javajs.api.GenericLineReader
public class WebMOReader extends MopacSlaterReader
http://www.webmo.net/demo/ right now WebMO files don't allow for multiple MOS, but we will assume here that that may change.
BasisFunctionReader.MOEnergySorter
SlaterReader.OrbitalSorter, SlaterReader.SlaterSorter
Modifier and Type | Field | Description |
---|---|---|
private static java.lang.String |
DC_LIST |
|
private static java.lang.String |
DS_LIST |
|
private static java.lang.String |
FC_LIST |
|
private static java.lang.String |
FS_LIST |
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
alphaBeta, dfCoefMaps, ignoreMOs, moData, nCoef, nOrbitals, orbitals, shells
atomicNumbers, MIN_COEF
slaterArray, slaters
Constructor | Description |
---|---|
WebMOReader() |
Modifier and Type | Method | Description |
---|---|---|
protected boolean |
checkLine() |
|
protected void |
finalizeSubclassReader() |
optional reader-specific method run first.
|
private boolean |
getLine() |
|
(package private) void |
readAtomicOrbitalOrder() |
|
(package private) void |
readAtoms() |
|
(package private) void |
readBonds() |
|
(package private) void |
readGaussianBasis() |
|
(package private) void |
readHeader() |
|
(package private) void |
readMolecularOrbital() |
|
(package private) void |
readSlaterBasis() |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, 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
canonicalizeQuantumSubshellTag, discardPreviousAtoms, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, getQuantumShellTag, getQuantumShellTagID, getQuantumShellTagIDSpherical, setMO
createSphericalSlaterByType, scaleSlater
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addSlater, addSlater, getSlaterConstCartesian, getSlaterConstDSpherical, setMOs, setSlaters, sortOrbitalCoefficients, sortOrbitals
private static java.lang.String DS_LIST
private static java.lang.String DC_LIST
private static java.lang.String FS_LIST
private static java.lang.String FC_LIST
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
protected void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
void readHeader() throws java.lang.Exception
java.lang.Exception
void readAtoms() throws java.lang.Exception
java.lang.Exception
void readBonds() throws java.lang.Exception
java.lang.Exception
void readAtomicOrbitalOrder() throws java.lang.Exception
java.lang.Exception
private boolean getLine() throws java.lang.Exception
java.lang.Exception
void readGaussianBasis() throws java.lang.Exception
java.lang.Exception
void readSlaterBasis() throws java.lang.Exception
java.lang.Exception
void readMolecularOrbital() throws java.lang.Exception
java.lang.Exception