java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.simple.InputReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

MopacArchiveReader
```
public class InputReader
extends AtomSetCollectionReader
```

Field Summary

Fields
Modifier and Type	Field	Description
`protected int`	`ac`
`private java.util.Map<java.lang.String,java.lang.Integer>`	`atomMap`
`private boolean`	`firstLine`
`private boolean`	`isHeader`
`private boolean`	`isJmolZformat`
`private boolean`	`isMopac`
`private javajs.util.Lst<java.lang.String[]>`	`lineBuffer`
`private javajs.util.P4`	`plane1`
`private javajs.util.P4`	`plane2`
`private javajs.util.P3`	`pt0`
`private java.util.Map<java.lang.String,java.lang.Float>`	`symbolicMap`
`private java.lang.String[]`	`tokens`
`private javajs.util.V3`	`v1`
`private javajs.util.V3`	`v2`
`protected javajs.util.Lst<Atom>`	`vAtoms`

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

InputReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`private java.lang.String`	`cleanLine()`
`protected void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`private Atom`	`getAtom()`
`private Atom`	`getAtomGeneral(Atom atom, int ia, int bondOrder)`
`private int`	`getAtomIndex(int i)`
`private void`	`getSymbolic()`
`private float`	`getSymbolic(java.lang.String key)`
`private float`	`getValue(int i)`
`private void`	`parseAtomTokens(Atom atom, java.lang.String element)`
`private boolean`	`readBlock(java.lang.String strEnd)`
`private void`	`readCFI()`
`private void`	`readConFile()`
`private boolean`	`readVFI()`
`protected Atom`	`setAtom(Atom atom, int ia, int ib, int ic, float d, float theta1, float theta2)`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

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

Field Detail

ac
```
protected int ac
```

vAtoms
```
protected javajs.util.Lst<Atom> vAtoms
```

atomMap

private java.util.Map<java.lang.String,java.lang.Integer> atomMap

tokens
```
private java.lang.String[] tokens
```

isJmolZformat
```
private boolean isJmolZformat
```

lineBuffer

private javajs.util.Lst<java.lang.String[]> lineBuffer

symbolicMap

private java.util.Map<java.lang.String,java.lang.Float> symbolicMap

isMopac
```
private boolean isMopac
```

isHeader
```
private boolean isHeader
```

firstLine
```
private boolean firstLine
```

pt0
```
private final javajs.util.P3 pt0
```

v1
```
private final javajs.util.V3 v1
```

v2
```
private final javajs.util.V3 v2
```

plane1
```
private final javajs.util.P4 plane1
```

plane2
```
private final javajs.util.P4 plane2
```

Constructor Detail
- InputReader
```
public InputReader()
```

Method Detail

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

readConFile

private void readConFile()
                  throws java.lang.Exception

Throws:: java.lang.Exception

readCFI

private void readCFI()
              throws java.lang.Exception

Throws:: java.lang.Exception

readVFI

private boolean readVFI()
                 throws java.lang.Exception

Throws:: java.lang.Exception

readBlock

private boolean readBlock(java.lang.String strEnd)
                   throws java.lang.Exception

Throws:: java.lang.Exception

cleanLine
```
private java.lang.String cleanLine()
```

finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               throws java.lang.Exception
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

getSymbolic
```
private void getSymbolic()
```

getAtom

private Atom getAtom()
              throws java.lang.Exception

Throws:: java.lang.Exception

parseAtomTokens

private void parseAtomTokens(Atom atom,
                             java.lang.String element)
                      throws java.lang.Exception

Throws:: java.lang.Exception

getAtomGeneral

private Atom getAtomGeneral(Atom atom,
                            int ia,
                            int bondOrder)
                     throws java.lang.Exception

Throws:: java.lang.Exception

getSymbolic

private float getSymbolic(java.lang.String key)

getValue

private float getValue(int i)
                throws java.lang.Exception

Throws:: java.lang.Exception

getAtomIndex
```
private int getAtomIndex(int i)
```

setAtom

protected Atom setAtom(Atom atom,
                       int ia,
                       int ib,
                       int ic,
                       float d,
                       float theta1,
                       float theta2)

Class InputReader

Field Summary

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

Methods inherited from class java.lang.Object

Field Detail

ac

vAtoms

atomMap

tokens

isJmolZformat

lineBuffer

symbolicMap

isMopac

isHeader

firstLine

pt0

v1

v2

plane1

plane2

Constructor Detail

InputReader

Method Detail

checkLine

readConFile

readCFI

readVFI

readBlock

cleanLine

finalizeSubclassReader

getSymbolic

getAtom

parseAtomTokens

getAtomGeneral

getSymbolic

getValue

getAtomIndex

setAtom