Package org.jmol.adapter.readers.pdb
Class PqrReader
java.lang.Object
org.jmol.adapter.smarter.AtomSetCollectionReader
org.jmol.adapter.readers.pdb.PdbReader
org.jmol.adapter.readers.pdb.PqrReader
- All Implemented Interfaces:
javajs.api.GenericLineReader
PQR file reader.
Angel Herraez, 2009 04 19
free form added Bob Hanson hansonr@stolaf.edu 2012 06 25
filter "FREE"
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
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Field Summary
Fields inherited from class org.jmol.adapter.readers.pdb.PdbReader
biomtChainAtomCounts, fileAtomIndex, gromacsWideFormat, htGroup1
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, CELL_TYPE_CONVENTIONAL, CELL_TYPE_PRIMITIVE, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterAllHetero, filterCased, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, is2D, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, merging, modDim, modelNumber, ms, mustFinalizeModelSet, next, noHydrogens, noPack, optimize2D, out, packingError, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
adaptable via subclassingMethods inherited from class org.jmol.adapter.readers.pdb.PdbReader
checkLine, checkRemark, deduceElementSymbol, filterPDBAtom, finalizeReaderPDB, finalizeSubclassReader, fixRadius, initializeReader, model, processAtom, processAtom2
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkAndRemoveFilterKey, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fill3x3, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFilterWithCase, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
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Constructor Details
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PqrReader
public PqrReader()
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Method Details
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setAdditionalAtomParameters
Description copied from class:PdbReader
adaptable via subclassing- Overrides:
setAdditionalAtomParameters
in classPdbReader
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