org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.molxyz.MolReader

All Implemented Interfaces:: GenericLineReader

Direct Known Subclasses:: JcampdxReader, Mol3DReader

public class MolReader extends AtomSetCollectionReader

A reader for MDLI mol and sdf files.

http://www.mdli.com/downloads/public/ctfile/ctfile.jsp

also: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf simple symmetry extension via load command: 9/2006 hansonr@stolaf.edu setAtomCoord(atom, x, y, z) applySymmetryAndSetTrajectory() simple 2D-->3D conversion using load "xxx.mol" FILTER "2D" Jmol 14.8.2 adds bond type 15 (quintuple) and 16 (sextuple)

Field Summary

Fields

Modifier and Type

Field

Description

protected boolean

allow2D

BS

bsDeleted

Fields inherited from class 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

MolReader()
Method Summary

Modifier and Type

Method

Description

Atom

addMolAtom(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z)

Bond

addMolBond(String iAtom1, String iAtom2, int order, int stereo)

protected boolean

checkLine()

void

deleteAtom(Atom atom)

protected void

finalizeReaderMR()

void

finalizeSubclassReader()

void

initializeReader()

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

Field Details
- allow2D
  
  protected boolean allow2D
- bsDeleted
  
  public BS bsDeleted
Constructor Details
- MolReader
  
  public MolReader()
Method Details
- initializeReader
  
  public void initializeReader() throws Exception
  
  Overrides:
  
  initializeReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- checkLine
  
  protected boolean checkLine() throws Exception
  
  Overrides:
  
  checkLine in class AtomSetCollectionReader
  
  Returns:
  
  true if need to read new line
  
  Throws:
  
  Exception
- finalizeSubclassReader
  
  public void finalizeSubclassReader() throws Exception
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- finalizeReaderMR
  
  protected void finalizeReaderMR() throws Exception
  
  Throws:
  
  Exception
- deleteAtom
  
  public void deleteAtom(Atom atom)
- addMolAtom
  
  public Atom addMolAtom(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z)
- addMolBond
  
  public Bond addMolBond(String iAtom1, String iAtom2, int order, int stereo)

Class MolReader

Field Summary

Fields inherited from class AtomSetCollectionReader

Constructor Summary

Method Summary

Methods inherited from class AtomSetCollectionReader

Methods inherited from class Object

Field Details

allow2D

bsDeleted

Constructor Details

MolReader

Method Details

initializeReader

checkLine

finalizeSubclassReader

finalizeReaderMR

deleteAtom

addMolAtom

addMolBond