org.jmol.adapter.readers.cifpdb
Class PqrReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.cifpdb.PdbReader
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) java.lang.String[] |
tokens
|
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 |
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, 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 |
tokens
java.lang.String[] tokens
PqrReader
public PqrReader()
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