org.jmol.adapter.readers.quantum

Class SpartanSmolReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.quantum.SpartanInputReader

org.jmol.adapter.readers.quantum.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 and Description
private java.lang.String	endCheck
private boolean	espCharges
private boolean	haveCharges
private boolean	iHaveModelStatement
private boolean	inputOnly
private boolean	isCompoundDocument
(package private) SpartanArchive	spartanArchive
private java.lang.String	title
(package private) java.util.Map<java.lang.String,java.lang.String>	titles

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

ac, bondData, constraints, modelAtomCount, modelName

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

alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells

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

addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor and Description
SpartanSmolReader()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkLine()
protected void	finalizeSubclassReader() optional reader-specific method run first.
private int	getModelNumber()
protected void	initializeReader()
private void	readArchive()
private boolean	readArchiveHeader()
private void	readMyTransform()
private void	readOutput()
private void	readProperties()
private void	setCharges()

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

readInputRecords

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

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getNewDfCoefMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

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, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, getElementSymbol, getFilter, 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, processDSSR, 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

iHaveModelStatement

private boolean iHaveModelStatement

isCompoundDocument

private boolean isCompoundDocument

inputOnly

private boolean inputOnly

espCharges

private boolean espCharges

endCheck

private java.lang.String endCheck

title

private java.lang.String title

spartanArchive

SpartanArchive spartanArchive

titles

java.util.Map<java.lang.String,java.lang.String> titles

haveCharges

private boolean haveCharges

Constructor Detail

SpartanSmolReader

public SpartanSmolReader()

Method Detail

initializeReader

protected void initializeReader()
                         throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

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

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

readMyTransform

private void readMyTransform()
                      throws java.lang.Exception

Throws:

java.lang.Exception

readOutput

private void readOutput()
                 throws java.lang.Exception

Throws:

java.lang.Exception

readArchive

private void readArchive()
                  throws java.lang.Exception

Throws:

java.lang.Exception

setCharges

private void setCharges()

readProperties

private void readProperties()
                     throws java.lang.Exception

Throws:

java.lang.Exception

getModelNumber

private int getModelNumber()

readArchiveHeader

private boolean readArchiveHeader()
                           throws java.lang.Exception

Throws:

java.lang.Exception