public class InputReader extends AtomSetCollectionReader
| Modifier and Type | Field and Description |
|---|---|
protected int |
ac |
private java.util.Map<java.lang.String,java.lang.Integer> |
atomMap |
private boolean |
firstLine |
private boolean |
isHeader |
private boolean |
isJmolZformat |
private boolean |
isMopac |
private javajs.util.Lst<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.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, 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, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr| Constructor and Description |
|---|
InputReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
private java.lang.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(java.lang.String key) |
private float |
getValue(int i) |
private void |
parseAtomTokens(Atom atom,
java.lang.String element) |
private boolean |
readBlock(java.lang.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, 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, setupASCRprotected int ac
protected javajs.util.Lst<Atom> vAtoms
private java.util.Map<java.lang.String,java.lang.Integer> atomMap
private java.lang.String[] tokens
private boolean isJmolZformat
private javajs.util.Lst<java.lang.String[]> lineBuffer
private java.util.Map<java.lang.String,java.lang.Float> symbolicMap
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 java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readConFile()
throws java.lang.Exception
java.lang.Exceptionprivate void readCFI()
throws java.lang.Exception
java.lang.Exceptionprivate boolean readVFI()
throws java.lang.Exception
java.lang.Exceptionprivate boolean readBlock(java.lang.String strEnd)
throws java.lang.Exception
java.lang.Exceptionprivate java.lang.String cleanLine()
protected void finalizeSubclassReader()
throws java.lang.Exception
AtomSetCollectionReaderfinalizeSubclassReader in class AtomSetCollectionReaderjava.lang.Exceptionprivate void getSymbolic()
private Atom getAtom() throws java.lang.Exception
java.lang.Exceptionprivate void parseAtomTokens(Atom atom, java.lang.String element) throws java.lang.Exception
java.lang.Exceptionprivate Atom getAtomGeneral(Atom atom, int ia, int bondOrder) throws java.lang.Exception
java.lang.Exceptionprivate float getSymbolic(java.lang.String key)
private float getValue(int i)
throws java.lang.Exception
java.lang.Exceptionprivate int getAtomIndex(int i)