org.jmol.adapter.readers.more
Class GhemicalMMReader

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

public class GhemicalMMReader
extends AtomSetCollectionReader

Reads Ghemical ( http://www.uku.fi/~thassine/ghemical) molecular mechanics (*.mm1gp) files. !Header mm1gp 100 !Info 1 !Atoms 6 0 6 1 6 2 1 3 1 4 1 5 1 !Bonds 5 1 0 D 2 0 S 3 0 S 4 1 S 5 1 S !Coord 0 0.06677 -0.00197151 4.968e-07 1 -0.0667699 0.00197154 -5.19252e-07 2 0.118917 -0.097636 2.03406e-06 3 0.124471 0.0904495 -4.84021e-07 4 -0.118917 0.0976359 -2.04017e-06 5 -0.124471 -0.0904493 5.12591e-07 !Charges 0 -0.2 1 -0.2 2 0.1 3 0.1 4 0.1 5 0.1 !End

Author:

Egon Willighagen

Field Summary

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

GhemicalMMReader()

Method Summary

(package private) void	processAtoms()
(package private) void	processBonds()
(package private) void	processCharges()
(package private) void	processCoord()
(package private) void	processHeader()
(package private) void	processInfo()
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

Constructor Detail

GhemicalMMReader

public GhemicalMMReader()

Method Detail

readAtomSetCollection

public AtomSetCollection readAtomSetCollection(java.io.BufferedReader reader)

Specified by:

readAtomSetCollection in class AtomSetCollectionReader

processHeader

void processHeader()

processInfo

void processInfo()

processAtoms

void processAtoms()
            throws java.lang.Exception

Throws:

java.lang.Exception

processBonds

void processBonds()
            throws java.lang.Exception

Throws:

java.lang.Exception

processCoord

void processCoord()
            throws java.lang.Exception

Throws:

java.lang.Exception

processCharges

void processCharges()
              throws java.lang.Exception

Throws:

java.lang.Exception