java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

AbinitReader, AimsReader, AlchemyReader, AmpacReader, BasisFunctionReader, BilbaoReader, BinaryDcdReader, CastepReader, CgdReader, CifReader, CrystalReader, CubeReader, DmolReader, EspressoReader, FAHReader, FoldingXyzReader, ForceFieldReader, GaussianWfnReader, GhemicalMMReader, GromacsReader, GulpReader, HyperChemReader, InputReader, JanaReader, JmeReader, JSONReader, MagresReader, MdCrdReader, MolReader, MopacReader, PdbReader, ShelxReader, SiestaReader, TlsDataOnlyReader, VaspOutcarReader, VaspPoscarReader, Wien2kReader, XcrysdenReader, XmlReader, XyzReader
```
public abstract class AtomSetCollectionReader
extends Object
implements javajs.api.GenericLineReader
```

Field Summary

Fields
Modifier and Type	Field	Description
`String`	`addedData`
`String`	`addedDataKey`
`protected boolean`	`addVibrations`
`boolean`	`allow_a_len_1`
`protected boolean`	`allowPDBFilter`
`static float`	`ANGSTROMS_PER_BOHR`
`boolean`	`applySymmetryToBonds`
`AtomSetCollection`	`asc`
`int`	`baseAtomIndex`
`protected javajs.api.GenericBinaryDocument`	`binaryDoc`
`protected javajs.util.BS`	`bsFilter`
`protected javajs.util.BS`	`bsModels`
`String`	`calculationType`
`(package private) boolean`	`centroidPacked`
`boolean`	`continuing`
`boolean`	`debugging`
`protected int`	`desiredModelNumber`
`int`	`desiredSpaceGroupIndex`
`int`	`desiredVibrationNumber`
`boolean`	`doApplySymmetry`
`protected boolean`	`doCentralize`
`(package private) boolean`	`doCentroidUnitCell`
`protected boolean`	`doCheckUnitCell`
`boolean`	`doConvertToFractional`
`private Object`	`domains`
`boolean`	`doPackUnitCell`
`boolean`	`doProcessLines`
`boolean`	`doReadMolecularOrbitals`
`private boolean`	`doSetOrientation`
`Object`	`dssr`
`(package private) boolean`	`fileCoordinatesAreFractional`
`protected String`	`fileName`
`protected javajs.util.P3`	`fileOffset`
`private javajs.util.P3`	`fileOffsetFractional`
`protected String`	`filePath`
`protected javajs.util.P3`	`fileScaling`
`Object`	`fillRange`
`String`	`filter`
`private String`	`filter1`
`private String`	`filter2`
`private boolean`	`filterAltLoc`
`private boolean`	`filterAtomName`
`private String`	`filterAtomNameTerminator`
`private boolean`	`filterAtomType`
`private String`	`filterAtomTypeStr`
`private boolean`	`filterChain`
`private boolean`	`filterElement`
`private boolean`	`filterEveryNth`
`private boolean`	`filterGroup3`
`protected boolean`	`filterHetero`
`private int`	`filterN`
`(package private) String`	`filterSymop`
`private int[]`	`firstLastStep`
`boolean`	`fixJavaFloat`
`protected boolean`	`forcePacked`
`protected boolean`	`getHeader`
`boolean`	`haveAtomFilter`
`protected boolean`	`haveModel`
`protected boolean`	`havePartialChargeFilter`
`Map<String,Object>`	`htParams`
`protected boolean`	`ignoreFileSpaceGroupName`
`protected boolean`	`ignoreFileSymmetryOperators`
`protected boolean`	`ignoreFileUnitCell`
`protected boolean`	`ignoreStructure`
`protected boolean`	`iHaveFractionalCoordinates`
`boolean`	`iHaveSymmetryOperators`
`boolean`	`iHaveUnitCell`
`boolean`	`isBinary`
`protected boolean`	`isConcatenated`
`protected boolean`	`isDSSP1`
`protected boolean`	`isFinalized`
`boolean`	`isMolecular`
`protected boolean`	`isPrimitive`
`protected boolean`	`isSequential`
`protected boolean`	`isTrajectory`
`private int`	`lastModelNumber`
`int[]`	`latticeCells`
`protected float`	`latticeScaling`
`protected String`	`latticeType`
`String`	`line`
`private javajs.util.SB`	`loadNote`
`javajs.util.Lst<javajs.util.M4>`	`lstNCS`
`private javajs.util.M3`	`matRot`
`protected javajs.util.M3`	`matUnitCellOrientation`
`(package private) boolean`	`merging`
`int`	`modDim`
`int`	`modelNumber`
`private javajs.util.Lst<String>`	`moreUnitCellInfo`
`MSInterface`	`ms`
`protected boolean`	`mustFinalizeModelSet`
`private String`	`nameRequired`
`protected int[]`	`next`
`private int`	`nFiltered`
`private int`	`nMatrixElements`
`protected javajs.util.OC`	`out`
`float`	`packingError`
`private String`	`previousScript`
`private String`	`previousSpaceGroup`
`private float[]`	`previousUnitCell`
`String`	`prevline`
`javajs.util.M3`	`primitiveToCrystal`
`protected int`	`ptLine`
`protected javajs.util.P3`	`ptSupercell`
`protected BufferedReader`	`reader`
`protected String`	`readerName`
`protected boolean`	`requiresBSFilter`
`protected boolean`	`reverseModels`
`protected boolean`	`rotateHexCell`
`protected String`	`sgName`
`private String`	`siteScript`
`protected int`	`stateScriptVersionInt`
`String`	`strSupercell`
`SymmetryInterface`	`symmetry`
`(package private) float`	`symmetryRange`
`protected int`	`templateAtomCount`
`Map<String,Object>`	`thisBiomolecule`
`javajs.util.Lst<javajs.util.P3[]>`	`trajectorySteps`
`float[]`	`ucItems`
`protected javajs.util.P3`	`unitCellOffset`
`private boolean`	`unitCellOffsetFractional`
`float[]`	`unitCellParams`
`protected boolean`	`useAltNames`
`protected boolean`	`useFileModelNumbers`
`Object`	`validation`
`int`	`vibrationNumber`
`boolean`	`vibsFractional`
`Viewer`	`vwr`

Constructor Summary

Constructors
Constructor Description

AtomSetCollectionReader()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Atom`	`addAtomXYZSymName(String[] tokens, int i, String sym, String name)`
`void`	`addExplicitLatticeVector(int i, float[] xyz, int i0)`
`void`	`addJmolScript(String script)`
`void`	`addSites(Map<String,Map<String,Object>> htSites)`
`protected void`	`addSiteScript(String script)`
`private boolean`	`allowAtomName(String atomName, String f)`
`void`	`appendLoadNote(String info)`
`void`	`appendUunitCellInfo(String info)`
`void`	`applySymmetryAndSetTrajectory()`
`SymmetryInterface`	`applySymTrajASCR()`
`void`	`checkCurrentLineForScript()`
`private boolean`	`checkFilter(Atom atom, String f)`
`boolean`	`checkFilterKey(String key)`
`boolean`	`checkLastModel()`	sets continuing and doProcessLines
`protected boolean`	`checkLine()`
`protected void`	`checkLineForScript(String line)`
`private boolean`	`checkUnitCell(int n)`
`private void`	`checkUnitCellOffset()`
`void`	`clearUnitCell()`
`protected int`	`cloneLastAtomSet(int ac, javajs.util.P3[] pts)`
`String`	`discardLinesUntilBlank()`
`String`	`discardLinesUntilContains(String containsMatch)`
`String`	`discardLinesUntilContains2(String s1, String s2)`
`String`	`discardLinesUntilNonBlank()`
`String`	`discardLinesUntilStartsWith(String startsWith)`
`protected void`	`discardPreviousAtoms()`
`boolean`	`doGetModel(int modelNumber, String title)`
`boolean`	`doGetVibration(int vibrationNumber)`
`protected void`	`doPreSymmetry()`
`protected double[][]`	`fill3x3(String[] tokens, int pt)`	fills a double[3][3]
`protected void`	`fillDataBlock(String[][] data, int minLineLen)`	fills an array with a pre-defined number of lines of token data, skipping blank lines in the process
`protected void`	`fillDataBlockFixed(String[][] data, int col0, int colWidth, int minLineLen)`	Fills an array with a predefined number of lines of data that is arranged in fixed FORTRAN-like column format.
`protected float[]`	`fillFloatArray(String s, int width, float[] data)`	fills a float array with string data from a file
`protected void`	`fillFrequencyData(int iAtom0, int ac, int modelAtomCount, boolean[] ignore, boolean isWide, int col0, int colWidth, int[] atomIndexes, int minLineLen, String[][] data)`	Extracts a block of frequency data from a file.
`protected boolean`	`filterAtom(Atom atom, int iAtom)`
`protected boolean`	`filterReject(String f, String code, String atomCode)`
`void`	`finalizeMOData(Map<String,Object> moData)`
`void`	`finalizeModelSet()`
`protected void`	`finalizeReaderASCR()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`protected void`	`finalizeSubclassSymmetry(boolean haveSymmetry)`
`private Object`	`finish()`
`private void`	`fixBaseIndices()`
`void`	`forceSymmetry(boolean andPack)`
`protected void`	`fractionalizeCoordinates(boolean toFrac)`
`static String`	`getElementSymbol(int elementNumber)`
`String`	`getFilter(String key)`
`protected static javajs.util.Lst<Integer>`	`getFortranFormatLengths(String s)`	get all integers after letters negative entries are spaces (1Xn)
`Object`	`getInterface(String className)`
`protected SymmetryInterface`	`getNewSymmetry()`
`protected static String[]`	`getStrings(String sinfo, int nFields, int width)`
`protected SymmetryInterface`	`getSymmetry()`
`String[]`	`getTokens()`
`static float[]`	`getTokensFloat(String s, float[] f, int n)`
`private void`	`initialize()`
`private void`	`initializeCartesianToFractional()`
`protected void`	`initializeReader()`
`protected void`	`initializeSymmetry()`
`protected void`	`initializeSymmetryOptions()`
`protected void`	`initializeTrajectoryFile()`
`boolean`	`isLastModel(int modelNumber)`	after reading a model, Q: Is this the last model?
`protected void`	`newAtomSet(String name)`
`protected float`	`parseFloat()`
`protected float`	`parseFloatRange(String s, int iStart, int iEnd)`
`float`	`parseFloatStr(String s)`
`protected int`	`parseInt()`
`int`	`parseIntAt(String s, int iStart)`
`protected int`	`parseIntRange(String s, int iStart, int iEnd)`
`int`	`parseIntStr(String s)`
`protected String`	`parseToken()`
`protected String`	`parseTokenNext(String s)`
`protected String`	`parseTokenRange(String s, int iStart, int iEnd)`
`protected String`	`parseTokenStr(String s)`
`protected void`	`processBinaryDocument()`
`protected void`	`processDOM(Object DOMNode)`
`String`	`rd()`
`protected javajs.util.V3[]`	`read3Vectors(boolean isBohr)`	read three vectors, as for unit cube definitions allows for non-numeric data preceding the number block
`(package private) Object`	`readData()`
`protected Object`	`readDataObject(Object node)`
`protected String`	`readLines(int nLines)`
`String`	`readNextLine()`
`boolean`	`rejectAtomName(String name)`
`String`	`RL()`
`protected void`	`set2D()`
`void`	`setAtomCoord(Atom atom)`
`Atom`	`setAtomCoordScaled(Atom atom, String[] tokens, int i, float f)`
`protected void`	`setAtomCoordTokens(Atom atom, String[] tokens, int i)`
`void`	`setAtomCoordXYZ(Atom atom, float x, float y, float z)`
`void`	`setChainID(Atom atom, String label)`
`protected void`	`setElementAndIsotope(Atom atom, String str)`	allow 13C, 15N, 2H, etc.
`private void`	`setError(Throwable e)`
`protected void`	`setFilter(String filter0)`
`protected void`	`setFilterAtomTypeStr(String s)`
`void`	`setFractionalCoordinates(boolean TF)`
`void`	`setIsPDB()`
`protected String`	`setLoadNote()`
`protected void`	`setModelPDB(boolean isPDB)`
`void`	`setSpaceGroupName(String name)`
`int`	`setSymmetryOperator(String xyz)`
`void`	`setTransform(float x1, float y1, float z1, float x2, float y2, float z2, float x3, float y3, float z3)`
`void`	`setUnitCell(float a, float b, float c, float alpha, float beta, float gamma)`
`void`	`setUnitCellItem(int i, float x)`
`protected void`	`setup(String fullPath, Map<String,Object> htParams, Object readerOrDocument)`
`protected void`	`setupASCR(String fullPath, Map<String,Object> htParams, Object readerOrDocument)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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 BufferedReader reader
```

binaryDoc

protected javajs.api.GenericBinaryDocument binaryDoc

readerName
```
protected String readerName
```

htParams
```
public Map<String,Object> htParams
```

trajectorySteps

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

domains
```
private Object domains
```

validation
```
public Object validation
```

dssr
```
public Object dssr
```

isConcatenated
```
protected boolean isConcatenated
```

addedData
```
public String addedData
```

addedDataKey
```
public String addedDataKey
```

fixJavaFloat
```
public boolean fixJavaFloat
```

thisBiomolecule

public Map<String,Object> thisBiomolecule

lstNCS

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

line
```
public String line
```

prevline
```
public String prevline
```

next
```
protected int[] next
```

ptLine
```
protected int ptLine
```

latticeType
```
protected String latticeType
```

latticeCells
```
public int[] latticeCells
```

fillRange
```
public 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 String calculationType
```

sgName
```
protected 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<String> moreUnitCellInfo

filePath
```
protected String filePath
```

fileName
```
protected String fileName
```

stateScriptVersionInt
```
protected int stateScriptVersionInt
```

baseAtomIndex
```
public int baseAtomIndex
```

isFinalized
```
protected boolean isFinalized
```

haveModel
```
protected boolean haveModel
```

previousSpaceGroup
```
private 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 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 String filterAtomTypeStr
```

filterAtomNameTerminator

private String filterAtomNameTerminator

filterElement
```
private boolean filterElement
```

filterHetero
```
protected boolean filterHetero
```

filterEveryNth
```
private boolean filterEveryNth
```

filterSymop
```
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 String nameRequired
```

doCentroidUnitCell
```
boolean doCentroidUnitCell
```

centroidPacked
```
boolean centroidPacked
```

strSupercell
```
public String strSupercell
```

allow_a_len_1
```
public boolean allow_a_len_1
```

filter1
```
private String filter1
```

filter2
```
private String filter2
```

matRot
```
private javajs.util.M3 matRot
```

ms
```
public MSInterface ms
```

vibsFractional
```
public boolean vibsFractional
```

previousScript
```
private String previousScript
```

siteScript
```
private String siteScript
```

Constructor Detail
- AtomSetCollectionReader
```
public AtomSetCollectionReader()
```

Method Detail

setup

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

setupASCR

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

readData

Object readData()
         throws Exception

Throws:: Exception

fixBaseIndices
```
private void fixBaseIndices()
```

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

optional reader-specific method run first.

Throws:: Exception

finalizeReaderASCR

protected void finalizeReaderASCR()
                           throws Exception

Throws:: Exception

setLoadNote
```
protected String setLoadNote()
```

setIsPDB
```
public void setIsPDB()
```

setModelPDB

protected void setModelPDB(boolean isPDB)

finish
```
private Object finish()
```

setError

private void setError(Throwable e)

Parameters:: e -

initialize
```
private void initialize()
```

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,
                               javajs.util.P3[] pts)
                        throws Exception

Throws:: Exception

setSpaceGroupName

public void setSpaceGroupName(String name)

setSymmetryOperator

public int setSymmetryOperator(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

protected 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(String s)

setFilter

protected void setFilter(String filter0)

getFilter

public String getFilter(String key)

checkFilterKey

public boolean checkFilterKey(String 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,
                            String f)

Parameters:: atom -; f -
Returns:: true if a filter is found

rejectAtomName

public boolean rejectAtomName(String name)

allowAtomName

private boolean allowAtomName(String atomName,
                              String f)

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 SymmetryInterface applySymTrajASCR()
                                   throws Exception

Throws:: Exception

finalizeSubclassSymmetry

protected void finalizeSubclassSymmetry(boolean haveSymmetry)
                                 throws Exception

Parameters:: haveSymmetry -
Throws:: Exception

doPreSymmetry

protected void doPreSymmetry()
                      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 - TODO

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 - TODO

data - TODO

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 javajs.util.Lst<Integer> getFortranFormatLengths(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 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 javajs.api.GenericLineReader

Throws:

Exception

appendUunitCellInfo

public void appendUunitCellInfo(String info)

getInterface

public Object getInterface(String className)

forceSymmetry

public void forceSymmetry(boolean andPack)

Class AtomSetCollectionReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

ANGSTROMS_PER_BOHR

isBinary

debugging

requiresBSFilter

primitiveToCrystal

asc

reader

binaryDoc

readerName

htParams

trajectorySteps

domains

validation

dssr

isConcatenated

addedData

addedDataKey

fixJavaFloat

thisBiomolecule

lstNCS

line

prevline

next

ptLine

latticeType

latticeCells

fillRange

doProcessLines

iHaveUnitCell

iHaveSymmetryOperators

continuing

vwr

doApplySymmetry

ignoreFileSymmetryOperators

isTrajectory

applySymmetryToBonds

doCheckUnitCell

getHeader

isSequential

isMolecular

templateAtomCount

modelNumber

vibrationNumber

desiredVibrationNumber

bsModels

useFileModelNumbers

havePartialChargeFilter

calculationType

sgName

ignoreFileUnitCell

ignoreFileSpaceGroupName

unitCellParams

desiredModelNumber

symmetry

out

iHaveFractionalCoordinates

doPackUnitCell

ptSupercell

mustFinalizeModelSet

forcePacked

packingError

rotateHexCell

isPrimitive

modDim

loadNote

doConvertToFractional

fileCoordinatesAreFractional

merging

symmetryRange

firstLastStep

lastModelNumber

desiredSpaceGroupIndex

fileScaling

latticeScaling