFloatRange​(java.lang.String s,
                                  int iStart,
                                  int iEnd)

• parseInt

  protected int parseInt()

• parseIntStr

  public int parseIntStr​(java.lang.String s)

• parseIntAt

  public int parseIntAt​(java.lang.String s,
                        int iStart)

• parseIntRange

  protected int parseIntRange​(java.lang.String s,
                              int iStart,
                              int iEnd)

• parseToken

  protected java.lang.String parseToken()

• parseTokenStr

  protected java.lang.String parseTokenStr​(java.lang.String s)

• parseTokenNext

  protected java.lang.String parseTokenNext​(java.lang.String s)

• parseTokenRange

  protected java.lang.String parseTokenRange​(java.lang.String s,
                                             int iStart,
                                             int iEnd)

• getFortranFormatLengths

  protected static javajs.util.Lst<java.lang.Integer> getFortranFormatLengths​(java.lang.String s)

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

  Parameters:

  s -

  Returns:

  Vector of integers

• read3Vectors

  protected javajs.util.V3[] read3Vectors​(boolean isBohr)
                                   throws java.lang.Exception

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

  Parameters:

  isBohr -

  Returns:

  three vectors

  Throws:

  java.lang.Exception

• setElementAndIsotope

  protected void setElementAndIsotope​(Atom atom,
                                      java.lang.String str)

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

  Parameters:

  atom -

  str -

• finalizeModelSet

  public void finalizeModelSet()

• setChainID

  public void setChainID​(Atom atom,
                         java.lang.String label)

• readNextLine

  public java.lang.String readNextLine()
                                throws java.lang.Exception

  Specified by:

  readNextLine in interface javajs.api.GenericLineReader

  Throws:

  java.lang.Exception

• appendUunitCellInfo

  public void appendUunitCellInfo​(java.lang.String info)

• getInterface

  public java.lang.Object getInterface​(java.lang.String className)

• forceSymmetry

  public void forceSymmetry​(boolean andPack)