org.jmol.api
Class JmolAdapter

java.lang.Object
  org.jmol.api.JmolAdapter

Direct Known Subclasses:

FrameExportJmolAdapter, SmarterJmolAdapter

public abstract class JmolAdapter
extends java.lang.Object

The JmolAdapter interface defines the API used by the JmolViewer to read external files and fetch atom properties necessary for rendering. A client of the JmolViewer implements this interface on top of their existing molecular model representation. The JmolViewer then requests information from the implementation using this API. Jmol will automatically calculate some atom properties if the client is not capable or does not want to supply them. Note: If you are seeing pink atoms that have lots of bonds, then your methods for getElementNumber(clientAtom) or getElementSymbol(clientAtom) are probably returning stray values. Therefore, these atoms are getting mapped to element 0 (Xx), which has color pink and a relatively large covalent bonding radius.

See Also:

JmolViewer

Nested Class Summary

class	JmolAdapter.AtomIterator AtomIterator is used to enumerate all the clientAtom objects in a specified frame.
class	JmolAdapter.BondIterator BondIterator is used to enumerate all the bonds
class	JmolAdapter.Logger Logger that writes to stdout
class	JmolAdapter.StructureIterator StructureIterator is used to enumerate Structures Helix, Sheet, Turn

Field Summary

JmolAdapter.Logger	logger
static short	ORDER_AROMATIC
static short	ORDER_COVALENT_DOUBLE
static short	ORDER_COVALENT_SINGLE
static short	ORDER_COVALENT_TRIPLE
static short	ORDER_HBOND
static short	ORDER_PARTIAL01
static short	ORDER_PARTIAL12
static short	ORDER_STEREO_FAR
static short	ORDER_STEREO_NEAR

Constructor Summary

JmolAdapter(java.lang.String adapterName, JmolAdapter.Logger logger)

Method Summary

static char	canonizeAlphaDigit(char ch)
static char	canonizeAlternateLocationID(char altLoc)
static char	canonizeChainID(char chainID)
static char	canonizeInsertionCode(char insertionCode)
boolean	coordinatesAreFractional(java.lang.Object clientFile) Get the boolean whether coordinates are fractional.
void	finish(java.lang.Object clientFile)
abstract JmolAdapter.AtomIterator	getAtomIterator(java.lang.Object clientFile) Get an AtomIterator for retrieval of all atoms in the file.
java.lang.String	getAtomSetCollectionName(java.lang.Object clientFile) Get the name of the atom set collection, if known.
java.util.Properties	getAtomSetCollectionProperties(java.lang.Object clientFile) Get the properties for this atomSetCollection.
int	getAtomSetCount(java.lang.Object clientFile) Get number of atomSets in the file.
java.lang.String	getAtomSetName(java.lang.Object clientFile, int atomSetIndex) Get the name of an atomSet.
int	getAtomSetNumber(java.lang.Object clientFile, int atomSetIndex) Get the number identifying each atomSet.
java.util.Properties	getAtomSetProperties(java.lang.Object clientFile, int atomSetIndex) Get the properties for an atomSet.
JmolAdapter.BondIterator	getBondIterator(java.lang.Object clientFile) Get a BondIterator for retrieval of all bonds in the file.
java.lang.String	getClientAtomStringProperty(java.lang.Object clientAtom, java.lang.String propertyName) Get a property from a clientAtom.
abstract int	getEstimatedAtomCount(java.lang.Object clientFile) Get the estimated number of atoms contained in the file.
java.lang.String	getFileTypeName(java.lang.Object clientFile) Get the type of this file or molecular model, if known.
float[]	getNotionalUnitcell(java.lang.Object clientFile) Get the notional unit cell.
float[]	getPdbScaleMatrix(java.lang.Object clientFile) Get the PDB scale matrix.
float[]	getPdbScaleTranslate(java.lang.Object clientFile) Get the PDB scale translation vector.
JmolAdapter.StructureIterator	getStructureIterator(java.lang.Object clientFile) Get a StructureIterator.
java.lang.Object	openBufferedReader(java.lang.String name, java.io.BufferedReader bufferedReader) Associate a clientFile object with a bufferedReader.
java.lang.Object	openBufferedReader(java.lang.String name, java.io.BufferedReader bufferedReader, JmolAdapter.Logger logger)
java.lang.Object	openBufferedReaders(java.lang.String[] name, java.io.BufferedReader[] bufferedReader) Associate a clientFile object with an array of BufferedReader.
java.lang.Object	openBufferedReaders(java.lang.String[] name, java.io.BufferedReader[] bufferedReader, JmolAdapter.Logger logger)
java.lang.Object	openDOMReader(java.lang.Object DOMNode)
java.lang.Object	openDOMReader(java.lang.Object DOMNode, JmolAdapter.Logger logger)

Methods inherited from class java.lang.Object

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

Field Detail

ORDER_COVALENT_SINGLE

public static final short ORDER_COVALENT_SINGLE

See Also:

Constant Field Values

ORDER_COVALENT_DOUBLE

public static final short ORDER_COVALENT_DOUBLE

See Also:

Constant Field Values

ORDER_COVALENT_TRIPLE

public static final short ORDER_COVALENT_TRIPLE

See Also:

Constant Field Values

ORDER_AROMATIC

public static final short ORDER_AROMATIC

See Also:

Constant Field Values

ORDER_HBOND

public static final short ORDER_HBOND

See Also:

Constant Field Values

ORDER_STEREO_NEAR

public static final short ORDER_STEREO_NEAR

See Also:

Constant Field Values

ORDER_STEREO_FAR

public static final short ORDER_STEREO_FAR

See Also:

Constant Field Values

ORDER_PARTIAL01

public static final short ORDER_PARTIAL01

See Also:

Constant Field Values

ORDER_PARTIAL12

public static final short ORDER_PARTIAL12

See Also:

Constant Field Values

logger

public JmolAdapter.Logger logger

Constructor Detail

JmolAdapter

public JmolAdapter(java.lang.String adapterName,
                   JmolAdapter.Logger logger)

Method Detail

openBufferedReader

public java.lang.Object openBufferedReader(java.lang.String name,
                                           java.io.BufferedReader bufferedReader)

Associate a clientFile object with a bufferedReader.

Given the BufferedReader, return an object which represents the file contents. The parameter name is assumed to be the file name or URL which is the source of reader. Note that this 'file' may have been automatically decompressed. Also note that the name may be 'String', representing a string constant. Therefore, few assumptions should be made about the name parameter. The return value is an object which represents a clientFile. This clientFile will be passed back in to other methods. If the return value is instanceof String then it is considered an error condition and the returned String is the error message.

Parameters:

name - File name, String or URL acting as the source of the reader

bufferedReader - The BufferedReader

Returns:

The clientFile or String with an error message

openBufferedReader

public java.lang.Object openBufferedReader(java.lang.String name,
                                           java.io.BufferedReader bufferedReader,
                                           JmolAdapter.Logger logger)

Parameters:

name - File name, String or URL acting as the source of the reader

bufferedReader - The BufferedReader

logger - The logger

Returns:

The clientFile or String with an error message

See Also:

openBufferedReader(String, BufferedReader)

openBufferedReaders

public java.lang.Object openBufferedReaders(java.lang.String[] name,
                                            java.io.BufferedReader[] bufferedReader)

Associate a clientFile object with an array of BufferedReader.

Given the array of BufferedReader, return an object which represents the concatenation of every file contents. The parameter name is assumed to be the file names or URL which are the source of each reader. Note that each of this 'file' may have been automatically decompressed. Also note that the name may be 'String', representing a string constant. Therefore, few assumptions should be made about the name parameter. The return value is an object which represents a clientFile. This clientFile will be passed back in to other methods. If the return value is instanceof String then it is considered an error condition and the returned String is the error message.

Parameters:

name - File names, String or URL acting as the source of each reader

bufferedReader - The array of BufferedReader

Returns:

The clientFile or String with an error message

openBufferedReaders

public java.lang.Object openBufferedReaders(java.lang.String[] name,
                                            java.io.BufferedReader[] bufferedReader,
                                            JmolAdapter.Logger logger)

Parameters:

name - File names, String or URL acting as the source of each reader

bufferedReader - The array of BufferedReader

logger - The logger

Returns:

The clientFile or String with an error message

See Also:

openBufferedReaders(String[], BufferedReader[])

openDOMReader

public java.lang.Object openDOMReader(java.lang.Object DOMNode)

openDOMReader

public java.lang.Object openDOMReader(java.lang.Object DOMNode,
                                      JmolAdapter.Logger logger)

finish

public void finish(java.lang.Object clientFile)

getFileTypeName

public java.lang.String getFileTypeName(java.lang.Object clientFile)

Get the type of this file or molecular model, if known.

Parameters:

clientFile - The client file

Returns:

The type of this file or molecular model, default "unknown"

getAtomSetCollectionName

public java.lang.String getAtomSetCollectionName(java.lang.Object clientFile)

Get the name of the atom set collection, if known.

Some file formats contain a formal name of the molecule in the file. If this method returns null then the JmolViewer will automatically supply the file/URL name as a default.

Parameters:

clientFile -

Returns:

The atom set collection name or null

getAtomSetCollectionProperties

public java.util.Properties getAtomSetCollectionProperties(java.lang.Object clientFile)

Get the properties for this atomSetCollection.

Not yet implemented everywhere, it is in the smarterJmolAdapter

Parameters:

clientFile - The client file

Returns:

The properties for this atomSetCollection or null

getAtomSetCount

public int getAtomSetCount(java.lang.Object clientFile)

Get number of atomSets in the file.

NOTE WARNING:
Not yet implemented everywhere, it is in the smarterJmolAdapter

Parameters:

clientFile - The client file

Returns:

The number of atomSets in the file, default 1

getAtomSetNumber

public int getAtomSetNumber(java.lang.Object clientFile,
                            int atomSetIndex)

Get the number identifying each atomSet.

For a PDB file, this is is the model number. For others it is a 1-based atomSet number.

Note that this is not currently implemented in PdbReader

Parameters:

clientFile - The client file

atomSetIndex - The atom set's index for which to get the atom set number

Returns:

The number identifying each atom set, default atomSetIndex+1.

getAtomSetName

public java.lang.String getAtomSetName(java.lang.Object clientFile,
                                       int atomSetIndex)

Get the name of an atomSet.

Parameters:

clientFile - The client file

atomSetIndex - The atom set index

Returns:

The name of the atom set, default the string representation of atomSetIndex

getAtomSetProperties

public java.util.Properties getAtomSetProperties(java.lang.Object clientFile,
                                                 int atomSetIndex)

Get the properties for an atomSet.

Parameters:

clientFile - The client file

atomSetIndex - The atom set index

Returns:

The properties for an atom set or null

getEstimatedAtomCount

public abstract int getEstimatedAtomCount(java.lang.Object clientFile)

Get the estimated number of atoms contained in the file.

Just return -1 if you don't know (or don't want to figure it out)

Parameters:

clientFile - The client file

Returns:

The estimated number of atoms in the file

coordinatesAreFractional

public boolean coordinatesAreFractional(java.lang.Object clientFile)

Get the boolean whether coordinates are fractional.

Parameters:

clientFile - The client file

Returns:

true if the coordinates are fractional, default false

getNotionalUnitcell

public float[] getNotionalUnitcell(java.lang.Object clientFile)

Get the notional unit cell.

This method returns the parameters that define a crystal unitcell the parameters are returned in a float[] in the following order a, b, c, alpha, beta, gamma
a, b, c : angstroms
alpha, beta, gamma : degrees
if there is no unit cell data then return null

Parameters:

clientFile - The client file

Returns:

The array of the values or null

getPdbScaleMatrix

public float[] getPdbScaleMatrix(java.lang.Object clientFile)

Get the PDB scale matrix.

Does not seem to be overriden by any descendent

Parameters:

clientFile - The client file

Returns:

The array of 9 floats for the matrix or null

getPdbScaleTranslate

public float[] getPdbScaleTranslate(java.lang.Object clientFile)

Get the PDB scale translation vector.

Does not seem to be overriden by any descendent

Parameters:

clientFile - The client file

Returns:

The x, y and z translation values or null

getClientAtomStringProperty

public java.lang.String getClientAtomStringProperty(java.lang.Object clientAtom,
                                                    java.lang.String propertyName)

Get a property from a clientAtom.

Parameters:

clientAtom - The clientAtom

propertyName - the key of the property

Returns:

The value of the property

getAtomIterator

public abstract JmolAdapter.AtomIterator getAtomIterator(java.lang.Object clientFile)

Get an AtomIterator for retrieval of all atoms in the file.

This method may not return null.

Parameters:

clientFile - The client file

Returns:

An AtomIterator

See Also:

JmolAdapter.AtomIterator

getBondIterator

public JmolAdapter.BondIterator getBondIterator(java.lang.Object clientFile)

Get a BondIterator for retrieval of all bonds in the file.

If this method returns null and no bonds are defined then the JmolViewer will automatically apply its rebonding code to build bonds between atoms.

Parameters:

clientFile - The client file

Returns:

A BondIterator or null

See Also:

JmolAdapter.BondIterator

getStructureIterator

public JmolAdapter.StructureIterator getStructureIterator(java.lang.Object clientFile)

Get a StructureIterator.

Parameters:

clientFile - The client file

Returns:

A StructureIterator or null

canonizeAlphaDigit

public static final char canonizeAlphaDigit(char ch)

canonizeChainID

public static final char canonizeChainID(char chainID)

canonizeInsertionCode

public static final char canonizeInsertionCode(char insertionCode)

canonizeAlternateLocationID

public static final char canonizeAlternateLocationID(char altLoc)