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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class CsfReader
extends MopacSlaterReader
```
CSF file reader based on CIF idea -- fluid property fields. note that, like CIF, the order of fields is totally unpredictable in addition, ID numbers are not sequential, requiring atomNames first crack at this 2006/04/13 added DGAUSS, MOPAC, EHT orbital/basis reading 2007/04/09 streamlined CSF dataset reading capabilities 2007/04/09

Author:

hansonr

Nested Class Summary
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.SlaterReader
  SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
- Nested classes/interfaces inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
  BasisFunctionReader.MOEnergySorter

Field Summary

Fields
Modifier and Type	Field	Description
`private static byte`	`ANUM`
`private static byte[]`	`atomFieldMap`
`private static java.lang.String[]`	`atomFields`
`private static byte`	`BFXN_ANGL`
`private static byte[]`	`bondFieldMap`
`private static java.lang.String[]`	`bondFields`
`private static byte`	`BTYPE`
`private static byte`	`CHRG`
`private static byte`	`COEF_INDICES`
`private static byte[]`	`connectorFieldMap`
`private static java.lang.String[]`	`connectorFields`
`private java.util.Map<java.lang.String,java.lang.String[]>`	`connectors`
`private static byte`	`CONTRACTIONS`
`private static byte`	`DIPOLE`
`private static byte`	`EIG_VAL`
`private static byte`	`EIG_VEC`
`private static byte`	`EIG_VEC_COMPRESSED`
`private int`	`fieldCount`
`private int[]`	`fieldTypes`
`private static byte`	`GTO_EXP`
`private java.util.Map<java.lang.String,Bond>`	`htBonds`
`private static byte`	`ID`
`private static byte`	`MO_OCC`
`private static byte[]`	`moFieldMap`
`private static java.lang.String[]`	`moFields`
`private int`	`nAtoms`
`private int`	`nGaussians`
`private static byte`	`NORMAL_MODE`
`private int`	`nSlaters`
`private int`	`nVibrations`
`private static byte`	`objCls1`
`private static byte`	`objCls2`
`private static byte`	`objID1`
`private static byte`	`objID2`
`private static byte`	`PCHRG`
`private java.util.Map<java.lang.String,java.lang.Integer>`	`propertyItemCounts`
`private static byte`	`SHELL`
`private static byte`	`STO_EXP`
`private java.lang.String`	`strAtomicNumbers`
`private static byte`	`SYM`
`private static byte`	`VIB_ENERGY`
`private static byte[]`	`vibFieldMap`
`private static java.lang.String[]`	`vibFields`
`private static byte`	`XYZ`

Fields inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
atomicNumbers, MIN_COEF

Fields inherited from class org.jmol.adapter.readers.quantum.SlaterReader
slaterArray, slaters

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, 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

CsfReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected boolean`	`checkLine()`
`private void`	`fillCsfArray(java.lang.String property, java.lang.String[] tokens, int i0, java.lang.Object f, boolean isInteger)`
`private int`	`getPropertyCount(java.lang.String what)`
`private int`	`parseLineParameters(java.lang.String[] fields, byte[] fieldMap)`
`private void`	`processAtomObject()`
`private void`	`processBasisObject(java.lang.String sto_gto)`
`private void`	`processBondObject()`
`private void`	`processConnectorObject()`
`private void`	`processLocalTransform()`
`private void`	`processMolecularOrbitalObject()`
`private void`	`processVibrationObject()`
`private void`	`setBond(Bond bond, java.lang.String[] connect)`

Methods inherited from class org.jmol.adapter.readers.quantum.MopacSlaterReader
createSphericalSlaterByType, scaleSlater

Methods inherited from class org.jmol.adapter.readers.quantum.SlaterReader
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, 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

nAtoms
```
private int nAtoms
```

strAtomicNumbers

private java.lang.String strAtomicNumbers

fieldCount
```
private int fieldCount
```

nVibrations
```
private int nVibrations
```

nGaussians
```
private int nGaussians
```

nSlaters
```
private int nSlaters
```

htBonds

private java.util.Map<java.lang.String,Bond> htBonds

propertyItemCounts

private java.util.Map<java.lang.String,java.lang.Integer> propertyItemCounts

fieldTypes
```
private final int[] fieldTypes
```

objCls1
```
private static final byte objCls1
```
See Also:

Constant Field Values

objID1
```
private static final byte objID1
```
See Also:

Constant Field Values

objCls2
```
private static final byte objCls2
```
See Also:

Constant Field Values

objID2
```
private static final byte objID2
```
See Also:

Constant Field Values

connectorFields

private static final java.lang.String[] connectorFields

connectorFieldMap

private static final byte[] connectorFieldMap

connectors

private java.util.Map<java.lang.String,java.lang.String[]> connectors

ID
```
private static final byte ID
```
See Also:

Constant Field Values

SYM
```
private static final byte SYM
```
See Also:

Constant Field Values

ANUM
```
private static final byte ANUM
```
See Also:

Constant Field Values

CHRG
```
private static final byte CHRG
```
See Also:

Constant Field Values

XYZ
```
private static final byte XYZ
```
See Also:

Constant Field Values

PCHRG
```
private static final byte PCHRG
```
See Also:

Constant Field Values

atomFields

private static final java.lang.String[] atomFields

atomFieldMap

private static final byte[] atomFieldMap

BTYPE
```
private static final byte BTYPE
```
See Also:

Constant Field Values

bondFields

private static final java.lang.String[] bondFields

bondFieldMap

private static final byte[] bondFieldMap

NORMAL_MODE
```
private static final byte NORMAL_MODE
```
See Also:

Constant Field Values

VIB_ENERGY
```
private static final byte VIB_ENERGY
```
See Also:

Constant Field Values

DIPOLE
```
private static final byte DIPOLE
```
See Also:

Constant Field Values

vibFields

private static final java.lang.String[] vibFields

vibFieldMap

private static final byte[] vibFieldMap

EIG_VAL
```
private static final byte EIG_VAL
```
See Also:

Constant Field Values

MO_OCC
```
private static final byte MO_OCC
```
See Also:

Constant Field Values

EIG_VEC
```
private static final byte EIG_VEC
```
See Also:

Constant Field Values

EIG_VEC_COMPRESSED
```
private static final byte EIG_VEC_COMPRESSED
```
See Also:

Constant Field Values

COEF_INDICES
```
private static final byte COEF_INDICES
```
See Also:

Constant Field Values

BFXN_ANGL
```
private static final byte BFXN_ANGL
```
See Also:

Constant Field Values

STO_EXP
```
private static final byte STO_EXP
```
See Also:

Constant Field Values

CONTRACTIONS
```
private static final byte CONTRACTIONS
```
See Also:

Constant Field Values

GTO_EXP
```
private static final byte GTO_EXP
```
See Also:

Constant Field Values

SHELL
```
private static final byte SHELL
```
See Also:

Constant Field Values

moFields

private static final java.lang.String[] moFields

moFieldMap
```
private static final byte[] moFieldMap
```

Constructor Detail
- CsfReader
```
public CsfReader()
```

Method Detail

checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

processLocalTransform

private void processLocalTransform()
                            throws java.lang.Exception

Throws:: java.lang.Exception

getPropertyCount

private int getPropertyCount(java.lang.String what)

parseLineParameters

private int parseLineParameters(java.lang.String[] fields,
                                byte[] fieldMap)
                         throws java.lang.Exception

Throws:: java.lang.Exception

fillCsfArray

private void fillCsfArray(java.lang.String property,
                          java.lang.String[] tokens,
                          int i0,
                          java.lang.Object f,
                          boolean isInteger)
                   throws java.lang.Exception

Throws:: java.lang.Exception

processConnectorObject

private void processConnectorObject()
                             throws java.lang.Exception

Throws:: java.lang.Exception

setBond

private void setBond(Bond bond,
                     java.lang.String[] connect)

processAtomObject

private void processAtomObject()
                        throws java.lang.Exception

Throws:: java.lang.Exception

processBondObject

private void processBondObject()
                        throws java.lang.Exception

Throws:: java.lang.Exception

processVibrationObject

private void processVibrationObject()
                             throws java.lang.Exception

Throws:: java.lang.Exception

processMolecularOrbitalObject

private void processMolecularOrbitalObject()
                                    throws java.lang.Exception

Throws:: java.lang.Exception

processBasisObject

private void processBasisObject(java.lang.String sto_gto)
                         throws java.lang.Exception

Throws:: java.lang.Exception

Class CsfReader

Nested Class Summary

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

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

Field Summary

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

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

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

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

Constructor Summary

Method Summary

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

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

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

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

Methods inherited from class java.lang.Object

Field Detail

nAtoms

strAtomicNumbers

fieldCount

nVibrations

nGaussians

nSlaters

htBonds

propertyItemCounts

fieldTypes

objCls1

objID1

objCls2

objID2

connectorFields

connectorFieldMap

connectors

ID

SYM

ANUM

CHRG

XYZ

PCHRG

atomFields

atomFieldMap

BTYPE

bondFields

bondFieldMap

NORMAL_MODE

VIB_ENERGY

DIPOLE

vibFields

vibFieldMap

EIG_VAL

MO_OCC

EIG_VEC

EIG_VEC_COMPRESSED

COEF_INDICES

BFXN_ANGL

STO_EXP

CONTRACTIONS

GTO_EXP

SHELL

moFields

moFieldMap

Constructor Detail

CsfReader

Method Detail

checkLine

processLocalTransform

getPropertyCount

parseLineParameters

fillCsfArray

processConnectorObject

setBond

processAtomObject

processBondObject

processVibrationObject

processMolecularOrbitalObject

processBasisObject