org.jmol.adapter.readers.more
Class AlchemyReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.more.AlchemyReader

public class AlchemyReader
extends AtomSetCollectionReader

TRIPOS simple Alchemy reader. atomtypes based on OpenBabel data/types.txt Somewhat flexible - for 3DNA compatibility. See http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp.alc) Bob Hanson 12/2008

Field Summary

(package private) int	atomCount
(package private) int	bondCount

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

ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, doApplySymmetry, filter, getHeader, haveAtomFilter, havePartialChargeFilter, htParams, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isTrajectory, latticeCells, line, modelNumber, needToApplySymmetry, next, prevline, reader, readerName, spaceGroup, templateAtomCount

Constructor Summary

AlchemyReader()

Method Summary

private void	readAtoms()
void	readAtomSetCollection(java.io.BufferedReader reader)
private void	readBonds()

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

addJmolScript, addPrimitiveLatticeVector, addSites, applySymmetryAndSetTrajectory, checkLineForScript, checkLineForScript, clearLatticeParameters, deducePdbElementSymbol, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, fillDataBlock, filterAtom, filterAtom, getElementSymbol, getStrings, getTokens, getTokens, getTokens, getTokensFloat, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readAtomSetCollectionFromDOM, readData, readData, readLine, readLineTrimmed, setAtomCoord, setAtomCoord, setError, 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

Field Detail

atomCount

int atomCount

bondCount

int bondCount

Constructor Detail

AlchemyReader

public AlchemyReader()

Method Detail

readAtomSetCollection

public void readAtomSetCollection(java.io.BufferedReader reader)

Specified by:

readAtomSetCollection in class AtomSetCollectionReader

readAtoms

private void readAtoms()
                throws java.lang.Exception

Throws:

java.lang.Exception

readBonds

private void readBonds()
                throws java.lang.Exception

Throws:

java.lang.Exception