org.jmol.adapter.smarter
Class SmarterJmolAdapter

java.lang.Object
  org.jmol.api.JmolAdapter
      org.jmol.adapter.smarter.SmarterJmolAdapter

public class SmarterJmolAdapter
extends JmolAdapter

Nested Class Summary

class

SmarterJmolAdapter.StructureIterator

Nested classes/interfaces inherited from class org.jmol.api.JmolAdapter

JmolAdapter.Logger

Field Summary

static java.lang.String	PATH_KEY
static java.lang.String	PATH_SEPARATOR

Fields inherited from class org.jmol.api.JmolAdapter

logger, ORDER_AROMATIC, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_STEREO_FAR, ORDER_STEREO_NEAR

Constructor Summary

SmarterJmolAdapter(JmolAdapter.Logger logger)

Method Summary

boolean	coordinatesAreFractional(java.lang.Object clientFile) Get the boolean whether coordinates are fractional.
void	finish(java.lang.Object clientFile)
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.
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	openBufferedReaders(java.lang.String[] name, java.io.BufferedReader[] bufferedReader) Associate a clientFile object with an array of BufferedReader.
java.lang.Object	openDOMReader(java.lang.Object DOMNode)

Methods inherited from class org.jmol.api.JmolAdapter

canonizeAlphaDigit, canonizeAlternateLocationID, canonizeChainID, canonizeInsertionCode, getClientAtomStringProperty, openBufferedReader, openBufferedReaders, openDOMReader

Methods inherited from class java.lang.Object

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

Field Detail

PATH_KEY

public static final java.lang.String PATH_KEY

See Also:

Constant Field Values

PATH_SEPARATOR

public static final java.lang.String PATH_SEPARATOR

Constructor Detail

SmarterJmolAdapter

public SmarterJmolAdapter(JmolAdapter.Logger logger)

Method Detail

finish

public void finish(java.lang.Object clientFile)

Overrides:

finish in class JmolAdapter

openBufferedReader

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

Description copied from class: JmolAdapter

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.

Overrides:

openBufferedReader in class JmolAdapter

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

openBufferedReaders

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

Description copied from class: JmolAdapter

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.

Overrides:

openBufferedReaders in class JmolAdapter

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

openDOMReader

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

Overrides:

openDOMReader in class JmolAdapter

getFileTypeName

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

Description copied from class: JmolAdapter

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

Overrides:

getFileTypeName in class JmolAdapter

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)

Description copied from class: JmolAdapter

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.

Overrides:

getAtomSetCollectionName in class JmolAdapter

Returns:

The atom set collection name or null

getAtomSetCollectionProperties

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

Description copied from class: JmolAdapter

Get the properties for this atomSetCollection.

Not yet implemented everywhere, it is in the smarterJmolAdapter

Overrides:

getAtomSetCollectionProperties in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The properties for this atomSetCollection or null

getAtomSetCount

public int getAtomSetCount(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get number of atomSets in the file.

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

Overrides:

getAtomSetCount in class JmolAdapter

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)

Description copied from class: JmolAdapter

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

Overrides:

getAtomSetNumber in class JmolAdapter

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)

Description copied from class: JmolAdapter

Get the name of an atomSet.

Overrides:

getAtomSetName in class JmolAdapter

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)

Description copied from class: JmolAdapter

Get the properties for an atomSet.

Overrides:

getAtomSetProperties in class JmolAdapter

Parameters:

clientFile - The client file

atomSetIndex - The atom set index

Returns:

The properties for an atom set or null

getEstimatedAtomCount

public int getEstimatedAtomCount(java.lang.Object clientFile)

Description copied from class: JmolAdapter

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)

Specified by:

getEstimatedAtomCount in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The estimated number of atoms in the file

coordinatesAreFractional

public boolean coordinatesAreFractional(java.lang.Object clientFile)

Description copied from class: JmolAdapter

Get the boolean whether coordinates are fractional.

Overrides:

coordinatesAreFractional in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

true if the coordinates are fractional, default false

getNotionalUnitcell

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

Description copied from class: JmolAdapter

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

Overrides:

getNotionalUnitcell in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The array of the values or null

getPdbScaleMatrix

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

Description copied from class: JmolAdapter

Get the PDB scale matrix.

Does not seem to be overriden by any descendent

Overrides:

getPdbScaleMatrix in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The array of 9 floats for the matrix or null

getPdbScaleTranslate

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

Description copied from class: JmolAdapter

Get the PDB scale translation vector.

Does not seem to be overriden by any descendent

Overrides:

getPdbScaleTranslate in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

The x, y and z translation values or null

getAtomIterator

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

Description copied from class: JmolAdapter

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

This method may not return null.

Specified by:

getAtomIterator in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

An AtomIterator

See Also:

JmolAdapter.AtomIterator

getBondIterator

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

Description copied from class: JmolAdapter

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.

Overrides:

getBondIterator in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

A BondIterator or null

See Also:

JmolAdapter.BondIterator

getStructureIterator

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

Description copied from class: JmolAdapter

Get a StructureIterator.

Overrides:

getStructureIterator in class JmolAdapter

Parameters:

clientFile - The client file

Returns:

A StructureIterator or null