org.jmol.adapter.readers.pdb.JmolDataReader

All Implemented Interfaces:: GenericLineReader

public class JmolDataReader extends PdbReader

JmolData file reader, for a modified PDB format This class also holds pseudo-static methods for spin

Field Summary

Fields inherited from class org.jmol.adapter.readers.pdb.PdbReader
biomtChainAtomCounts, fileAtomIndex, gromacsWideFormat, pdbID

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, CELL_TYPE_SUPER, cellSlop, centroidPacked, checkNearAtoms, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filteredPrecision, filterHetero, floatifyJavaDouble, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isSUPERCELL, isTrajectory, latticeCells, latticeScaling, latticeType, line, lowPrecision, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noMinimize, noPack, optimize2D, out, paramsCentroid, paramsLattice, precision, 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

JmolDataReader()
Method Summary

Modifier and Type

Method

Description

protected void

checkRemark()

protected void

finalizeSubclassReader()

Object[]

getJmolDataFrameProperties(ScriptEval e, int tok, int[] propToks, String[] props, BS bs, P3 minXYZ, P3 maxXYZ, String format, boolean isPdbFormat)

String[]

getJmolDataFrameScripts(Viewer vwr, int tok, int modelIndex, int modelCount, String type, String qFrame, String[] props, boolean isSpinPointGroup)

BS

getPlotSpinSet(Viewer vwr, BS bs, int modelIndex, P3 minXYZ, P3 maxXYZ)

remove non-spin atoms and atoms with duplicated spin and set min/max XYZ for the plot

protected void

processAtom2(Atom atom, int serial, float x, float y, float z, int charge)

protected void

setAdditionalAtomParameters(Atom atom)

adaptable via subclassing

void

setJmolDataFrame(ModelSet ms, String type, int modelIndex, int modelDataIndex)

Set up the JmolDataFrame initially

Methods inherited from class org.jmol.adapter.readers.pdb.PdbReader
checkLine, deduceElementSymbol, filterPDBAtom, finalizeReaderPDB, fixRadius, initializeReader, model, processAtom

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, fixDoubleA, fixFloatA, fixFloatPt, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getPackingRangeValue, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parsePrecision, 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, setPrecision, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR, warnSkippingOperation

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

Constructor Details
- JmolDataReader
  
  public JmolDataReader()
Method Details
- checkRemark
  
  protected void checkRemark()
  
  Overrides:
  
  checkRemark in class PdbReader
- processAtom2
  
  protected void processAtom2(Atom atom, int serial, float x, float y, float z, int charge)
  
  Overrides:
  
  processAtom2 in class PdbReader
- setAdditionalAtomParameters
  
  protected void setAdditionalAtomParameters(Atom atom)
  
  Description copied from class: PdbReader
  
  adaptable via subclassing
  
  Overrides:
  
  setAdditionalAtomParameters in class PdbReader
  
  Parameters:
  
  atom -
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  Overrides:
  
  finalizeSubclassReader in class PdbReader
  
  Throws:
  
  Exception
- getJmolDataFrameScripts
  
  public String[] getJmolDataFrameScripts(Viewer vwr, int tok, int modelIndex, int modelCount, String type, String qFrame, String[] props, boolean isSpinPointGroup)
- getJmolDataFrameProperties
  
  public Object[] getJmolDataFrameProperties(ScriptEval e, int tok, int[] propToks, String[] props, BS bs, P3 minXYZ, P3 maxXYZ, String format, boolean isPdbFormat) throws ScriptException
  
  Throws:
  
  ScriptException
- setJmolDataFrame
  
  public void setJmolDataFrame(ModelSet ms, String type, int modelIndex, int modelDataIndex)
  
  Set up the JmolDataFrame initially
  
  Parameters:
  
  ms -
  
  type -
  
  modelIndex -
  
  modelDataIndex -
- getPlotSpinSet
  
  public BS getPlotSpinSet(Viewer vwr, BS bs, int modelIndex, P3 minXYZ, P3 maxXYZ)
  
  remove non-spin atoms and atoms with duplicated spin and set min/max XYZ for the plot
  
  Parameters:
  
  vwr -
  
  bs -
  
  modelIndex -
  
  minXYZ -
  
  maxXYZ -
  
  Returns:
  
  bitset for plot

Class JmolDataReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.pdb.PdbReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.pdb.PdbReader

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

Methods inherited from class java.lang.Object

Constructor Details

JmolDataReader

Method Details

checkRemark

processAtom2

setAdditionalAtomParameters

finalizeSubclassReader

getJmolDataFrameScripts

getJmolDataFrameProperties

setJmolDataFrame

getPlotSpinSet