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 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 |
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 and Description |
---|
ZMatrixReader() |
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) |
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
protected int atomCount
protected java.util.List<Atom> vAtoms
private java.util.Map<java.lang.String,java.lang.Integer> atomMap
private java.lang.String[] tokens
private boolean isJmolZformat
private java.util.List<java.lang.String[]> lineBuffer
private java.util.Map<java.lang.String,java.lang.Float> symbolicMap
private boolean isMopac
private boolean isHeader
private final javax.vecmath.Point3f pt0
private final javax.vecmath.Vector3f v1
private final javax.vecmath.Vector3f v2
private final javax.vecmath.Point4f plane1
private final javax.vecmath.Point4f 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
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)