org.jmol.adapter.readers.cif.BCIFReader

All Implemented Interfaces:: GenericLineReader

public class BCIFReader extends MMCifReader

A very simple Binary CIF file reader extention of MMCifReader extends CifReader.

Author:: Bob Hanson (hansonr@stolaf.edu)

Field Summary

Fields

Modifier and Type

Field

Description

protected static int[]

temp

Fields inherited from class org.jmol.adapter.readers.cif.MMCifReader
CAT_ASSEM, CAT_CHEMCOMP, CAT_COMPBOND, CAT_NCS, CAT_OPER, CAT_SEQUENCEDIF, CAT_SHEET, CAT_STRUCSITE, CAT_STRUCTCONF, CAT_STRUCTCONN, done, htHetero, htSites, isBiomolecule, vBiomolecules

Fields inherited from class org.jmol.adapter.readers.cif.CifReader
ac, CAT_ATOM_SITE, CAT_ATOM_SITES, CAT_ATOM_TYPE, CAT_CELL, EMPTY, firstChar, htGroup1, iHaveDesiredModel, isCourseGrained, isLigand, isLoop, isMagCIF, isMMCIF, isSpinCIF, lastDataSetName, maxSerial, modelMap, nAtoms, nAtoms0, NONE, pdbID, skipping, symops, thisDataSetName, useAuthorChainID

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

BCIFReader()
Method Summary

Modifier and Type

Method

Description

protected void

finalizeSubclassReader()

protected GenericCifDataParser

getCifDataParser()

protected float

getFloatColumnData(int i)

Called by processAtomSites to retrieve individual matrix elements and set them by name.

protected boolean

isFieldValid()

protected float

parseCartesianField()

protected float

parseFloatField()

protected int

parseIntField()

protected int

parseIntFieldTok(byte tok)

Get a specific column's item for this category on this row.

protected void

parseLoopParameters(String[] fields)

This is the callback the that the MMCifReader and CifReader process.....() methods call initially.

protected void

processBinaryDocument()

The primare method initiating this reader

protected void

setup(String fullPath, Map<String,Object> htParams, Object reader)

binary must set up initially

Methods inherited from class org.jmol.adapter.readers.cif.MMCifReader
addAssembly, addHetero, addMatrix, checkFilterAssembly, checkPDBModelField, checkSubclassSymmetry, finalizeSubclass, incrementModel, initSubclass, processAssemblyGenBlock, processChemCompLoopBlock, processCompBondLoopBlock, processSequence, processStructConfLoopBlock, processStructConnLoopBlock, processStructOperListBlock, processStructSheetRangeLoopBlock, processStructSiteBlock, processSubclassAtom, processSubclassEntry, processSubclassLoopBlock, sortAssemblyModels

Methods inherited from class org.jmol.adapter.readers.cif.CifReader
addCifAtom, addHeader, applySymmetryAndSetTrajectory, checkAllFieldsPresent, doPreSymmetry, fieldProperty, filterCIFAtom, finalizeSubclassSymmetry, fullTrim, getBondOrder, getFieldString, initializeReader, isLoopKey, isNull, newModel, nextAtomSet, processAtomTypeLoopBlock, processCellParameter, processCitationListBlock, processLoopBlock, processUnitCellTransformMatrix, setSymmetryOperator, skipLoop, skipLoopKeyword

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addMoreUnitCellInfo, addSites, addSiteScript, appendLoadNote, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setPrecision, setSpaceGroupName, setTransform, setUnitCell, setUnitCellItem, setupASCR, warnSkippingOperation

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

Field Details
- temp
  
  protected static int[] temp
Constructor Details
- BCIFReader
  
  public BCIFReader()
Method Details
- getCifDataParser
  
  protected GenericCifDataParser getCifDataParser()
  
  Overrides:
  
  getCifDataParser in class CifReader
- setup
  
  protected void setup(String fullPath, Map<String,Object> htParams, Object reader)
  
  binary must set up initially
  
  Overrides:
  
  setup in class AtomSetCollectionReader
  
  Parameters:
  
  fullPath -
  
  htParams -
  
  reader -
- processBinaryDocument
  
  protected void processBinaryDocument() throws Exception
  
  The primare method initiating this reader
  
  Overrides:
  
  processBinaryDocument in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  protected void finalizeSubclassReader() throws Exception
  
  Overrides:
  
  finalizeSubclassReader in class CifReader
  
  Throws:
  
  Exception
- parseLoopParameters
  
  protected void parseLoopParameters(String[] fields) throws Exception
  
  This is the callback the that the MMCifReader and CifReader process.....() methods call initially. Pass this on to our psuedo-parser.
  
  Overrides:
  
  parseLoopParameters in class CifReader
  
  Parameters:
  
  fields -
  
  Throws:
  
  Exception
- isFieldValid
  
  protected boolean isFieldValid()
  
  Overrides:
  
  isFieldValid in class CifReader
- parseIntField
  
  protected int parseIntField()
  
  Overrides:
  
  parseIntField in class CifReader
- parseFloatField
  
  protected float parseFloatField()
  
  Overrides:
  
  parseFloatField in class CifReader
- parseCartesianField
  
  protected float parseCartesianField()
  
  Overrides:
  
  parseCartesianField in class CifReader
- parseIntFieldTok
  
  protected int parseIntFieldTok(byte tok)
  
  Get a specific column's item for this category on this row. In contrast to MMCifReader, we already have the integer; we don't have to parse it.
  
  Overrides:
  
  parseIntFieldTok in class MMCifReader
- getFloatColumnData
  
  protected float getFloatColumnData(int i)
  
  Called by processAtomSites to retrieve individual matrix elements and set them by name.
  
  Overrides:
  
  getFloatColumnData in class CifReader

Class BCIFReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.cif.MMCifReader

Fields inherited from class org.jmol.adapter.readers.cif.CifReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.cif.MMCifReader

Methods inherited from class org.jmol.adapter.readers.cif.CifReader

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

Methods inherited from class java.lang.Object

Field Details

temp

Constructor Details

BCIFReader

Method Details

getCifDataParser

setup

processBinaryDocument

finalizeSubclassReader

parseLoopParameters

isFieldValid

parseIntField

parseFloatField

parseCartesianField

parseIntFieldTok

getFloatColumnData