org.jmol.adapter.readers.more
Class FFReader

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

Direct Known Subclasses:

MdTopReader, Mol2Reader

abstract class FFReader
extends AtomSetCollectionReader

Field Summary

private java.util.Properties	atomTypes
private static java.lang.String	ffTypes
private static java.lang.String	secondCharOnly
private static java.lang.String	specialTypes
private static java.lang.String	twoChar
private java.lang.String	userAtomTypes

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

FFReader()

Method Summary

protected boolean	getElementSymbol(Atom atom, java.lang.String atomType)
protected void	setUserAtomTypes()

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, readAtomSetCollection, 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

ffTypes

private static final java.lang.String ffTypes

See Also:

Constant Field Values

twoChar

private static final java.lang.String twoChar

See Also:

Constant Field Values

specialTypes

private static final java.lang.String specialTypes

See Also:

Constant Field Values

secondCharOnly

private static final java.lang.String secondCharOnly

See Also:

Constant Field Values

userAtomTypes

private java.lang.String userAtomTypes

atomTypes

private java.util.Properties atomTypes

Constructor Detail

FFReader

FFReader()

Method Detail

setUserAtomTypes

protected void setUserAtomTypes()

getElementSymbol

protected boolean getElementSymbol(Atom atom,
                                   java.lang.String atomType)