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

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

MOReader, SlaterReader, SpartanInputReader, SpartanReader
```
public abstract class BasisFunctionReader
extends AtomSetCollectionReader
```
Author:

hansonr

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class BasisFunctionReader.MOEnergySorter

Field Summary

Fields
Modifier and Type	Field	Description
`protected java.lang.String`	`alphaBeta`
`protected int[][]`	`dfCoefMaps`
`private boolean`	`filterIsNot`
`private java.lang.String[]`	`filterTokens`
`protected boolean`	`ignoreMOs`
`java.util.Map<java.lang.String,java.lang.Object>`	`moData`
`protected int`	`nCoef`
`protected int`	`nOrbitals`
`javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>>`	`orbitals`
`javajs.util.Lst<int[]>`	`shells`
`private java.lang.String`	`spin`

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

Constructor Summary

Constructors
Constructor Description

BasisFunctionReader()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected static java.lang.String`	`canonicalizeQuantumSubshellTag(java.lang.String tag)`
`protected void`	`discardPreviousAtoms()`
`protected boolean`	`filterMO()`	check line for filter options
`protected int`	`fixSlaterTypes(int typeOld, int typeNew)`
`int[][]`	`getDfCoefMaps()`
`protected boolean`	`getDFMap(java.lang.String fileList, int shellType, java.lang.String jmolList, int minLength)`	finds the position in the Jmol-required list of function types.
`static java.lang.String`	`getQuantumShellTag(int id)`
`static int`	`getQuantumShellTagID(java.lang.String tag)`
`static int`	`getQuantumShellTagIDSpherical(java.lang.String tag)`
`void`	`setMO(java.util.Map<java.lang.String,java.lang.Object> mo)`

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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

shells
```
public javajs.util.Lst<int[]> shells
```

moData

public java.util.Map<java.lang.String,java.lang.Object> moData

orbitals

public javajs.util.Lst<java.util.Map<java.lang.String,java.lang.Object>> orbitals

nOrbitals
```
protected int nOrbitals
```

ignoreMOs
```
protected boolean ignoreMOs
```

alphaBeta
```
protected java.lang.String alphaBeta
```

dfCoefMaps
```
protected int[][] dfCoefMaps
```

filterTokens

private java.lang.String[] filterTokens

filterIsNot
```
private boolean filterIsNot
```

spin
```
private java.lang.String spin
```

nCoef
```
protected int nCoef
```

Constructor Detail
- BasisFunctionReader
```
public BasisFunctionReader()
```

Method Detail

filterMO
```
protected boolean filterMO()
```
check line for filter options

Returns:

true if a match

setMO

public void setMO(java.util.Map<java.lang.String,java.lang.Object> mo)

getDFMap

protected boolean getDFMap(java.lang.String fileList,
                           int shellType,
                           java.lang.String jmolList,
                           int minLength)

finds the position in the Jmol-required list of function types. This list is reader-dependent.

Parameters:: fileList -; shellType -; jmolList -; minLength -
Returns:: true if successful

getDfCoefMaps
```
public int[][] getDfCoefMaps()
```

canonicalizeQuantumSubshellTag

protected static final java.lang.String canonicalizeQuantumSubshellTag(java.lang.String tag)

fixSlaterTypes

protected int fixSlaterTypes(int typeOld,
                             int typeNew)

getQuantumShellTagIDSpherical

public static int getQuantumShellTagIDSpherical(java.lang.String tag)

getQuantumShellTagID

public static int getQuantumShellTagID(java.lang.String tag)

getQuantumShellTag

public static java.lang.String getQuantumShellTag(int id)

discardPreviousAtoms
```
protected void discardPreviousAtoms()
```
Overrides:

discardPreviousAtoms in class AtomSetCollectionReader

Class BasisFunctionReader

Nested Class Summary

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

shells

moData

orbitals

nOrbitals

ignoreMOs

alphaBeta

dfCoefMaps

filterTokens

filterIsNot

spin

nCoef

Constructor Detail

BasisFunctionReader

Method Detail

filterMO

setMO

getDFMap

getDfCoefMaps

canonicalizeQuantumSubshellTag

fixSlaterTypes

getQuantumShellTagIDSpherical

getQuantumShellTagID

getQuantumShellTag

discardPreviousAtoms