org.jmol.adapter.readers.simple

Class GhemicalMMReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.simple.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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
GhemicalMMReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
(package private) void	processAtoms()
(package private) void	processBonds()
(package private) void	processCharges()
(package private) void	processCoord()
(package private) void	processHeader()
(package private) void	processInfo()

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

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, 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

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

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