public class MagresReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
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private static int |
BLOCK_ATOMS |
private static int |
BLOCK_CALC |
private static int |
BLOCK_MAGRES |
private static int |
BLOCK_NEW |
private static int |
BLOCK_NONE |
private float[] |
cellParams |
private int |
currentBlock |
private javajs.util.SB |
header |
private javajs.util.Lst<Tensor> |
interactionTensors |
private java.util.Map<java.lang.String,java.lang.String> |
magresUnits |
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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MagresReader() |
Modifier and Type | Method and Description |
---|---|
private int |
checkBlock()
looking for tags here.
|
protected boolean |
checkLine()
Valid blocks include [calculation] [atoms] [magres];
all magres entries must be prefaced with a corresponding unit;
Use of < > instead of [ ] is allowed.
|
protected void |
finalizeSubclassReader()
Set final auxiliary info and symmetry, including
"fileHeader", "magresUnits", and "interactionTensors";
note that print getProperty("auxiliaryInfo.models[1].magresUnits")
should return a catalog of tensor types.
|
private static java.lang.String |
getAtomName(java.lang.String name,
java.lang.String index)
combine name and index
|
protected void |
initializeReader()
not sure how to work with symmetry here...
|
private boolean |
readAtom()
Allowing for BOHR units here; probably unnecessary.
|
private boolean |
readCellParams() |
private boolean |
readSymmetry()
not doing anything with this -- P1 assumed
|
private boolean |
readTensor()
Read a tensor line.
|
private boolean |
setUnits(boolean isMagresBlock)
catalog units
|
private boolean |
trimLine()
All characters after hash ignored; lines are trimmed.
|
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 static final int BLOCK_NEW
private static final int BLOCK_NONE
private static final int BLOCK_CALC
private static final int BLOCK_ATOMS
private static final int BLOCK_MAGRES
private int currentBlock
private float[] cellParams
private java.util.Map<java.lang.String,java.lang.String> magresUnits
private javajs.util.Lst<Tensor> interactionTensors
private javajs.util.SB header
protected void initializeReader()
initializeReader
in class AtomSetCollectionReader
protected void finalizeSubclassReader() throws java.lang.Exception
finalizeSubclassReader
in class AtomSetCollectionReader
java.lang.Exception
protected boolean checkLine() throws java.lang.Exception
checkLine
in class AtomSetCollectionReader
java.lang.Exception
private boolean trimLine()
private int checkBlock()
private boolean setUnits(boolean isMagresBlock)
isMagresBlock
- private boolean readSymmetry()
private boolean readCellParams() throws java.lang.Exception
java.lang.Exception
private boolean readAtom()
private static java.lang.String getAtomName(java.lang.String name, java.lang.String index)
name
- index
- private boolean readTensor() throws java.lang.Exception
java.lang.Exception