org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.molxyz.MolReader

All Implemented Interfaces:: javajs.api.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

private int

atomCount

private String[]

atomData

javajs.util.BS

bsDeleted

private boolean

fixN

fix charges for RN(=O)(O), =N(O)*, =N

private boolean

haveAtomSerials

private int

iatom0

private V3000Rdr

vr

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

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()

optional reader-specific method run first.

(package private) int

fixOrder(int order, int stereo)

void

initializeReader()

private void

processCtab(boolean isMDL)

private void

processMolSdHeader()

private void

readAtomsAndBonds(int ac, int bc)

private void

readAtomValues()

Read all V nnn lines as string data; user can adapt as needed.

private void

readIsotopes()

Read all M ISO lines.

private void

readMolData(Map<String,Object> molData, javajs.util.Lst<String> _keyList)

Read the SDF data with name in lower case

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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, 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
- haveAtomSerials
  
  private boolean haveAtomSerials
- allow2D
  
  protected boolean allow2D
- iatom0
  
  private int iatom0
- vr
  
  private V3000Rdr vr
- atomCount
  
  private int atomCount
- atomData
  
  private String[] atomData
- bsDeleted
  
  public javajs.util.BS bsDeleted
- fixN
  
  private boolean fixN
  
  fix charges for RN(=O)(O), =N(O)*, =N
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
  
  Description copied from class: AtomSetCollectionReader
  
  optional reader-specific method run first.
  
  Overrides:
  
  finalizeSubclassReader in class AtomSetCollectionReader
  
  Throws:
  
  Exception
- finalizeReaderMR
  
  protected void finalizeReaderMR() throws Exception
  
  Throws:
  
  Exception
- processMolSdHeader
  
  private void processMolSdHeader() throws Exception
  
  Throws:
  
  Exception
- processCtab
  
  private void processCtab(boolean isMDL) throws Exception
  
  Throws:
  
  Exception
- readAtomsAndBonds
  
  private void readAtomsAndBonds(int ac, int bc) throws Exception
  
  Throws:
  
  Exception
- readAtomValues
  
  private void readAtomValues() throws Exception
  
  Read all V nnn lines as string data; user can adapt as needed.
  
  Throws:
  
  Exception
- readIsotopes
  
  private void readIsotopes() throws Exception
  
  Read all M ISO lines. These are absolute isotope numbers.
  
  Throws:
  
  Exception
- deleteAtom
  
  public void deleteAtom(Atom atom)
- readMolData
  
  private void readMolData(Map<String,Object> molData, javajs.util.Lst<String> _keyList) throws Exception
  
  Read the SDF data with name in lower case
  
  Parameters:
  
  molData -
  
  _keyList -
  
  Throws:
  
  Exception
- addMolAtom
  
  public Atom addMolAtom(int iAtom, int isotope, String elementSymbol, int charge, float x, float y, float z)
- fixOrder
  
  int fixOrder(int order, int stereo)
- addMolBond
  
  public Bond addMolBond(String iAtom1, String iAtom2, int order, int stereo)

Class MolReader

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

haveAtomSerials

allow2D

iatom0

vr

atomCount

atomData

bsDeleted

fixN

Constructor Details

MolReader

Method Details

initializeReader

checkLine

finalizeSubclassReader

finalizeReaderMR

processMolSdHeader

processCtab

readAtomsAndBonds

readAtomValues

readIsotopes

deleteAtom

readMolData

addMolAtom

fixOrder

addMolBond