Package org.jmol.adapter.readers.spartan
Class SpartanSmolReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.quantum.BasisFunctionReader
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- org.jmol.adapter.readers.spartan.SpartanInputReader
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- org.jmol.adapter.readers.spartan.SpartanSmolReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class SpartanSmolReader extends SpartanInputReader
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Nested Class Summary
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Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
BasisFunctionReader.MOEnergySorter
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Field Summary
Fields Modifier and Type Field Description private static java.lang.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 java.lang.String
title
(package private) java.util.Map<java.lang.String,java.lang.String>
titles
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Fields inherited from class org.jmol.adapter.readers.spartan.SpartanInputReader
bondData, constraints, modelAtomCount
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Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells, slaterArray, slaters
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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, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noPack, 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
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Constructor Summary
Constructors Constructor Description SpartanSmolReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
checkLine()
protected void
finalizeSubclassReader()
optional reader-specific method run first.protected void
initializeReader()
private void
makeNewAtomSet()
private java.lang.String
readArchive()
private java.lang.String
readArchiveHeader()
private void
readMyTransform()
private void
readOutput()
private void
readProperties()
private void
setCharges()
void
setEnergy(float value)
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Methods inherited from class org.jmol.adapter.readers.spartan.SpartanInputReader
readInputRecords, readTransform
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Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, clearOrbitals, discardPreviousAtoms, enableShell, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
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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
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Field Detail
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iHaveModelStatement
private boolean iHaveModelStatement
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isCompoundDocument
private boolean isCompoundDocument
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inputOnly
private boolean inputOnly
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espCharges
private boolean espCharges
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natCharges
private boolean natCharges
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isInputFirst
private boolean isInputFirst
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iHaveNewDir
private boolean iHaveNewDir
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endCheck
private static final java.lang.String endCheck
- See Also:
- Constant Field Values
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title
private java.lang.String title
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spartanArchive
SpartanArchive spartanArchive
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titles
java.util.Map<java.lang.String,java.lang.String> titles
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haveCharges
private boolean haveCharges
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
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makeNewAtomSet
private void makeNewAtomSet()
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finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readMyTransform
private void readMyTransform() throws java.lang.Exception
- Throws:
java.lang.Exception
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readOutput
private void readOutput() throws java.lang.Exception
- Throws:
java.lang.Exception
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readArchive
private java.lang.String readArchive() throws java.lang.Exception
- Throws:
java.lang.Exception
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setCharges
private void setCharges()
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readProperties
private void readProperties() throws java.lang.Exception
- Throws:
java.lang.Exception
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readArchiveHeader
private java.lang.String readArchiveHeader() throws java.lang.Exception
- Throws:
java.lang.Exception
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setEnergy
public void setEnergy(float value)
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