org.jmol.adapter.readers.molxyz
Class MolReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.molxyz.MolReader
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 |
private 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, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, discardLines, 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, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
is2D
boolean is2D
isV3000
private boolean isV3000
dimension
private java.lang.String dimension
MolReader
public MolReader()
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
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