Package org.jmol.adapter.readers.xtal
Class OptimadeReader
- java.lang.Object
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- org.jmol.adapter.smarter.AtomSetCollectionReader
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- org.jmol.adapter.readers.xtal.OptimadeReader
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- All Implemented Interfaces:
javajs.api.GenericLineReader
public class OptimadeReader extends AtomSetCollectionReader
A (preliminary) reader for OPTIMADE resources. load Optimade::https://aiida.materialscloud.org/2dtopo/optimade/v1/structures?filter=nperiodic_dimensions=2&page_limit=1- Author:
- Bob Hanson hansonr@stolaf.edu
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Field Summary
Fields Modifier and Type Field Description private boolean
iHaveDesiredModel
private boolean
isPolymer
private boolean
isSlab
private int
modelNo
private boolean
noSlab
private int
permutation
values 0, 1, or 2 indicate how to permute the lattice vectors to be of the form [1,0,0] for polymers or [1,1,0] for slabsprivate float[]
xyz
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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, filterAllHetero, 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, merging, 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
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Constructor Summary
Constructors Constructor Description OptimadeReader()
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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 void
checkDimensionType(float[] dt)
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)
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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
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Field Detail
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modelNo
private int modelNo
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iHaveDesiredModel
private boolean iHaveDesiredModel
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permutation
private int permutation
values 0, 1, or 2 indicate how to permute the lattice vectors to be of the form [1,0,0] for polymers or [1,1,0] for slabs
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isPolymer
private boolean isPolymer
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isSlab
private boolean isSlab
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noSlab
private boolean noSlab
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xyz
private float[] xyz
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Method Detail
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initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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readModel
private void readModel(java.util.Map<java.lang.String,java.lang.Object> map) throws java.lang.Exception
- Throws:
java.lang.Exception
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checkDimensionType
private void checkDimensionType(float[] dt)
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readLattice
private boolean readLattice(java.util.List<java.lang.Object> lattice)
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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)
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addAtom
private Atom addAtom(float[] xyz, java.lang.String sym, java.lang.String name)
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toFloatArray
private static boolean toFloatArray(java.util.List<java.lang.Number> list, float[] a)
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finalizeSubclassSymmetry
protected void finalizeSubclassSymmetry(boolean haveSymmetry) throws java.lang.Exception
- Overrides:
finalizeSubclassSymmetry
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
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