org.jmol.adapter.readers.more
Class HinReader

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

public class HinReader
extends AtomSetCollectionReader

Support for .hin, HyperChem's native file format. http://www.hyper.com

Record format is: atom 1 - C ** - -0.06040 0.00000 0.00000 0.00000 3 2 a 6 a 38 s ... atom 67 - H ** - 0.17710 -7.10260 -3.74840 2.24660 1 34 s endmol 1 interesting fields are partialCharge, x, y, z, bondCount
bonds are atom number and s/d/t/a for single/double/triple/aromatic

Field Summary

(package private) int	atomIndex
(package private) int	baseAtomIndex

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

Constructor Summary

HinReader()

Method Summary

(package private) java.lang.String	getMolName()
(package private) void	processAtom()
(package private) void	processEndmol()
(package private) void	processMol()
(package private) void	readAtoms()
AtomSetCollection	readAtomSetCollection(java.io.BufferedReader reader)

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

Field Detail

atomIndex

int atomIndex

baseAtomIndex

int baseAtomIndex

Constructor Detail

HinReader

public HinReader()

Method Detail

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)

Specified by:

readAtomSetCollection in class AtomSetCollectionReader

readAtoms

void readAtoms()
         throws java.lang.Exception

Throws:

java.lang.Exception

processMol

void processMol()
          throws java.lang.Exception

Throws:

java.lang.Exception

getMolName

java.lang.String getMolName()

processAtom

void processAtom()
           throws java.lang.Exception

Throws:

java.lang.Exception

processEndmol

void processEndmol()