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. load Optimade::https://aiida.materialscloud.org/2dtopo/optimade/v1/structures?filter=nperiodic_dimensions=2&page_limit=1

Author:: Bob Hanson hansonr@stolaf.edu

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 slabs

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, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, 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

Modifier and Type

Method

Description

private Atom

addAtom(float[] xyz, String sym, String name)

private void

checkDimensionType(float[] dt)

protected void

finalizeSubclassSymmetry(boolean haveSymmetry)

protected void

initializeReader()

private void

readAtoms(List<Object> species, List<Object> sites, List<Object> coords)

private boolean

readLattice(List<Object> lattice)

private void

readModel(Map<String,Object> map)

private static boolean

toFloatArray(List<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 Details
- modelNo
  
  private int modelNo
- iHaveDesiredModel
  
  private boolean iHaveDesiredModel
- 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
- isPolymer
  
  private boolean isPolymer
- isSlab
  
  private boolean isSlab
- noSlab
  
  private boolean noSlab
- xyz
  
  private float[] xyz
Constructor Details
- OptimadeReader
  
  public OptimadeReader()
Method Details
- initializeReader
  
  protected void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- readModel
  
  private void readModel(Map<String,Object> map) throws Exception
  
  Throws:
  
  Exception
- checkDimensionType
  
  private void checkDimensionType(float[] dt)
- readLattice
  
  private boolean readLattice(List<Object> lattice)
- readAtoms
  
  private void readAtoms(List<Object> species, List<Object> sites, List<Object> coords)
- addAtom
  
  private Atom addAtom(float[] xyz, String sym, String name)
- toFloatArray
  
  private static boolean toFloatArray(List<Number> list, float[] a)
- finalizeSubclassSymmetry
  
  protected void finalizeSubclassSymmetry(boolean haveSymmetry) throws Exception
  
  Overrides:
  
  finalizeSubclassSymmetry in class AtomSetCollectionReader
  
  Throws:
  
  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 Details

modelNo

iHaveDesiredModel

permutation

isPolymer

isSlab

noSlab

xyz

Constructor Details

OptimadeReader

Method Details

initializeReader

readModel

checkDimensionType

readLattice

readAtoms

addAtom

toFloatArray

finalizeSubclassSymmetry