org.jmol.adapter.readers.xtal

Class MagresReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xtal.MagresReader

public class MagresReader
extends AtomSetCollectionReader

Field Summary

Fields

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 SB	header
private JmolList<Tensor>	interactionTensors
private java.util.Map<java.lang.String,java.lang.String>	magresUnits

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterAtomTypeStr, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, mustFinalizeModelSet, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer

Constructor Summary

Constructors

Constructor and Description
MagresReader()

Method Summary

Methods

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	finalizeReader() 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.

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, processDOM, read3Vectors, readDataObject, readLine, readLines, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setLoadNote, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

BLOCK_NEW

private static final int BLOCK_NEW

See Also:

Constant Field Values

BLOCK_NONE

private static final int BLOCK_NONE

See Also:

Constant Field Values

BLOCK_CALC

private static final int BLOCK_CALC

See Also:

Constant Field Values

BLOCK_ATOMS

private static final int BLOCK_ATOMS

See Also:

Constant Field Values

BLOCK_MAGRES

private static final int BLOCK_MAGRES

See Also:

Constant Field Values

currentBlock

private int currentBlock

cellParams

private float[] cellParams

magresUnits

private java.util.Map<java.lang.String,java.lang.String> magresUnits

interactionTensors

private JmolList<Tensor> interactionTensors

header

private SB header

Constructor Detail

MagresReader

public MagresReader()

Method Detail

initializeReader

protected void initializeReader()

not sure how to work with symmetry here...

Overrides:

initializeReader in class AtomSetCollectionReader

finalizeReader

protected void finalizeReader()
                       throws java.lang.Exception

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.

Overrides:

finalizeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

checkLine

protected boolean checkLine()
                     throws java.lang.Exception

Valid blocks include [calculation] [atoms] [magres]; all magres entries must be prefaced with a corresponding unit; Use of < > instead of [ ] is allowed.

Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true to read another line (some readers return false because they have over-read a line)

Throws:

java.lang.Exception

trimLine

private boolean trimLine()

All characters after hash ignored; lines are trimmed.

Returns:

true if line has content

checkBlock

private int checkBlock()

looking for tags here.

Returns:

currentBlock if not a tag or BLOCK_NEW otherwise

setUnits

private boolean setUnits(boolean isMagresBlock)

catalog units

Parameters:

isMagresBlock -

Returns:

true

readSymmetry

private boolean readSymmetry()

not doing anything with this -- P1 assumed

Returns:

true

readCellParams

private boolean readCellParams()
                        throws java.lang.Exception

Returns:

true;

Throws:

java.lang.Exception

readAtom

private boolean readAtom()

Allowing for BOHR units here; probably unnecessary.

Returns:

true

getAtomName

private static java.lang.String getAtomName(java.lang.String name,
                           java.lang.String index)

combine name and index

Parameters:

name -

index -

Returns:

name_index

readTensor

private boolean readTensor()
                    throws java.lang.Exception

Read a tensor line. Note that a corresponding unit line must have appeared first.

Returns:

true;

Throws:

java.lang.Exception