public class InputReader extends AtomSetCollectionReader
Modifier and Type | Field and 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 |
addedData, addedDataKey, addVibrations, 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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
InputReader() |
Modifier and Type | Method and 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) |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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
protected int ac
protected javajs.util.Lst<Atom> vAtoms
private String[] tokens
private boolean isJmolZformat
private javajs.util.Lst<String[]> lineBuffer
private boolean isMopac
private boolean isHeader
private boolean firstLine
private final javajs.util.P3 pt0
private final javajs.util.V3 v1
private final javajs.util.V3 v2
private final javajs.util.P4 plane1
private final javajs.util.P4 plane2
protected boolean checkLine() throws Exception
checkLine
in class AtomSetCollectionReader
Exception
private String cleanLine()
protected void finalizeSubclassReader() throws Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
Exception
private void getSymbolic()
private void parseAtomTokens(Atom atom, String element) throws Exception
Exception
private Atom getAtomGeneral(Atom atom, int ia, int bondOrder) throws Exception
Exception
private float getSymbolic(String key)
private int getAtomIndex(int i)