org.jmol.adapter.readers.more
Class PqrReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.cifpdb.PdbReader
          extended by org.jmol.adapter.readers.more.PqrReader

public class PqrReader
extends PdbReader

PQR file reader.

http://www.rcsb.org

Author:
Miguel, Egon, and Bob (hansonr@stolaf.edu) symmetry added by Bob Hanson: setFractionalCoordinates() setSpaceGroupName() setUnitCell() initializeCartesianToFractional(); setUnitCellItem() setAtomCoord() applySymmetryAndSetTrajectory()

Field Summary
protected  java.lang.String fileType
           
 
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
PqrReader()
           
 
Method Summary
protected  float readBFactor()
           
protected  int readOccupancy()
           
protected  float readPartialCharge()
           
protected  float readRadius()
           
 
Methods inherited from class org.jmol.adapter.readers.cifpdb.PdbReader
applySymmetryAndSetTrajectory, readAtomSetCollection
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, 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, 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

fileType

protected java.lang.String fileType
Constructor Detail

PqrReader

public PqrReader()
Method Detail

readOccupancy

protected int readOccupancy()
Overrides:
readOccupancy in class PdbReader

readBFactor

protected float readBFactor()
Overrides:
readBFactor in class PdbReader

readPartialCharge

protected float readPartialCharge()
Overrides:
readPartialCharge in class PdbReader

readRadius

protected float readRadius()
Overrides:
readRadius in class PdbReader