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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class JanaReader
extends AtomSetCollectionReader
```
A reader for Jana M50+M40 file pairs. TODO: rigid-body rotation TLS, local symmetry, and local axes

Author:

Bob Hanson hansonr@stolaf.edu 8/7/2013

Field Summary

Fields
Modifier and Type	Field	Description
`(package private) static int`	`CELL`
`(package private) static int`	`END`
`private boolean`	`firstPosition`
`private float[]`	`floats`
`private boolean`	`haveM40Data`
`private boolean`	`isLegendre`
`(package private) static int`	`LATT`
`private javajs.util.Lst<float[]>`	`lattvecs`
`private javajs.util.M3`	`matR`
`private java.lang.String`	`modAxes`
`private int`	`modDim`
`private javajs.util.Lst<javajs.util.P3>`	`modelMolecule`
`private javajs.util.Lst<Atom>`	`molAtoms`
`private boolean`	`molHasTLS`
`private java.lang.String`	`molName`
`private javajs.util.Lst<java.lang.Integer>`	`molTtypes`
`(package private) static int`	`NDIM`
`(package private) static int`	`QI`
`private int`	`qicount`
`(package private) static java.lang.String`	`records`
`private javajs.util.P3`	`rho`
`(package private) static int`	`SPG`
`(package private) static int`	`SYM`
`private int`	`thisSub`
`(package private) static int`	`TITLE`
`static java.lang.String`	`U_LIST`
`private javajs.util.V3`	`v0Cart`
`private javajs.util.V3`	`vR`
`(package private) static int`	`WMATRIX`
`private static java.lang.String[]`	`XYZ`

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

JanaReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`addSinCos(int j, java.lang.String key, java.lang.String label, boolean isPos)`	Add x, y, and z modulations as [ csin, ccos, 0 ] or, possibly Legendre [ coef, order, 0 ]
`private void`	`adjustM40Occupancies()`	M40 occupancies are divided by the site multiplicity; here we factor that back in.
`private void`	`cartesianProduct(javajs.util.T3 vA, javajs.util.T3 vB)`	dual-purpose function for cross products, proper rotations, and improper rotations
`private void`	`cell()`
`protected boolean`	`checkLine()`
`private double[]`	`combineModulation(java.lang.String key, float csin, float ccos)`	Retrieve cataloged displacement and add in this component, returning a new double[3].
`private void`	`copyModulations(java.lang.String label, java.lang.String newLabel)`	Create a new catalog entry for an atom's modulation components.
`void`	`doPreSymmetry()`
`private void`	`ensureFourier(int j)`	Make sure that F_n record is present.
`void`	`finalizeSubclassReader()`	optional reader-specific method run first.
`protected void`	`finalizeSubclassSymmetry(boolean haveSymmetry)`
`private boolean`	`getFlag(int i)`	safely get a one-character 0 or 1 as a boolean
`private int`	`getInt(int col1, int col2)`	safe int parsing of line.substring(col1, col2);
`private java.lang.String`	`getStr(int col1, int col2)`	safe string parsing of line.substring(col1, col2);
`void`	`initializeReader()`
`private void`	`ndim()`
`private void`	`parseM40Floats()`
`private void`	`processPosition(java.lang.String posName, Atom pos, boolean isAxial)`	We process the Pos#n record here.
`private void`	`qi()`
`private float[][]`	`readAtomRecord(Atom atom, javajs.util.P3 rm, javajs.util.P3 rp, boolean isPos)`	Read the atom or pos# record, including occupancy, various flags, and, especially, modulations.
`private void`	`readM40Data(boolean haveReader)`	read the M40 file, possibly as the extension of M50+M40
`private float[][]`	`readM40FloatLines(int nLines, int nFloats)`
`private java.lang.String`	`readM40Floats()`
`private void`	`readM40WaveVectors()`
`private void`	`setMolecularModulation(java.lang.String key, float csin, float ccos)`	Add the modulation after applying rigid-body phase correction
`private double[]`	`setRigidBodyPhase(java.lang.String key, double[] v)`	Adjust phases to match the difference between the atom's position and the rigid molecular fragment's reference point.
`private void`	`setRigidBodyRotations(java.lang.String label, float[][] params)`	Transform unphased Fourier x,y,z cos/sin coefficients in a rigid body system based on distance from center.
`private java.lang.String`	`skipToNextAtom()`
`private void`	`symmetry()`

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, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, 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
  - lattvecs
```
private javajs.util.Lst<float[]> lattvecs
```
  - thisSub
```
private int thisSub
```
  - modAxes
```
private java.lang.String modAxes
```
  - modDim
```
private int modDim
```
  - haveM40Data
```
private boolean haveM40Data
```
  - records
```
static final java.lang.String records
```
    See Also:
    
    Constant Field Values
  - TITLE
```
static final int TITLE
```
    See Also:
    
    Constant Field Values
  - CELL
```
static final int CELL
```
    See Also:
    
    Constant Field Values
  - NDIM
```
static final int NDIM
```
    See Also:
    
    Constant Field Values
  - QI
```
static final int QI
```
    See Also:
    
    Constant Field Values
  - LATT
```
static final int LATT
```
    See Also:
    
    Constant Field Values
  - SYM
```
static final int SYM
```
    See Also:
    
    Constant Field Values
  - SPG
```
static final int SPG
```
    See Also:
    
    Constant Field Values
  - END
```
static final int END
```
    See Also:
    
    Constant Field Values
  - WMATRIX
```
static final int WMATRIX
```
    See Also:
    
    Constant Field Values
  - qicount
```
private int qicount
```
  - molName
```
private java.lang.String molName
```
  - molAtoms
```
private javajs.util.Lst<Atom> molAtoms
```
  - molTtypes
```
private javajs.util.Lst<java.lang.Integer> molTtypes
```
  - modelMolecule
```
private javajs.util.Lst<javajs.util.P3> modelMolecule
```
  - molHasTLS
```
private boolean molHasTLS
```
  - matR
```
private javajs.util.M3 matR
```
  - rho
```
private javajs.util.P3 rho
```
  - firstPosition
```
private boolean firstPosition
```
  - vR
```
private javajs.util.V3 vR
```
  - v0Cart
```
private javajs.util.V3 v0Cart
```
  - isLegendre
```
private boolean isLegendre
```
  - U_LIST
```
public static final java.lang.String U_LIST
```
    See Also:
    
    Constant Field Values
  - XYZ
```
private static java.lang.String[] XYZ
```
  - floats
```
private float[] floats
```
- Constructor Detail
  - JanaReader
```
public JanaReader()
```
- Method Detail
  - initializeReader
```
public void initializeReader()
                      throws java.lang.Exception
```
    Overrides:
    
    initializeReader in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception
  - checkLine
```
protected boolean checkLine()
                     throws java.lang.Exception
```
    Overrides:
    
    checkLine in class AtomSetCollectionReader
    
    Returns:
    
    true if need to read new line
    
    Throws:
    
    java.lang.Exception
  - doPreSymmetry
```
public void doPreSymmetry()
                   throws java.lang.Exception
```
    Overrides:
    
    doPreSymmetry in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception
  - finalizeSubclassReader
```
public void finalizeSubclassReader()
                            throws java.lang.Exception
```
    Description copied from class: AtomSetCollectionReader
    
    optional reader-specific method run first.
    
    Overrides:
    
    finalizeSubclassReader in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception
  - finalizeSubclassSymmetry
```
protected void finalizeSubclassSymmetry(boolean haveSymmetry)
                                 throws java.lang.Exception
```
    Overrides:
    
    finalizeSubclassSymmetry in class AtomSetCollectionReader
    
    Throws:
    
    java.lang.Exception
  - cell
```
private void cell()
           throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - ndim
```
private void ndim()
           throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - qi
```
private void qi()
         throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - symmetry
```
private void symmetry()
               throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readM40Data
```
private void readM40Data(boolean haveReader)
                  throws java.lang.Exception
```
    read the M40 file, possibly as the extension of M50+M40
    
    Parameters:
    
    haveReader -
    
    Throws:
    
    java.lang.Exception
  - getInt
```
private int getInt(int col1,
                   int col2)
```
    safe int parsing of line.substring(col1, col2);
    
    Parameters:
    
    col1 -
    
    col2 -
    
    Returns:
    
    value or 0
  - getStr
```
private java.lang.String getStr(int col1,
                                int col2)
```
    safe string parsing of line.substring(col1, col2);
    
    Parameters:
    
    col1 -
    
    col2 -
    
    Returns:
    
    value or ""
  - getFlag
```
private boolean getFlag(int i)
```
    safely get a one-character 0 or 1 as a boolean
    
    Parameters:
    
    i -
    
    Returns:
    
    true if it was a 1
  - skipToNextAtom
```
private java.lang.String skipToNextAtom()
                                 throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - readM40WaveVectors
```
private void readM40WaveVectors()
                         throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - processPosition
```
private void processPosition(java.lang.String posName,
                             Atom pos,
                             boolean isAxial)
                      throws java.lang.Exception
```
    We process the Pos#n record here. This involves cloning the free atoms, translating and rotating them to the proper locations, and copying the modulations. Jmol uses the alternative location PDB option (%1, %2,...) to specify the group, enabling the Jmol command DISPLAY configuration=1, for example. We also set a flag to prevent autobonding between alt-loc sets. This is not perfect, as in some cases "pos#2" would be better than "pos#1" in terms of bonding. At this point we only support systType=1 (basic coordinates)
    
    Parameters:
    
    posName -
    
    pos -
    
    isAxial -
    
    Throws:
    
    java.lang.Exception
  - cartesianProduct
```
private void cartesianProduct(javajs.util.T3 vA,
                              javajs.util.T3 vB)
```
    dual-purpose function for cross products, proper rotations, and improper rotations
    
    Parameters:
    
    vA -
    
    vB -
  - readAtomRecord
```
private float[][] readAtomRecord(Atom atom,
                                 javajs.util.P3 rm,
                                 javajs.util.P3 rp,
                                 boolean isPos)
                          throws java.lang.Exception
```
    Read the atom or pos# record, including occupancy, various flags, and, especially, modulations. Not implemented: TLS, space groups, and local position rotation axes.
    
    Parameters:
    
    atom -
    
    rm - // rotation vector/point not implemented
    
    rp - // rotation point not implemented
    
    isPos -
    
    Returns:
    
    pos# record's rotational displacement data
    
    Throws:
    
    java.lang.Exception
  - addSinCos
```
private void addSinCos(int j,
                       java.lang.String key,
                       java.lang.String label,
                       boolean isPos)
                throws java.lang.Exception
```
    Add x, y, and z modulations as [ csin, ccos, 0 ] or, possibly Legendre [ coef, order, 0 ]
    
    Parameters:
    
    j -
    
    key -
    
    label -
    
    isPos -
    
    Throws:
    
    java.lang.Exception
  - ensureFourier
```
private void ensureFourier(int j)
```
    Make sure that F_n record is present.
    
    Parameters:
    
    j -
  - readM40Floats
```
private java.lang.String readM40Floats()
                                throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - parseM40Floats
```
private void parseM40Floats()
```
  - readM40FloatLines
```
private float[][] readM40FloatLines(int nLines,
                                    int nFloats)
                             throws java.lang.Exception
```
    Throws:
    
    java.lang.Exception
  - adjustM40Occupancies
```
private void adjustM40Occupancies()
```
    M40 occupancies are divided by the site multiplicity; here we factor that back in.
  - copyModulations
```
private void copyModulations(java.lang.String label,
                             java.lang.String newLabel)
```
    Create a new catalog entry for an atom's modulation components. Just occupation and displacement here.
    
    Parameters:
    
    label -
    
    newLabel -
  - setRigidBodyPhase
```
private double[] setRigidBodyPhase(java.lang.String key,
                                   double[] v)
```
    Adjust phases to match the difference between the atom's position and the rigid molecular fragment's reference point. We have: a' = g + vR Here we want just the local rotational part, vR
    
    Parameters:
    
    key -
    
    v -
    
    Returns:
    
    phase-adjusted parameters
  - setRigidBodyRotations
```
private void setRigidBodyRotations(java.lang.String label,
                                   float[][] params)
```
    Transform unphased Fourier x,y,z cos/sin coefficients in a rigid body system based on distance from center. We have: a' = g + vR = g + R(v0) Here we need just the original atom offset from the reference point, v0, as a Cartesian vector.
    
    Parameters:
    
    label - ";atomName"
    
    params - block of [nDisp][6] rotational parameters
  - combineModulation
```
private double[] combineModulation(java.lang.String key,
                                   float csin,
                                   float ccos)
```
    Retrieve cataloged displacement and add in this component, returning a new double[3].
    
    Parameters:
    
    key -
    
    csin -
    
    ccos -
    
    Returns:
    
    new array
  - setMolecularModulation
```
private void setMolecularModulation(java.lang.String key,
                                    float csin,
                                    float ccos)
```
    Add the modulation after applying rigid-body phase correction
    
    Parameters:
    
    key -
    
    csin -
    
    ccos -

Class JanaReader

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

lattvecs

thisSub

modAxes

modDim

haveM40Data

records

TITLE

CELL

NDIM

QI

LATT

SYM

SPG

END

WMATRIX

qicount

molName

molAtoms

molTtypes

modelMolecule

molHasTLS

matR

rho

firstPosition

vR

v0Cart

isLegendre

U_LIST

XYZ

floats

Constructor Detail

JanaReader

Method Detail

initializeReader

checkLine

doPreSymmetry

finalizeSubclassReader

finalizeSubclassSymmetry

cell

ndim

qi

symmetry

readM40Data

getInt

getStr

getFlag

skipToNextAtom

readM40WaveVectors

processPosition

cartesianProduct

readAtomRecord

addSinCos

ensureFourier

readM40Floats

parseM40Floats

readM40FloatLines

adjustM40Occupancies

copyModulations

setRigidBodyPhase

setRigidBodyRotations

combineModulation

setMolecularModulation