org.jmol.adapter.smarter

Class SmarterJmolAdapter

java.lang.Object

org.jmol.api.JmolAdapter

org.jmol.adapter.smarter.SmarterJmolAdapter

public class SmarterJmolAdapter
extends JmolAdapter

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	PATH_KEY AtomSetCollectionReader.readData() will close any BufferedReader
static java.lang.String	PATH_SEPARATOR

Fields inherited from class org.jmol.api.JmolAdapter

cellParamNames, NOTE_SCRIPT_FILE, ORDER_AROMATIC, ORDER_AROMATIC_DOUBLE, ORDER_AROMATIC_SINGLE, ORDER_AS_SINGLE, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_PARTIAL23, ORDER_PARTIAL32, ORDER_STEREO_FAR, ORDER_STEREO_NEAR, ORDER_UNSPECIFIED, SHELL_D_CARTESIAN, SHELL_D_SPHERICAL, SHELL_F_CARTESIAN, SHELL_F_SPHERICAL, SHELL_G_CARTESIAN, SHELL_G_SPHERICAL, SHELL_L, SHELL_P, SHELL_S, SHELL_SP, SUPPORTED_BASIS_FUNCTIONS

Constructor Summary

Constructors

Constructor and Description
SmarterJmolAdapter()

Method Summary

Methods

Modifier and Type	Method and Description
static void	close(java.lang.Object bufferedReader)
boolean	coordinatesAreFractional(java.lang.Object atomSetCollection) Get the boolean whether coordinates are fractional.
void	finish(java.lang.Object atomSetCollection)
int	getAtomCount(java.lang.Object atomSetCollection) Get the estimated number of atoms contained in the file.
JmolAdapterAtomIterator	getAtomIterator(java.lang.Object atomSetCollection) Get an AtomIterator for retrieval of all atoms in the file.
java.util.Map<java.lang.String,java.lang.Object>	getAtomSetAuxiliaryInfo(java.lang.Object atomSetCollection, int atomSetIndex) Get the auxiliary information for a particular atomSet.
java.lang.Object	getAtomSetCollection(java.lang.Object atomSetCollectionReader) Create the AtomSetCollection and return it
java.util.Map<java.lang.String,java.lang.Object>	getAtomSetCollectionAuxiliaryInfo(java.lang.Object atomSetCollection) Get the auxiliary information for this atomSetCollection.
java.lang.Object	getAtomSetCollectionFromDOM(java.lang.Object DOMNode, java.util.Map<java.lang.String,java.lang.Object> htParams) Direct DOM HTML4 page reading; Egon was interested in this at one point.
java.lang.Object	getAtomSetCollectionFromReader(java.lang.String fname, java.lang.Object reader, java.util.Map<java.lang.String,java.lang.Object> htParams)
java.lang.Object	getAtomSetCollectionFromSet(java.lang.Object readerSet, java.lang.Object atomsets, java.util.Map<java.lang.String,java.lang.Object> htParams) needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]
java.lang.String	getAtomSetCollectionName(java.lang.Object atomSetCollection) Get the name of the atom set collection, if known.
java.lang.Object	getAtomSetCollectionReader(java.lang.String name, java.lang.String type, java.lang.Object bufferedReader, java.util.Map<java.lang.String,java.lang.Object> htParams) Read an atomSetCollection object from a bufferedReader and close the reader.
java.lang.Object	getAtomSetCollectionReaders(JmolFilesReaderInterface filesReader, java.lang.String[] names, java.lang.String[] types, java.util.Map<java.lang.String,java.lang.Object> htParams, boolean getReadersOnly) primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader
int	getAtomSetCount(java.lang.Object atomSetCollection) Get number of atomSets in the file.
java.lang.String	getAtomSetName(java.lang.Object atomSetCollection, int atomSetIndex) Get the name of an atomSet.
int	getAtomSetNumber(java.lang.Object atomSetCollection, int atomSetIndex) Get the number identifying each atomSet.
JmolAdapterBondIterator	getBondIterator(java.lang.Object atomSetCollection) Get a BondIterator for retrieval of all bonds in the file.
java.lang.String[][]	getBondList(java.lang.Object atomSetCollection)
java.lang.String	getFileTypeName(java.lang.Object atomSetCollectionOrReader) Just get the resolved file type; if a file, does NOT close the reader
int	getHydrogenAtomCount(java.lang.Object atomSetCollection) Get the hydrogen atom count -- for ligand files
float[]	getNotionalUnitcell(java.lang.Object atomSetCollection) Get the notional unit cell.
float[]	getPdbScaleMatrix(java.lang.Object atomSetCollection) Get the PDB scale matrix.
float[]	getPdbScaleTranslate(java.lang.Object atomSetCollection) Get the PDB scale translation vector.
JmolAdapterStructureIterator	getStructureIterator(java.lang.Object atomSetCollection) Get a StructureIterator.
static java.lang.Object	staticGetAtomSetCollection(AtomSetCollectionReader a)
static java.lang.Object	staticGetAtomSetCollectionReader(java.lang.String name, java.lang.String type, java.lang.Object bufferedReader, java.util.Map<java.lang.String,java.lang.Object> htParams) The primary file or string reader -- returns just the reader now

Methods inherited from class org.jmol.api.JmolAdapter

canonizeAlternateLocationID, canonizeInsertionCode, getAdapterName, getAtomSetCollectionFromReader, getBondingRadiusFloat, getElementNumber, getElementSymbol, getNaturalIsotope, getNewDfCoefMap, getQuantumShellTagID, getQuantumShellTagIDSpherical, getShellEnumeration, isHetero, lookupGroupID, openBufferedReader, openBufferedReader, openBufferedReader

Methods inherited from class java.lang.Object

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

Field Detail

PATH_KEY

public static final java.lang.String PATH_KEY

AtomSetCollectionReader.readData() will close any BufferedReader

See Also:

Constant Field Values

PATH_SEPARATOR

public static final java.lang.String PATH_SEPARATOR

Constructor Detail

SmarterJmolAdapter

public SmarterJmolAdapter()

Method Detail

getFileTypeName

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

Just get the resolved file type; if a file, does NOT close the reader

Specified by:

getFileTypeName in class JmolAdapter

Parameters:

atomSetCollectionOrReader -

Returns:

a file type or null

getAtomSetCollectionReader

public java.lang.Object getAtomSetCollectionReader(java.lang.String name,
                                          java.lang.String type,
                                          java.lang.Object bufferedReader,
                                          java.util.Map<java.lang.String,java.lang.Object> htParams)

Description copied from class: JmolAdapter

Read an atomSetCollection object from a bufferedReader and close the reader.

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 atomSetCollection. This atomSetCollection 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.

Specified by:

getAtomSetCollectionReader in class JmolAdapter

Parameters:

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

type - File type, if known, or null

bufferedReader - The BufferedReader

htParams - a hash table containing parameter information

Returns:

The atomSetCollection or String with an error message

staticGetAtomSetCollectionReader

public static java.lang.Object staticGetAtomSetCollectionReader(java.lang.String name,
                                                java.lang.String type,
                                                java.lang.Object bufferedReader,
                                                java.util.Map<java.lang.String,java.lang.Object> htParams)

The primary file or string reader -- returns just the reader now

Parameters:

name -

type -

bufferedReader -

htParams -

Returns:

an AtomSetCollectionReader or an error string

getAtomSetCollectionFromReader

public java.lang.Object getAtomSetCollectionFromReader(java.lang.String fname,
                                              java.lang.Object reader,
                                              java.util.Map<java.lang.String,java.lang.Object> htParams)
                                                throws java.lang.Exception

Specified by:

getAtomSetCollectionFromReader in class JmolAdapter

Throws:

java.lang.Exception

getAtomSetCollection

public java.lang.Object getAtomSetCollection(java.lang.Object atomSetCollectionReader)

Create the AtomSetCollection and return it

Specified by:

getAtomSetCollection in class JmolAdapter

Parameters:

atomSetCollectionReader -

Returns:

an AtomSetCollection or an error string

staticGetAtomSetCollection

public static java.lang.Object staticGetAtomSetCollection(AtomSetCollectionReader a)

getAtomSetCollectionReaders

public java.lang.Object getAtomSetCollectionReaders(JmolFilesReaderInterface filesReader,
                                           java.lang.String[] names,
                                           java.lang.String[] types,
                                           java.util.Map<java.lang.String,java.lang.Object> htParams,
                                           boolean getReadersOnly)

primary for String[] or File[] reading -- two options are implemented --- return a set of simultaneously open readers, or return one single collection using a single reader

Specified by:

getAtomSetCollectionReaders in class JmolAdapter

Parameters:

filesReader -

names -

types -

htParams -

getReadersOnly - TRUE for a set of readers; FALSE for one atomSetCollection

Returns:

a set of AtomSetCollectionReaders, a single AtomSetCollection, or an error string

getAtomSetCollectionFromSet

public java.lang.Object getAtomSetCollectionFromSet(java.lang.Object readerSet,
                                           java.lang.Object atomsets,
                                           java.util.Map<java.lang.String,java.lang.Object> htParams)

needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]

Specified by:

getAtomSetCollectionFromSet in class JmolAdapter

Parameters:

readerSet -

atomsets -

htParams -

Returns:

a single AtomSetCollection or an error string

getAtomSetCollectionFromDOM

public java.lang.Object getAtomSetCollectionFromDOM(java.lang.Object DOMNode,
                                           java.util.Map<java.lang.String,java.lang.Object> htParams)

Direct DOM HTML4 page reading; Egon was interested in this at one point.

Specified by:

getAtomSetCollectionFromDOM in class JmolAdapter

Parameters:

DOMNode -

htParams -

Returns:

a single AtomSetCollection or an error string

finish

public void finish(java.lang.Object atomSetCollection)

Specified by:

finish in class JmolAdapter

getAtomSetCollectionName

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

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.

Specified by:

getAtomSetCollectionName in class JmolAdapter

Returns:

The atom set collection name or null

getAtomSetCollectionAuxiliaryInfo

public java.util.Map<java.lang.String,java.lang.Object> getAtomSetCollectionAuxiliaryInfo(java.lang.Object atomSetCollection)

Description copied from class: JmolAdapter

Get the auxiliary information for this atomSetCollection.

Via the smarterJmolAdapter

Specified by:

getAtomSetCollectionAuxiliaryInfo in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

The auxiliaryInfo Hashtable that may be available for particular filetypes for this atomSetCollection or null

getAtomSetCount

public int getAtomSetCount(java.lang.Object atomSetCollection)

Description copied from class: JmolAdapter

Get number of atomSets in the file.

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

Specified by:

getAtomSetCount in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

The number of atomSets in the file

getAtomSetNumber

public int getAtomSetNumber(java.lang.Object atomSetCollection,
                   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

Specified by:

getAtomSetNumber in class JmolAdapter

Parameters:

atomSetCollection - The client file

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

Returns:

The number identifying each atom set.

getAtomSetName

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

Description copied from class: JmolAdapter

Get the name of an atomSet.

Specified by:

getAtomSetName in class JmolAdapter

Parameters:

atomSetCollection - The client file

atomSetIndex - The atom set index

Returns:

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

getAtomSetAuxiliaryInfo

public java.util.Map<java.lang.String,java.lang.Object> getAtomSetAuxiliaryInfo(java.lang.Object atomSetCollection,
                                                                       int atomSetIndex)

Description copied from class: JmolAdapter

Get the auxiliary information for a particular atomSet.

Via the smarterJmolAdapter

Specified by:

getAtomSetAuxiliaryInfo in class JmolAdapter

Parameters:

atomSetCollection - The client file

atomSetIndex - The atom set index

Returns:

The auxiliaryInfo Hashtable that may be available for particular filetypes for this atomSet or null

getHydrogenAtomCount

public int getHydrogenAtomCount(java.lang.Object atomSetCollection)

Description copied from class: JmolAdapter

Get the hydrogen atom count -- for ligand files

Specified by:

getHydrogenAtomCount in class JmolAdapter

Returns:

number of hydrogen atoms in this model

getBondList

public java.lang.String[][] getBondList(java.lang.Object atomSetCollection)

Specified by:

getBondList in class JmolAdapter

Returns:

[ [atomName1 atomName2 order] ...]

getAtomCount

public int getAtomCount(java.lang.Object atomSetCollection)

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:

getAtomCount in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

The estimated number of atoms in the file

coordinatesAreFractional

public boolean coordinatesAreFractional(java.lang.Object atomSetCollection)

Description copied from class: JmolAdapter

Get the boolean whether coordinates are fractional.

Specified by:

coordinatesAreFractional in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

true if the coordinates are fractional, default false

getNotionalUnitcell

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

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

Specified by:

getNotionalUnitcell in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

The array of the values or null

getPdbScaleMatrix

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

Description copied from class: JmolAdapter

Get the PDB scale matrix.

Does not seem to be overriden by any descendent

Specified by:

getPdbScaleMatrix in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

The array of 9 floats for the matrix or null

getPdbScaleTranslate

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

Description copied from class: JmolAdapter

Get the PDB scale translation vector.

Does not seem to be overriden by any descendent

Specified by:

getPdbScaleTranslate in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

The x, y and z translation values or null

getAtomIterator

public JmolAdapterAtomIterator getAtomIterator(java.lang.Object atomSetCollection)

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:

atomSetCollection - The client file

Returns:

An AtomIterator

See Also:

JmolAdapterAtomIterator

getBondIterator

public JmolAdapterBondIterator getBondIterator(java.lang.Object atomSetCollection)

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.

Specified by:

getBondIterator in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

A BondIterator or null

See Also:

JmolAdapterBondIterator

getStructureIterator

public JmolAdapterStructureIterator getStructureIterator(java.lang.Object atomSetCollection)

Description copied from class: JmolAdapter

Get a StructureIterator.

Specified by:

getStructureIterator in class JmolAdapter

Parameters:

atomSetCollection - The client file

Returns:

A StructureIterator or null

close

public static void close(java.lang.Object bufferedReader)
                  throws java.io.IOException

Throws:

java.io.IOException