org.jmol.adapter.readers.simple

Class ZMatrixReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.simple.ZMatrixReader

Direct Known Subclasses:

MopacArchiveReader

public class ZMatrixReader
extends AtomSetCollectionReader

Field Summary

Fields

Modifier and Type	Field and Description
protected int	atomCount
private java.util.Map<java.lang.String,java.lang.Integer>	atomMap
private boolean	isHeader
private boolean	isJmolZformat
private boolean	isMopac
private java.util.List<java.lang.String[]>	lineBuffer
private javax.vecmath.Point4f	plane1
private javax.vecmath.Point4f	plane2
private javax.vecmath.Point3f	pt0
private java.util.Map<java.lang.String,java.lang.Float>	symbolicMap
private java.lang.String[]	tokens
private javax.vecmath.Vector3f	v1
private javax.vecmath.Vector3f	v2
protected java.util.List<Atom>	vAtoms

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

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
ZMatrixReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected boolean	checkLine()
private void	cleanLine()
protected void	finalizeReader()
private void	getAtom()
private int	getAtomIndex(int i)
private void	getSymbolic()
private float	getSymbolic(java.lang.String key)
private float	getValue(int i)
protected Atom	setAtom(Atom atom, int ia, int ib, int ic, float d, float theta1, float theta2)

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, filterAtom, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, initializeTrajectoryFile, 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, setElementAndIsotope, 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

atomCount

protected int atomCount

vAtoms

protected java.util.List<Atom> vAtoms

atomMap

private java.util.Map<java.lang.String,java.lang.Integer> atomMap

tokens

private java.lang.String[] tokens

isJmolZformat

private boolean isJmolZformat

lineBuffer

private java.util.List<java.lang.String[]> lineBuffer

symbolicMap

private java.util.Map<java.lang.String,java.lang.Float> symbolicMap

isMopac

private boolean isMopac

isHeader

private boolean isHeader

pt0

private final javax.vecmath.Point3f pt0

v1

private final javax.vecmath.Vector3f v1

v2

private final javax.vecmath.Vector3f v2

plane1

private final javax.vecmath.Point4f plane1

plane2

private final javax.vecmath.Point4f plane2

Constructor Detail

ZMatrixReader

public ZMatrixReader()

Method Detail

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

java.lang.Exception

cleanLine

private void cleanLine()

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

getSymbolic

private void getSymbolic()

getAtom

private void getAtom()
              throws java.lang.Exception

Throws:

java.lang.Exception

getSymbolic

private float getSymbolic(java.lang.String key)

getValue

private float getValue(int i)
                throws java.lang.Exception

Throws:

java.lang.Exception

getAtomIndex

private int getAtomIndex(int i)

setAtom

protected Atom setAtom(Atom atom,
           int ia,
           int ib,
           int ic,
           float d,
           float theta1,
           float theta2)