GulpReader

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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class GulpReader
extends AtomSetCollectionReader
```
Problems identified (Bob Hanson) -- -- Coordinates for the asymmetric unit are conventional. Default right now is to read conventional cell, not primitive celll -- Frequency data number of atoms does not correspond to initial atom count. It looks like there is a missing report of symmetry-generated atoms. see https://projects.ivec.org/gulp/

Version:

1.0

Author:

Pieremanuele Canepa, Room 104, FM Group School of Physical Sciences, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH United Kingdom, pc229@kent.ac.uk

Field Summary

Fields
Modifier and Type	Field and Description
`private float`	`a`
`private float`	`alpha`
`private Map<String,Float>`	`atomCharges`
`private float`	`b`
`private float`	`beta`
`private boolean`	`bTest`
`private float`	`c`
`private boolean`	`coordinatesArePrimitive`
`private String`	`energyUnits`
`private float`	`gamma`
`private boolean`	`isPolymer`
`private boolean`	`isPrimitive`
`private boolean`	`isSlab`
`private float[]`	`primitiveData`
`private String`	`sep`
`private static String[]`	`tags`
`private Double`	`totEnergy`

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 and Description

GulpReader()

Constructors
Constructor and Description
`GulpReader()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`applySymmetryAndSetTrajectory()`
`protected boolean`	`checkLine()`
`protected void`	`finalizeSubclassReader()` optional reader-specific method run first.
`protected void`	`initializeReader()`
`private void`	`newAtomSet(boolean doSetUnitCell)`
`private static int`	`parameterIndex(String key)`
`private void`	`readAtomicPos(boolean finalizeSymmetry)`
`private void`	`readCellParameters(boolean isLatticeVectors)`
`private boolean`	`readDimensionality()`
`private void`	`readEnergy()`
`private void`	`readFinalCell()`
`private void`	`readPartialCharges()`
`private void`	`readSpaceGroup()`
`private void`	`scalePrimitiveData(int i, float value)`
`private void`	`setEnergy()`
`private void`	`setModelParameters(boolean isPrimitive)`
`private void`	`setParameter(String key, float value)`

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, 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

isSlab
```
private boolean isSlab
```

isPolymer
```
private boolean isPolymer
```

isPrimitive
```
private boolean isPrimitive
```

sep
```
private String sep
```

coordinatesArePrimitive

private boolean coordinatesArePrimitive

atomCharges
```
private Map<String,Float> atomCharges
```

bTest
```
private boolean bTest
```

a
```
private float a
```

b
```
private float b
```

c
```
private float c
```

alpha
```
private float alpha
```

beta
```
private float beta
```

gamma
```
private float gamma
```

primitiveData
```
private float[] primitiveData
```

tags
```
private static final String[] tags
```

totEnergy
```
private Double totEnergy
```

energyUnits
```
private String energyUnits
```

Constructor Detail
- GulpReader
```
public GulpReader()
```

Method Detail

initializeReader
```
protected void initializeReader()
                         throws Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

Exception

finalizeSubclassReader
```
protected void finalizeSubclassReader()
```
Description copied from class: AtomSetCollectionReader

optional reader-specific method run first.

Overrides:

finalizeSubclassReader in class AtomSetCollectionReader

checkLine
```
protected boolean checkLine()
                     throws Exception
```
Overrides:

checkLine in class AtomSetCollectionReader

Returns:

true if need to read new line

Throws:

Exception

readDimensionality

private boolean readDimensionality()
                            throws Exception

Throws:: Exception

readSpaceGroup

private void readSpaceGroup()
                     throws Exception

Throws:: Exception

parameterIndex

private static int parameterIndex(String key)

setParameter

private void setParameter(String key,
                          float value)

newAtomSet

private void newAtomSet(boolean doSetUnitCell)

setModelParameters

private void setModelParameters(boolean isPrimitive)

readCellParameters

private void readCellParameters(boolean isLatticeVectors)
                         throws Exception

Throws:: Exception

readFinalCell

private void readFinalCell()
                    throws Exception

Throws:: Exception

scalePrimitiveData

private void scalePrimitiveData(int i,
                                float value)

applySymmetryAndSetTrajectory
```
public void applySymmetryAndSetTrajectory()
                                   throws Exception
```
Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

Throws:

Exception

readAtomicPos

private void readAtomicPos(boolean finalizeSymmetry)
                    throws Exception

Throws:: Exception

readPartialCharges

private void readPartialCharges()
                         throws Exception

Throws:: Exception

readEnergy

private void readEnergy()
                 throws Exception

Throws:: Exception

setEnergy
```
private void setEnergy()
```

Class GulpReader

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

isSlab

isPolymer

isPrimitive

sep

coordinatesArePrimitive

atomCharges

bTest

a

b

c

alpha

beta

gamma

primitiveData

tags

totEnergy

energyUnits

Constructor Detail

GulpReader

Method Detail

initializeReader

finalizeSubclassReader

checkLine

readDimensionality

readSpaceGroup

parameterIndex

setParameter

newAtomSet

setModelParameters

readCellParameters

readFinalCell

scalePrimitiveData

applySymmetryAndSetTrajectory

readAtomicPos

readPartialCharges

readEnergy

setEnergy