org.jmol.adapter.readers.molxyz

Class MolReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.molxyz.MolReader

Direct Known Subclasses:

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
(package private) boolean	allow2D
protected java.lang.String	dimension
(package private) boolean	is2D
private boolean	isV3000

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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
MolReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
private void	checkLineContinuation()
void	finalizeReader()
void	initializeReader()
(package private) void	processCtab(boolean isMDL)
(package private) void	processMolSdHeader()
(package private) void	readAtoms(int atomCount)
(package private) void	readBonds(int atom0, int bondCount)
private void	readUserData(int atom0)

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem

Methods inherited from class java.lang.Object

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

Field Detail

is2D

boolean is2D

isV3000

private boolean isV3000

dimension

protected java.lang.String dimension

allow2D

boolean allow2D

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

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

processMolSdHeader

void processMolSdHeader()
                  throws java.lang.Exception

Throws:

java.lang.Exception

processCtab

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

Throws:

java.lang.Exception

readAtoms

void readAtoms(int atomCount)
         throws java.lang.Exception

Throws:

java.lang.Exception

checkLineContinuation

private void checkLineContinuation()
                            throws java.lang.Exception

Throws:

java.lang.Exception

readBonds

void readBonds(int atom0,
             int bondCount)
         throws java.lang.Exception

Throws:

java.lang.Exception