public class MdCrdReader extends AtomSetCollectionReader
| Modifier and Type | Field and Description |
|---|---|
private int |
lenLine |
private int |
ptFloat |
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 |
|---|
MdCrdReader() |
| Modifier and Type | Method and Description |
|---|---|
protected boolean |
checkLine() |
private float |
getFloat() |
private javajs.util.P3 |
getPoint() |
private boolean |
getTrajectoryStep(javajs.util.P3[] trajectoryStep,
boolean isPeriodic) |
protected void |
initializeReader() |
private void |
readCoordinates() |
protected void |
setup(java.lang.String fullPath,
java.util.Map<java.lang.String,java.lang.Object> htParams,
java.lang.Object readerOrDocument) |
private boolean |
skipFloats(int n) |
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, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, 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, 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, setupASCRprotected void setup(java.lang.String fullPath,
java.util.Map<java.lang.String,java.lang.Object> htParams,
java.lang.Object readerOrDocument)
setup in class AtomSetCollectionReaderprotected void initializeReader()
initializeReader in class AtomSetCollectionReaderprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate void readCoordinates()
throws java.lang.Exception
java.lang.Exceptionprivate float getFloat()
throws java.lang.Exception
java.lang.Exceptionprivate javajs.util.P3 getPoint()
throws java.lang.Exception
java.lang.Exceptionprivate boolean getTrajectoryStep(javajs.util.P3[] trajectoryStep,
boolean isPeriodic)
throws java.lang.Exception
java.lang.Exceptionprivate boolean skipFloats(int n)
throws java.lang.Exception
java.lang.Exception