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	ac
private java.util.Map<java.lang.String,java.lang.Integer>	atomMap
private boolean	isHeader
private boolean	isJmolZformat
private boolean	isMopac
private javajs.util.List<java.lang.String[]>	lineBuffer
private javajs.util.P4	plane1
private javajs.util.P4	plane2
private javajs.util.P3	pt0
private java.util.Map<java.lang.String,java.lang.Float>	symbolicMap
private java.lang.String[]	tokens
private javajs.util.V3	v1
private javajs.util.V3	v2
protected javajs.util.List<Atom>	vAtoms

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

addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, vwr

Constructor Summary

Constructors

Constructor and Description
ZMatrixReader()

Method Summary

Modifier and Type	Method and Description
protected boolean	checkLine()
private void	cleanLine()
protected void	finalizeReader() optional reader-specific method run first.
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

addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeReader, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, rd, read3Vectors, readDataObject, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ac

protected int ac

vAtoms

protected javajs.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 javajs.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 javajs.util.P3 pt0

v1

private final javajs.util.V3 v1

v2

private final javajs.util.V3 v2

plane1

private final javajs.util.P4 plane1

plane2

private final javajs.util.P4 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

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

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)