public class ZMatrixReader extends AtomSetCollectionReader
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 JmolList<java.lang.String[]> |
lineBuffer |
private P4 |
plane1 |
private P4 |
plane2 |
private P3 |
pt0 |
private java.util.Map<java.lang.String,java.lang.Float> |
symbolicMap |
private java.lang.String[] |
tokens |
private V3 |
v1 |
private V3 |
v2 |
protected JmolList<Atom> |
vAtoms |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
ZMatrixReader() |
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) |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeReader, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
protected int atomCount
private java.util.Map<java.lang.String,java.lang.Integer> atomMap
private java.lang.String[] tokens
private boolean isJmolZformat
private JmolList<java.lang.String[]> lineBuffer
private java.util.Map<java.lang.String,java.lang.Float> symbolicMap
private boolean isMopac
private boolean isHeader
private final P3 pt0
private final V3 v1
private final V3 v2
private final P4 plane1
private final P4 plane2
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private void cleanLine()
protected void finalizeReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeReader
in class AtomSetCollectionReader
java.lang.Exception
private void getSymbolic()
private void getAtom() throws java.lang.Exception
java.lang.Exception
private float getSymbolic(java.lang.String key)
private float getValue(int i) throws java.lang.Exception
java.lang.Exception
private int getAtomIndex(int i)