java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.OptimadeReader

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class OptimadeReader
extends AtomSetCollectionReader
```
A (preliminary) reader for OPTIMADE resources.

Author:

Bob Hanson hansonr@stolaf.edu

Field Summary

Fields
Modifier and Type	Field	Description
`private float[]`	`dimensionType`
`private boolean`	`iHaveDesiredModel`
`private boolean`	`isPolymer`
`private boolean`	`isSlab`
`private int`	`modelNo`
`private float`	`ndims`
`private float[]`	`xyz`

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, 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, 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

Constructor Summary

Constructors
Constructor Description

OptimadeReader()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private Atom`	`addAtom(float[] xyz, java.lang.String sym, java.lang.String name)`
`private boolean`	`checkDimensionType()`
`protected void`	`finalizeSubclassSymmetry(boolean haveSymmetry)`
`protected void`	`initializeReader()`
`private void`	`readAtoms(java.util.List<java.lang.Object> species, java.util.List<java.lang.Object> sites, java.util.List<java.lang.Object> coords)`
`private boolean`	`readLattice(java.util.List<java.lang.Object> lattice)`
`private void`	`readModel(java.util.Map<java.lang.String,java.lang.Object> map)`
`private static boolean`	`toFloatArray(java.util.List<java.lang.Number> list, float[] a)`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, 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

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

Field Detail

modelNo
```
private int modelNo
```

iHaveDesiredModel
```
private boolean iHaveDesiredModel
```

dimensionType
```
private float[] dimensionType
```

ndims
```
private float ndims
```

isPolymer
```
private boolean isPolymer
```

isSlab
```
private boolean isSlab
```

xyz
```
private float[] xyz
```

Constructor Detail
- OptimadeReader
```
public OptimadeReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
                         throws java.lang.Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

readModel

private void readModel(java.util.Map<java.lang.String,java.lang.Object> map)
                throws java.lang.Exception

Throws:: java.lang.Exception

checkDimensionType
```
private boolean checkDimensionType()
```

readLattice

private boolean readLattice(java.util.List<java.lang.Object> lattice)

readAtoms

private void readAtoms(java.util.List<java.lang.Object> species,
                       java.util.List<java.lang.Object> sites,
                       java.util.List<java.lang.Object> coords)

addAtom

private Atom addAtom(float[] xyz,
                     java.lang.String sym,
                     java.lang.String name)

toFloatArray

private static boolean toFloatArray(java.util.List<java.lang.Number> list,
                                    float[] a)

finalizeSubclassSymmetry

protected void finalizeSubclassSymmetry(boolean haveSymmetry)
                                 throws java.lang.Exception

Overrides:: finalizeSubclassSymmetry in class AtomSetCollectionReader
Throws:: java.lang.Exception

Class OptimadeReader

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

modelNo

iHaveDesiredModel

dimensionType

ndims

isPolymer

isSlab

xyz

Constructor Detail

OptimadeReader

Method Detail

initializeReader

readModel

checkDimensionType

readLattice

readAtoms

addAtom

toFloatArray

finalizeSubclassSymmetry