org.jmol.adapter.readers.more

Class P2nReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.cifpdb.PdbReader

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

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
P2nReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	finalizeReader()
protected void	setAdditionalAtomParameters(Atom atom) adaptable via subclassing

Methods inherited from class org.jmol.adapter.readers.cifpdb.PdbReader

checkLine, filterAtom, initializeReader

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, 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