org.jmol.adapter.readers.spartan.SpartanSmolReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class SpartanSmolReader extends SpartanInputReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
Field Summary

Fields

Modifier and Type

Field

Description

private static final String

endCheck

private boolean

espCharges

private boolean

haveCharges

private boolean

iHaveModelStatement

private boolean

iHaveNewDir

private boolean

inputOnly

private boolean

isCompoundDocument

private boolean

isInputFirst

private boolean

natCharges

(package private) SpartanArchive

spartanArchive

private String

title

(package private) Map<String,String>

titles

Fields inherited from class org.jmol.adapter.readers.spartan.SpartanInputReader
bondData, constraints, modelAtomCount

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells, slaterArray, slaters

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

SpartanSmolReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkLine()

protected void

finalizeSubclassReader()

optional reader-specific method run first.

protected void

initializeReader()

private void

makeNewAtomSet()

private String

readArchive()

private String

readArchiveHeader()

private void

readMyTransform()

private void

readOutput()

private void

readProperties()

private void

setCharges()

void

setEnergy(float value)

Methods inherited from class org.jmol.adapter.readers.spartan.SpartanInputReader
readInputRecords, readTransform

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

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, 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, 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
- iHaveModelStatement
  
  private boolean iHaveModelStatement
- isCompoundDocument
  
  private boolean isCompoundDocument
- inputOnly
  
  private boolean inputOnly
- espCharges
  
  private boolean espCharges
- natCharges
  
  private boolean natCharges
- isInputFirst
  
  private boolean isInputFirst
- iHaveNewDir
  
  private boolean iHaveNewDir
- endCheck
  
  private static final String endCheck
  See Also:
  
  Constant Field Values
- title
  
  private String title
- spartanArchive
  
  SpartanArchive spartanArchive
- titles
  
  Map<String,String> titles
- haveCharges
  
  private boolean haveCharges
Constructor Details
- SpartanSmolReader
  
  public SpartanSmolReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- makeNewAtomSet
  
  private void makeNewAtomSet()
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- readMyTransform
  
  private void readMyTransform() throws Exception
  
  Throws:
  
  Exception
- readOutput
  
  private void readOutput() throws Exception
  
  Throws:
  
  Exception
- readArchive
  
  private String readArchive() throws Exception
  
  Throws:
  
  Exception
- setCharges
  
  private void setCharges()
- readProperties
  
  private void readProperties() throws Exception
  
  Throws:
  
  Exception
- readArchiveHeader
  
  private String readArchiveHeader() throws Exception
  
  Throws:
  
  Exception
- setEnergy
  
  public void setEnergy(float value)

Class SpartanSmolReader

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.spartan.SpartanInputReader

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.spartan.SpartanInputReader

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

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

Methods inherited from class java.lang.Object

Field Details

iHaveModelStatement

isCompoundDocument

inputOnly

espCharges

natCharges

isInputFirst

iHaveNewDir

endCheck

title

spartanArchive

titles

haveCharges

Constructor Details

SpartanSmolReader

Method Details

initializeReader

checkLine

makeNewAtomSet

finalizeSubclassReader

readMyTransform

readOutput

readArchive

setCharges

readProperties

readArchiveHeader

setEnergy