org.jmol.adapter.readers.more
Class PqrReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.cifpdb.PdbReader
          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
(package private) java.lang.String[]	tokens

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

tokens

java.lang.String[] tokens

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