Package org.jmol.adapter.readers.xtal
Class PWmatReader
- java.lang.Object
-
- org.jmol.adapter.smarter.AtomSetCollectionReader
-
- org.jmol.adapter.readers.xtal.PWmatReader
-
- All Implemented Interfaces:
javajs.api.GenericLineReader
public class PWmatReader extends AtomSetCollectionReader
crude PWmat atom.config reader http://pwmatus.com/manual- Author:
- hansonr
-
-
Field Summary
Fields Modifier and Type Field Description private boolean
haveLattice
private boolean
haveMagnetic
private boolean
havePositions
private int
nAtoms
-
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addedData, addedDataKey, addVibrations, allow_a_len_1, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, baseBondIndex, binaryDoc, bsFilter, bsModels, calculationType, centroidPacked, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCentroidUnitCell, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterCased, 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, paramsCentroid, paramsLattice, prevline, primitiveToCrystal, ptLine, ptSupercell, reader, readerName, requiresBSFilter, reverseModels, rotateHexCell, sgName, slabXY, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, ucItems, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
-
-
Constructor Summary
Constructors Constructor Description PWmatReader()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
applySymmetryAndSetTrajectory()
protected boolean
checkLine()
protected void
finalizeSubclassReader()
optional reader-specific method run first.private java.lang.String
getLine()
protected void
initializeReader()
private void
readCoordinates()
private void
readDataBlock(java.lang.String name)
private void
readItems(java.lang.String name, int offset, float[] values)
private void
readUnitCell()
private void
readVectors(java.lang.String name, int offset, boolean haveLine)
private java.lang.String
removeComments()
private void
setProperties(java.lang.String name, float[] values, int iSet, int n)
private void
setVectors(java.lang.String name, float[] valuesX, float[] valuesY, float[] valuesZ, int n)
-
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addExplicitLatticeVector, addJmolScript, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkAndRemoveFilterKey, 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, getFilterWithCase, 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, setupASCR
-
-
-
-
Method Detail
-
initializeReader
protected void initializeReader() throws java.lang.Exception
- Overrides:
initializeReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
-
checkLine
protected boolean checkLine() throws java.lang.Exception
- Overrides:
checkLine
in classAtomSetCollectionReader
- Returns:
- true if need to read new line
- Throws:
java.lang.Exception
-
readUnitCell
private void readUnitCell() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readCoordinates
private void readCoordinates() throws java.lang.Exception
- Throws:
java.lang.Exception
-
readDataBlock
private void readDataBlock(java.lang.String name) throws java.lang.Exception
- Throws:
java.lang.Exception
-
readItems
private void readItems(java.lang.String name, int offset, float[] values) throws java.lang.Exception
- Throws:
java.lang.Exception
-
setProperties
private void setProperties(java.lang.String name, float[] values, int iSet, int n)
-
readVectors
private void readVectors(java.lang.String name, int offset, boolean haveLine) throws java.lang.Exception
- Throws:
java.lang.Exception
-
getLine
private java.lang.String getLine() throws java.lang.Exception
- Throws:
java.lang.Exception
-
removeComments
private java.lang.String removeComments()
-
setVectors
private void setVectors(java.lang.String name, float[] valuesX, float[] valuesY, float[] valuesZ, int n)
-
applySymmetryAndSetTrajectory
public void applySymmetryAndSetTrajectory() throws java.lang.Exception
- Overrides:
applySymmetryAndSetTrajectory
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
-
finalizeSubclassReader
protected void finalizeSubclassReader() throws java.lang.Exception
Description copied from class:AtomSetCollectionReader
optional reader-specific method run first.- Overrides:
finalizeSubclassReader
in classAtomSetCollectionReader
- Throws:
java.lang.Exception
-
-