Package org.jmol.adapter.writers

Class QCJSONWriter

java.lang.Object

org.jmol.util.JSONWriter

org.jmol.adapter.writers.QCJSONWriter

public class QCJSONWriter
extends JSONWriter

A very experimental class for writing QCJSON files. This standard is in the process of being developed, so any of this could change at any time. All we have here is Bob Hanson's experiment with getting Jmol to save and restore structures, vibrations, and molecular orbitals. Data set Bob is using is at https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/qcjson

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	QCJSONWriter.SparseArray

Field Summary

Fields

Modifier and Type	Field	Description
private int	basisID
private int[][]	dfCoefMaps
private boolean	filterMOs
private Map<String,String>	htBasisMap
private static Map<String,String>	integrationKeyMap
private Map<String,Object>	moBases
private javajs.util.Lst<int[]>	shells
private Viewer	vwr

Fields inherited from class org.jmol.util.JSONWriter

indent, oc

Constructor Summary

Constructors

Constructor	Description
QCJSONWriter()

Method Summary

Modifier and Type	Method	Description
private String	addBasis(Map<String,Object> moData)	Add a basis to the associative array moBases keyed on its hashcode
void	closeSchema()
private Object	fixCoefficients(double[] coeffs)	Jmol allows for a set of arrays that map coefficient indicies with nonstandard order to Gaussian/Molden order.
private static Map<String,String>	fixIntegration()	When an MO is calculated in Jmol, Jmol will check the integration so that it can be checked to be close to 1.0000.
private String	formatNumber(float x)
protected Object	getAndCheckValue(Map<String,Object> map, String key)
private Object	getAuxiliaryData(int modelIndex, String key)
Object	getProperty(int modelIndex, String key)
private boolean	haveMOData(int modelIndex)
private boolean	isVibration(int modelIndex)
void	openSchema()
void	set(Viewer viewer, OutputStream os)
private void	setDFCoord(Map<String,Object> moData)
String	toString()
void	writeAtoms(int modelIndex)
void	writeBonds(int modelIndex)
void	writeJob(int iJob)
void	writeJobMetadata()
void	writeJobs()
void	writeJSON()
void	writeMagic()
private void	writeMapKeyValueUnits(String key, Object value, String units)
void	writeMOBases()
private void	writeMOData(int modelIndex)
int	writeModel(int modelIndex)
void	writeModelMetadata(int modelIndex)
void	writeModels()
void	writeObject(Object o)
private void	writePrefix_Units(String prefix, String units)
void	writeSchemaMetadata()
void	writeTopology(int modelIndex)
int	writeVibrations(int modelIndex)

Methods inherited from class org.jmol.util.JSONWriter

append, arrayAdd, arrayClose, arrayOpen, closeStream, mapAddKey, mapAddKeyValue, mapAddKeyValueRaw, mapAddMapAllExcept, mapClose, mapOpen, setModifyKeys, setStream, setWhiteSpace, setWriteNullAsString, writeArray, writeBoolean, writeList, writeMap, writeNull, writeNumber, writeString, writeString

Methods inherited from class java.lang.Object

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

Field Detail

moBases

private Map<String,Object> moBases

htBasisMap

private Map<String,String> htBasisMap

filterMOs

private boolean filterMOs

vwr

private Viewer vwr

basisID

private int basisID

shells

private javajs.util.Lst<int[]> shells

dfCoefMaps

private int[][] dfCoefMaps

integrationKeyMap

private static Map<String,String> integrationKeyMap

Constructor Detail

QCJSONWriter

public QCJSONWriter()

Method Detail

set

public void set(Viewer viewer,
                OutputStream os)

toString

public String toString()

Overrides:

toString in class Object

writeJSON

public void writeJSON()

writeSchemaMetadata

public void writeSchemaMetadata()

openSchema

public void openSchema()

writeMagic

public void writeMagic()

closeSchema

public void closeSchema()

writeJobs

public void writeJobs()

writeJob

public void writeJob(int iJob)

writeJobMetadata

public void writeJobMetadata()

writeModels

public void writeModels()

writeModel

public int writeModel(int modelIndex)

writeTopology

public void writeTopology(int modelIndex)

getProperty

public Object getProperty(int modelIndex,
                          String key)

isVibration

private boolean isVibration(int modelIndex)

writeModelMetadata

public void writeModelMetadata(int modelIndex)

writeAtoms

public void writeAtoms(int modelIndex)

formatNumber

private String formatNumber(float x)

writePrefix_Units

private void writePrefix_Units(String prefix,
                               String units)

writeBonds

public void writeBonds(int modelIndex)

writeVibrations

public int writeVibrations(int modelIndex)

writeMapKeyValueUnits

private void writeMapKeyValueUnits(String key,
                                   Object value,
                                   String units)

haveMOData

private boolean haveMOData(int modelIndex)

getAuxiliaryData

private Object getAuxiliaryData(int modelIndex,
                                String key)

writeMOData

private void writeMOData(int modelIndex)

fixIntegration

private static Map<String,String> fixIntegration()

When an MO is calculated in Jmol, Jmol will check the integration so that it can be checked to be close to 1.0000. This integration value is saved back in the MO data, but it is not a standard key. (As though anything is here!) So we set a key mapping to replace it.

Returns:

the "integration" key map

getAndCheckValue

protected Object getAndCheckValue(Map<String,Object> map,
                                  String key)

Overrides:

getAndCheckValue in class JSONWriter

fixCoefficients

private Object fixCoefficients(double[] coeffs)

Jmol allows for a set of arrays that map coefficient indicies with nonstandard order to Gaussian/Molden order. Here we do the conversion upon writing so that the order is always Gaussian/Molden order.

Parameters:

coeffs -

Returns:

setDFCoord

private void setDFCoord(Map<String,Object> moData)

addBasis

private String addBasis(Map<String,Object> moData)

Add a basis to the associative array moBases keyed on its hashcode

Parameters:

moData -

Returns:

ID for this basis.

writeMOBases

public void writeMOBases()

writeObject

public void writeObject(Object o)

Overrides:

writeObject in class JSONWriter