SpartanInputReader

java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.quantum.BasisFunctionReader
  - - org.jmol.adapter.readers.spartan.SpartanInputReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

OdysseyReader, SpartanSmolReader
```
public abstract class SpartanInputReader
extends BasisFunctionReader
```

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

protected java.lang.String bondData

protected java.lang.String constraints

protected int modelAtomCount
- Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
  addedData, addedDataKey, addVibrations, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
- Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells

Fields
Modifier and Type	Field	Description
`protected java.lang.String`	`bondData`
`protected java.lang.String`	`constraints`
`protected int`	`modelAtomCount`

Constructor Summary

Constructors
Constructor Description

SpartanInputReader()

Constructors
Constructor	Description
`SpartanInputReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`readAtomNames()`
`private void`	`readBonds(int ac0)`
`private void`	`readConstraints()`
`private void`	`readInputAtoms()`
`private java.lang.String`	`readInputHeader()`
`protected java.lang.String`	`readInputRecords()`
`private void`	`readTransform()`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, 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 org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

modelAtomCount
```
protected int modelAtomCount
```

bondData
```
protected java.lang.String bondData
```

constraints
```
protected java.lang.String constraints
```

Constructor Detail
- SpartanInputReader
```
public SpartanInputReader()
```

Method Detail

readInputRecords

protected java.lang.String readInputRecords()
                                     throws java.lang.Exception

Throws:: java.lang.Exception

readConstraints

private void readConstraints()
                      throws java.lang.Exception

Throws:: java.lang.Exception

readTransform

private void readTransform()
                    throws java.lang.Exception

Throws:: java.lang.Exception

readInputHeader

private java.lang.String readInputHeader()
                                  throws java.lang.Exception

Throws:: java.lang.Exception

readInputAtoms

private void readInputAtoms()
                     throws java.lang.Exception

Throws:: java.lang.Exception

readAtomNames

private void readAtomNames()
                    throws java.lang.Exception

Throws:: java.lang.Exception

readBonds

private void readBonds(int ac0)
                throws java.lang.Exception

Throws:: java.lang.Exception

Class SpartanInputReader

Nested Class Summary

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

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

modelAtomCount

bondData

constraints

Constructor Detail

SpartanInputReader

Method Detail

readInputRecords

readConstraints

readTransform

readInputHeader

readInputAtoms

readAtomNames

readBonds