org.jmol.adapter.readers.cifpdb
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.cifpdb.PqrReader

public class PqrReader
extends PdbReader

PQR file reader. Angel Herraez, 2009 04 19 PQR format is a format based on pdb, where the occupancy is replaced with the atomic charge and the temperature (or B factor) is replaced with atomic radius (however, the column positions in many pqr files do not match those of pdb files). This gives the acronym: P for pdb, Q for charge, R for radius. Jmol interprets the charge values (property partialcharge) and the radii (property vanderwaals), and can hence use them e.g. in color atoms partialCharge and spacefill. The PQR format has somewhat uncertain origins, but is used by several computational biology packages, including MEAD, AutoDock and APBS[1], for which it is the primary input format. PQR format description[2] within APBS documentation. Note that APBS reads PQR loosely, based only on white space delimiters, but Jmol may be more strict about column positions. PDB files can be converted to PQR by the PDB2PQR software[3], which adds missing hydrogen atoms and calculates the charge and radius parameters from a variety of force fields. 1.- http://apbs.sourceforge.net/ 2.- http://apbs.sourceforge.net/doc/user-guide/index.html#pqr-format 3.- http://pdb2pqr.sourceforge.net/ 4.- http://cardon.wustl.edu/MediaWiki/index.php/PQR_format

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

Field Summary
(package private)  String[] tokens
           
 
Fields inherited from class org.jmol.adapter.readers.cifpdb.PdbReader
compnd, sbIgnored, sbSelected
 
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
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, checkLine, filterAtom, finalizeReader, initializeReader
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, 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

tokens

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