java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.AbinitReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class AbinitReader extends AtomSetCollectionReader

Field Summary

Fields

Modifier and Type

Field

Description

(package private) float[]

cellLattice

private boolean

inputOnly

private int

nAtom

private int

nType

private float[]

typeArray

private float[]

znucl

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

AbinitReader()
Method Summary

Modifier and Type

Method

Description

private void

applySymmetry()

protected boolean

checkLine()

protected void

initializeReader()

private void

readAtoms()

private void

readAtomSpecies()

private void

readIntiallattice()

private void

readNoatom()

private void

readNotypes()

private void

readSpaceGroup()

private void

readTypesequence()

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, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, 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
- znucl
  
  private float[] znucl
- inputOnly
  
  private boolean inputOnly
- nAtom
  
  private int nAtom
- nType
  
  private int nType
- typeArray
  
  private float[] typeArray
- cellLattice
  
  float[] cellLattice
Constructor Details
- AbinitReader
  
  public AbinitReader()
Method Details
- initializeReader
  
  protected void initializeReader()
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- readNoatom
  
  private void readNoatom() throws Exception
  
  Throws:
  
  Exception
- readNotypes
  
  private void readNotypes() throws Exception
  
  Throws:
  
  Exception
- readTypesequence
  
  private void readTypesequence() throws Exception
  
  Throws:
  
  Exception
- readAtomSpecies
  
  private void readAtomSpecies() throws Exception
  
  Throws:
  
  Exception
- readSpaceGroup
  
  private void readSpaceGroup() throws Exception
  
  Throws:
  
  Exception
- readIntiallattice
  
  private void readIntiallattice() throws Exception
  
  Throws:
  
  Exception
- applySymmetry
  
  private void applySymmetry() throws Exception
  
  Throws:
  
  Exception
- readAtoms
  
  private void readAtoms() throws Exception
  
  Throws:
  
  Exception

Class AbinitReader

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

znucl

inputOnly

nAtom

nType

typeArray

cellLattice

Constructor Details

AbinitReader

Method Details

initializeReader

checkLine

readNoatom

readNotypes

readTypesequence

readAtomSpecies

readSpaceGroup

readIntiallattice

applySymmetry

readAtoms