Package org.jmol.adapter.readers.simple

Class InputReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.simple.InputReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

MopacArchiveReader

public class InputReader
extends AtomSetCollectionReader

Field Summary

Fields

Modifier and Type	Field	Description
protected int	ac
private Map<String,Integer>	atomMap
private boolean	firstLine
private boolean	isHeader
private boolean	isJmolZformat
private boolean	isMopac
private javajs.util.Lst<String[]>	lineBuffer
private javajs.util.P4	plane1
private javajs.util.P4	plane2
private javajs.util.P3	pt0
private Map<String,Float>	symbolicMap
private String[]	tokens
private javajs.util.V3	v1
private javajs.util.V3	v2
protected javajs.util.Lst<Atom>	vAtoms

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

addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isPrimitive, isSequential, isTrajectory, latticeCells, latticeScaling, latticeType, line, lstNCS, matUnitCellOrientation, modDim, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors

Constructor	Description
InputReader()

Method Summary

Modifier and Type	Method	Description
protected boolean	checkLine()
private String	cleanLine()
protected void	finalizeSubclassReader()	optional reader-specific method run first.
private Atom	getAtom()
private Atom	getAtomGeneral(Atom atom, int ia, int bondOrder)
private int	getAtomIndex(int i)
private void	getSymbolic()
private float	getSymbolic(String key)
private float	getValue(int i)
private void	parseAtomTokens(Atom atom, String element)
private boolean	readBlock(String strEnd)
private void	readCFI()
private void	readConFile()
private boolean	readVFI()
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, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, 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, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeReader, 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

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.Lst<Atom> vAtoms

atomMap

private Map<String,Integer> atomMap

tokens

private String[] tokens

isJmolZformat

private boolean isJmolZformat

lineBuffer

private javajs.util.Lst<String[]> lineBuffer

symbolicMap

private Map<String,Float> symbolicMap

isMopac

private boolean isMopac

isHeader

private boolean isHeader

firstLine

private boolean firstLine

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

InputReader

public InputReader()

Method Detail

checkLine

protected boolean checkLine()
                     throws Exception

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readConFile

private void readConFile()
                  throws Exception

Throws:

Exception

readCFI

private void readCFI()
              throws Exception

Throws:

Exception

readVFI

private boolean readVFI()
                 throws Exception

Throws:

Exception

readBlock

private boolean readBlock(String strEnd)
                   throws Exception

Throws:

Exception

cleanLine

private String cleanLine()

finalizeSubclassReader

protected void finalizeSubclassReader()
                               throws Exception

Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

Throws:

Exception

getSymbolic

private void getSymbolic()

getAtom

private Atom getAtom()
              throws Exception

Throws:

Exception

parseAtomTokens

private void parseAtomTokens(Atom atom,
                             String element)
                      throws Exception

Throws:

Exception

getAtomGeneral

private Atom getAtomGeneral(Atom atom,
                            int ia,
                            int bondOrder)
                     throws Exception

Throws:

Exception

getSymbolic

private float getSymbolic(String key)

getValue

private float getValue(int i)
                throws Exception

Throws:

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)