org.jmol.adapter.readers.molxyz
Class MolReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by 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
(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
MolReader()
           
 
Method Summary
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