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 Map<String,Integer>

atomMap

private boolean

firstLine

private boolean

isHeader

private boolean

isJmolZformat

private boolean

isMopac

private javajs.util.Lst<String[]>

lineBuffer

private final javajs.util.P4

plane1

private final javajs.util.P4

plane2

private final javajs.util.P3

pt0

private Map<String,Float>

symbolicMap

private String[]

tokens

private final javajs.util.V3

v1

private final javajs.util.V3

v2

protected javajs.util.Lst<Atom>

vAtoms

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor Summary

Constructors

Constructor

Description

InputReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

private 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(String key)

private float

getValue(int i)

private void

parseAtomTokens(Atom atom, String element)

private boolean

readBlock(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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, 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 Details
- ac
  
  protected int ac
- vAtoms
  
  protected javajs.util.Lst<Atom> vAtoms
- atomMap
  
  private Map<String,Integer> atomMap
- tokens
  
  private String[] tokens
- isJmolZformat
  
  private boolean isJmolZformat
- lineBuffer
  
  private javajs.util.Lst<String[]> lineBuffer
- symbolicMap
  
  private Map<String,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 Details
- InputReader
  
  public InputReader()
Method Details
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readConFile
  
  private void readConFile() throws Exception
  
  Throws:
  
  Exception
- readCFI
  
  private void readCFI() throws Exception
  
  Throws:
  
  Exception
- readVFI
  
  private boolean readVFI() throws Exception
  
  Throws:
  
  Exception
- readBlock
  
  private boolean readBlock(String strEnd) throws Exception
  
  Throws:
  
  Exception
- cleanLine
  
  private String cleanLine()
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- getSymbolic
  
  private void getSymbolic()
- getAtom
  
  private Atom getAtom() throws Exception
  
  Throws:
  
  Exception
- parseAtomTokens
  
  private void parseAtomTokens(Atom atom, String element) throws Exception
  
  Throws:
  
  Exception
- getAtomGeneral
  
  private Atom getAtomGeneral(Atom atom, int ia, int bondOrder) throws Exception
  
  Throws:
  
  Exception
- getSymbolic
  
  private float getSymbolic(String key)
- getValue
  
  private float getValue(int i) throws Exception
  
  Throws:
  
  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 Details

ac

vAtoms

atomMap

tokens

isJmolZformat

lineBuffer

symbolicMap

isMopac

isHeader

firstLine

pt0

v1

v2

plane1

plane2

Constructor Details

InputReader

Method Details

checkLine

readConFile

readCFI

readVFI

readBlock

cleanLine

finalizeSubclassReader

getSymbolic

getAtom

parseAtomTokens

getAtomGeneral

getSymbolic

getValue

getAtomIndex

setAtom