org.jmol.adapter.readers.more
Class HinReader

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