org.jmol.adapter.readers.more
Class ForceFieldReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.more.ForceFieldReader
Direct Known Subclasses:
MdTopReader, Mol2Reader

public abstract class ForceFieldReader
extends AtomSetCollectionReader


Field Summary
private  Properties atomTypes
           
private static String ffTypes
           
private static String secondCharOnly
           
private static String specialTypes
           
private static String twoChar
           
private  String userAtomTypes
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
ForceFieldReader()
           
 
Method Summary
protected static String deducePdbElementSymbol(boolean isHetero, String XX, String group3)
           
protected  boolean getElementSymbol(Atom atom, String atomType)
           
protected  void setUserAtomTypes()
           
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, 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, readAtomSetCollectionFromDOM, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, 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 String ffTypes
See Also:
Constant Field Values

twoChar

private static final String twoChar
See Also:
Constant Field Values

specialTypes

private static final String specialTypes
See Also:
Constant Field Values

secondCharOnly

private static final String secondCharOnly
See Also:
Constant Field Values

userAtomTypes

private String userAtomTypes

atomTypes

private Properties atomTypes
Constructor Detail

ForceFieldReader

public ForceFieldReader()
Method Detail

setUserAtomTypes

protected void setUserAtomTypes()

getElementSymbol

protected boolean getElementSymbol(Atom atom,
                                   String atomType)

deducePdbElementSymbol

protected static String deducePdbElementSymbol(boolean isHetero,
                                               String XX,
                                               String group3)