public class CgdReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
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private javajs.util.Lst<java.lang.String> |
edgeData |
private java.util.Map<Atom,javajs.util.V3[]> |
htEdges |
private java.lang.String |
lastName |
private boolean |
noBondSym |
private static java.lang.String |
SG_ALIASES |
private java.lang.String[] |
tokens |
private static javajs.util.V3[] |
vecs |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
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CgdReader() |
Modifier and Type | Method and Description |
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private void |
atom() |
protected boolean |
checkLine() |
private void |
finalizeEdges()
Now that we have all the edge data we can add edges to atoms
|
private void |
finalizeNet()
Using atom.vib as a proxy indicating rotation,
make all the bonds indicated in the atom's htEdges
|
void |
finalizeSubclassReader()
optional reader-specific method run first.
|
private Atom |
findAtom(javajs.util.P3 pt) |
private javajs.util.P3 |
getCoord(int i) |
private java.lang.String |
getName(java.lang.String name) |
private java.lang.String |
group(java.lang.String name) |
void |
initializeReader() |
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, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, processDOM, processDSSR, 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
private boolean noBondSym
private java.lang.String[] tokens
private java.util.Map<Atom,javajs.util.V3[]> htEdges
private java.lang.String lastName
private javajs.util.Lst<java.lang.String> edgeData
private static final java.lang.String SG_ALIASES
private static final javajs.util.V3[] vecs
public void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private java.lang.String group(java.lang.String name)
private void atom()
private java.lang.String getName(java.lang.String name)
public void finalizeSubclassReader() throws java.lang.Exception
AtomSetCollectionReader
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
private void finalizeEdges()
private javajs.util.P3 getCoord(int i)
private void finalizeNet()
private Atom findAtom(javajs.util.P3 pt)