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 ascOrReader)

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

  Specified by:

  getFileTypeName in class JmolAdapter

  Parameters:

  ascOrReader -

  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 readerOrDocument,
                                                         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 ascReader)

  Create the AtomSetCollection and return it

  Specified by:

  getAtomSetCollection in class JmolAdapter

  Parameters:

  ascReader -

  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 asc

  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 asc)

  Specified by:

  finish in class JmolAdapter

• getAtomSetCollectionName

  public java.lang.String getAtomSetCollectionName​(java.lang.Object asc)

  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 asc)

  Description copied from class: JmolAdapter
  Get the auxiliary information for this atomSetCollection.

  Via the smarterJmolAdapter

  Specified by:

  getAtomSetCollectionAuxiliaryInfo in class JmolAdapter

  Parameters:

  asc - 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 asc)

  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:

  asc - The client file

  Returns:

  The number of atomSets in the file

• getAtomSetNumber

  public int getAtomSetNumber​(java.lang.Object asc,
                              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:

  asc - 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 asc,
                                         int atomSetIndex)

  Description copied from class: JmolAdapter
  Get the name of an atomSet.

  Specified by:

  getAtomSetName in class JmolAdapter

  Parameters:

  asc - 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 asc,
                                                                                        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:

  asc - 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 asc)

  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 asc)

  Specified by:

  getBondList in class JmolAdapter

  Returns:

  [ [atomName1 atomName2 order] ...]

• getAtomCount

  public int getAtomCount​(java.lang.Object asc)

  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:

  asc - The client file

  Returns:

  The estimated number of atoms in the file

• coordinatesAreFractional

  public boolean coordinatesAreFractional​(java.lang.Object asc)

  Description copied from class: JmolAdapter
  Get the boolean whether coordinates are fractional.

  Specified by:

  coordinatesAreFractional in class JmolAdapter

  Parameters:

  asc - The client file

  Returns:

  true if the coordinates are fractional, default false

• getAtomIterator

  public JmolAdapterAtomIterator getAtomIterator​(java.lang.Object asc)

  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:

  asc - The client file

  Returns:

  An AtomIterator

  See Also:

  JmolAdapterAtomIterator

• getBondIterator

  public JmolAdapterBondIterator getBondIterator​(java.lang.Object asc)

  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:

  asc - The client file

  Returns:

  A BondIterator or null

  See Also:

  JmolAdapterBondIterator

• getStructureIterator

  public JmolAdapterStructureIterator getStructureIterator​(java.lang.Object asc)

  Description copied from class: JmolAdapter
  Get a StructureIterator.

  Specified by:

  getStructureIterator in class JmolAdapter

  Parameters:

  asc - 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