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)
applySymmetry()
Field Summary |
(package private) java.lang.String |
header
|
private static java.lang.String |
isotopeMap0
|
private static java.lang.String |
isotopeMap1
|
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, desiredModelNumber, desiredSpaceGroupIndex, doApplySymmetry, filter, getHeader, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveDesiredModel, iHaveSymmetryOperators, iHaveUnitCell, latticeCells, line, modelNumber, needToApplySymmetry, next, notionalUnitCell, prevline, primitiveLatticeVectors, ptLine, reader, readerName, spaceGroup |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetry, checkLineForScript, checkLineForScript, clearLatticeParameters, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, fillDataBlock, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, initialize, initialize, initializeCartesianToFractional, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setUnitCell, setUnitCellItem |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
header
java.lang.String header
isotopeMap0
private static final java.lang.String isotopeMap0
- See Also:
- Constant Field Values
isotopeMap1
private static final java.lang.String isotopeMap1
- See Also:
- Constant Field Values
MolReader
public MolReader()
readAtomSetCollection
public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)
- Specified by:
readAtomSetCollection
in class AtomSetCollectionReader
processMolSdHeader
void processMolSdHeader()
throws java.lang.Exception
- Throws:
java.lang.Exception
processRgHeader
void processRgHeader()
throws java.lang.Exception
- Throws:
java.lang.Exception
processCtab
void processCtab()
throws java.lang.Exception
- Throws:
java.lang.Exception
flushLines
void flushLines()
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtoms
void readAtoms(int atomCount)
throws java.lang.Exception
- Throws:
java.lang.Exception
readBonds
void readBonds(int atom0,
int bondCount)
throws java.lang.Exception
- Throws:
java.lang.Exception