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 booleaniHaveDesiredModelprivate booleanisPolymerprivate booleanisSlabprivate intmodelNoprivate booleannoSlabprivate intpermutationvalues 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-
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 AtomaddAtom(float[] xyz, java.lang.String sym, java.lang.String name)private voidcheckDimensionType(float[] dt)protected voidfinalizeSubclassSymmetry(boolean haveSymmetry)protected voidinitializeReader()private voidreadAtoms(java.util.List<java.lang.Object> species, java.util.List<java.lang.Object> sites, java.util.List<java.lang.Object> coords)private booleanreadLattice(java.util.List<java.lang.Object> lattice)private voidreadModel(java.util.Map<java.lang.String,java.lang.Object> map)private static booleantoFloatArray(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
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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:
initializeReaderin 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:
finalizeSubclassSymmetryin classAtomSetCollectionReader- Throws:
java.lang.Exception
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