Package org.jmol.adapter.readers.spartan

Class SpartanSmolReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

org.jmol.adapter.readers.spartan.SpartanInputReader

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 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

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

addedData, addedDataKey, addVibrations, allow_a_len_1, 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, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, 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, 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, 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 Detail

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 Detail

SpartanSmolReader

public SpartanSmolReader()

Method Detail

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)