org.jmol.adapter.readers.more
Class P2nReader

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.P2nReader

public class P2nReader
extends PdbReader

P2N file reader. This format is the input for Resp ESP Charge Derive server http://q4md-forcefieldtools.org/


Field Summary
private  java.util.List<java.lang.String> altNames
           
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer
 
Constructor Summary
P2nReader()
           
 
Method Summary
protected  void finalizeReader()
           
protected  void setAdditionalAtomParameters(Atom atom)
          adaptable via subclassing
 
Methods inherited from class org.jmol.adapter.readers.cifpdb.PdbReader
applySymmetryAndSetTrajectory, checkLine, filterAtom, initializeReader
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, checkFilter, checkLastModel, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, 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, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, 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

altNames

private java.util.List<java.lang.String> altNames
Constructor Detail

P2nReader

public P2nReader()
Method Detail

setAdditionalAtomParameters

protected void setAdditionalAtomParameters(Atom atom)
Description copied from class: PdbReader
adaptable via subclassing

Overrides:
setAdditionalAtomParameters in class PdbReader

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception
Overrides:
finalizeReader in class PdbReader
Throws:
java.lang.Exception