java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xtal.MagresReader

All Implemented Interfaces:: javajs.api.GenericLineReader

public class MagresReader
extends AtomSetCollectionReader

Field Summary

Fields
Modifier and Type	Field	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`

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
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, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr

Constructor Summary

Constructors
Constructor Description

MagresReader()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	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.

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymmetryAndSetTrajectory, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, 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, 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 javajs.util.Lst<Tensor> interactionTensors
```
  - header
```
private javajs.util.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
  - finalizeSubclassReader
```
protected void finalizeSubclassReader()
                               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:
    
    finalizeSubclassReader 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

Class MagresReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

BLOCK_NEW

BLOCK_NONE

BLOCK_CALC

BLOCK_ATOMS

BLOCK_MAGRES

currentBlock

cellParams

magresUnits

interactionTensors

header

Constructor Detail

MagresReader

Method Detail

initializeReader

finalizeSubclassReader

checkLine

trimLine

checkBlock

setUnits

readSymmetry

readCellParams

readAtom

getAtomName

readTensor