java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.quantum.BasisFunctionReader

All Implemented Interfaces:: GenericLineReader

Direct Known Subclasses:: MOReader, SpartanInputReader, SpartanReader

public abstract class BasisFunctionReader extends AtomSetCollectionReader

Author:: hansonr invalid input: '<'hansonr@stolaf.edu>

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

class

BasisFunctionReader.MOEnergySorter
Field Summary

Fields

Modifier and Type

Field

Description

protected String

alphaBeta

protected int[][]

dfCoefMaps

protected boolean

haveCoefs

protected boolean

ignoreMOs

Map<String,Object>

moData

protected int

nCoef

protected int

nOrbitals

Lst<Map<String,Object>>

orbitals

Lst<int[]>

shells

protected SlaterData[]

slaterArray

protected Lst<SlaterData>

slaters

Fields inherited from class 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, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, 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
Constructor Summary

Constructors

Constructor

Description

BasisFunctionReader()
Method Summary

Modifier and Type

Method

Description

protected static final String

canonicalizeQuantumSubshellTag(String tag)

protected void

clearOrbitals()

protected void

discardPreviousAtoms()

protected void

enableShell(int shellType)

This flag must be explicitly set when a reader has been verified to properly sort G, H, I,...

protected boolean

filterMO()

check line for filter options

protected int

fixSlaterTypes(int typeOld, int typeNew)

Only for 5D, 10F, 15G designations.

int[][]

getDfCoefMaps()

protected boolean

getDFMap(String shell, String fileList, int shellType, String jmolList, int minLength)

finds the position in the Jmol-required list of function types.

static String

getQuantumShellTag(int id)

static int

getQuantumShellTagID(String tag)

static int

getQuantumShellTagIDSpherical(String tag)

void

setMO(Map<String,Object> mo)

Methods inherited from class AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR, warnSkippingOperation

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

Field Details
- shells
  
  public Lst<int[]> shells
- slaters
  
  protected Lst<SlaterData> slaters
- slaterArray
  
  protected SlaterData[] slaterArray
- moData
  
  public Map<String,Object> moData
- orbitals
  
  public Lst<Map<String,Object>> orbitals
- nOrbitals
  
  protected int nOrbitals
- ignoreMOs
  
  protected boolean ignoreMOs
- alphaBeta
  
  protected String alphaBeta
- dfCoefMaps
  
  protected int[][] dfCoefMaps
- nCoef
  
  protected int nCoef
- haveCoefs
  
  protected boolean haveCoefs
Constructor Details
- BasisFunctionReader
  
  public BasisFunctionReader()
Method Details
- filterMO
  
  protected boolean filterMO()
  
  check line for filter options
  
  Returns:
  
  true if a match
- setMO
  
  public void setMO(Map<String,Object> mo)
- getDFMap
  
  protected boolean getDFMap(String shell, String fileList, int shellType, String jmolList, int minLength)
  
  finds the position in the Jmol-required list of function types. This list is reader-dependent.
  
  Parameters:
  
  shell - TODO
  
  fileList -
  
  shellType -
  
  jmolList -
  
  minLength -
  
  Returns:
  
  true if successful
- enableShell
  
  protected void enableShell(int shellType)
  
  This flag must be explicitly set when a reader has been verified to properly sort G, H, I,... orbitals.
  
  Parameters:
  
  shellType -
- getDfCoefMaps
  
  public int[][] getDfCoefMaps()
- canonicalizeQuantumSubshellTag
  
  protected static final String canonicalizeQuantumSubshellTag(String tag)
- fixSlaterTypes
  
  protected int fixSlaterTypes(int typeOld, int typeNew)
  
  Only for 5D, 10F, 15G designations. Each time this method is run through, additional changes are made in the orbital count. So only the final reading is significant.
  
  Parameters:
  
  typeOld -
  
  typeNew -
  
  Returns:
  
  the number of coefficients overall, for all orbital types
- getQuantumShellTagIDSpherical
  
  public static int getQuantumShellTagIDSpherical(String tag)
- getQuantumShellTagID
  
  public static int getQuantumShellTagID(String tag)
- getQuantumShellTag
  
  public static String getQuantumShellTag(int id)
- discardPreviousAtoms
  
  protected void discardPreviousAtoms()
  
  Overrides:
  
  discardPreviousAtoms in class AtomSetCollectionReader
- clearOrbitals
  
  protected void clearOrbitals()

Class BasisFunctionReader

Nested Class Summary

Field Summary

Fields inherited from class AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class AtomSetCollectionReader

Methods inherited from class Object

Field Details

shells

slaters

slaterArray

moData

orbitals

nOrbitals

ignoreMOs

alphaBeta

dfCoefMaps

nCoef

haveCoefs

Constructor Details

BasisFunctionReader

Method Details

filterMO

setMO

getDFMap

enableShell

getDfCoefMaps

canonicalizeQuantumSubshellTag

fixSlaterTypes

getQuantumShellTagIDSpherical

getQuantumShellTagID

getQuantumShellTag

discardPreviousAtoms

clearOrbitals