org.jmol.adapter.readers.molxyz

Class MolReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.molxyz.MolReader

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"

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	allow2D
protected java.lang.String	dimension
private boolean	haveAtomSerials
private int	iatom0
private boolean	is2D
private boolean	isV3000

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

addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr

Constructor Summary

Constructors

Constructor and Description
MolReader()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkLine()
private void	checkLineContinuation()
void	finalizeReader() optional reader-specific method run first.
protected void	finalizeReaderMR()
private int	fixOrder(int order, int stereo)
void	initializeReader()
private void	processCtab(boolean isMDL)
private void	processMolSdHeader()
private void	readAtoms(int ac)
private void	readBonds(int bondCount)
private void	readUserData(int atom0)

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

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

is2D

private boolean is2D

isV3000

private boolean isV3000

haveAtomSerials

private boolean haveAtomSerials

dimension

protected java.lang.String dimension

allow2D

protected boolean allow2D

iatom0

private int iatom0

Constructor Detail

MolReader

public MolReader()

Method Detail

initializeReader

public void initializeReader()
                      throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

readUserData

private void readUserData(int atom0)
                   throws java.lang.Exception

Throws:

java.lang.Exception

finalizeReader

public void finalizeReader()
                    throws java.lang.Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

finalizeReaderMR

protected void finalizeReaderMR()
                         throws java.lang.Exception

Throws:

java.lang.Exception

processMolSdHeader

private void processMolSdHeader()
                         throws java.lang.Exception

Throws:

java.lang.Exception

processCtab

private void processCtab(boolean isMDL)
                  throws java.lang.Exception

Throws:

java.lang.Exception

readAtoms

private void readAtoms(int ac)
                throws java.lang.Exception

Throws:

java.lang.Exception

checkLineContinuation

private void checkLineContinuation()
                            throws java.lang.Exception

Throws:

java.lang.Exception

readBonds

private void readBonds(int bondCount)
                throws java.lang.Exception

Throws:

java.lang.Exception

fixOrder

private int fixOrder(int order,
                     int stereo)