public class MagresReader extends AtomSetCollectionReader
| Modifier and Type | Field and Description |
|---|---|
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, 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 |
|---|
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, 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, 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, setupASCRprivate 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 AtomSetCollectionReaderprotected void finalizeSubclassReader()
throws java.lang.Exception
finalizeSubclassReader in class AtomSetCollectionReaderjava.lang.Exceptionprotected boolean checkLine()
throws java.lang.Exception
checkLine in class AtomSetCollectionReaderjava.lang.Exceptionprivate boolean trimLine()
private int checkBlock()
private boolean setUnits(boolean isMagresBlock)
isMagresBlock - private boolean readSymmetry()
private boolean readCellParams()
throws java.lang.Exception
java.lang.Exceptionprivate 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