Class SmarterJmolAdapter
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
AtomSetCollectionReader.readData() will close any BufferedReaderstatic final String
Fields inherited from class org.jmol.api.JmolAdapter
cellParamNames, ORDER_AROMATIC, ORDER_AROMATIC_DOUBLE, ORDER_AROMATIC_SINGLE, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_HEX, ORDER_COVALENT_QUAD, ORDER_COVALENT_QUINT, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_PARTIAL23, ORDER_PARTIAL32, ORDER_PYMOL_MULT, ORDER_PYMOL_SINGLE, ORDER_STEREO_EITHER, ORDER_STEREO_FAR, ORDER_STEREO_NEAR, ORDER_UNSPECIFIED
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic void
boolean
Get the boolean whether coordinates are fractional.void
int
getAtomCount
(Object asc, int atomSetIndex) Get the number of atoms contained in the file.getAtomIterator
(Object asc) Get an AtomIterator for retrieval of all atoms in the file.getAtomSetAuxiliaryInfo
(Object asc, int atomSetIndex) Get the auxiliary information for a particular atomSet.getAtomSetCollection
(Object ascReader) Create the AtomSetCollection and return itGet the auxiliary information for this atomSetCollection.getAtomSetCollectionFromDOM
(Object DOMNode, Map<String, Object> htParams) Direct DOM HTML4 page reading; Egon was interested in this at one point.needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]Get the name of the atom set collection, if known.getAtomSetCollectionReader
(String name, String type, Object bufferedReader, Map<String, Object> htParams) Read an atomSetCollection object from a bufferedReader and close the reader.getAtomSetCollectionReaders
(JmolFilesReaderInterface filesReader, String[] names, String[] types, Map<String, 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 readerint
getAtomSetCount
(Object asc) Get number of atomSets in the file or specific model index in filegetAtomSetName
(Object asc, int atomSetIndex) Get the name of an atomSet.int
getAtomSetNumber
(Object asc, int atomSetIndex) Get the number identifying each atomSet.getBondIterator
(Object asc) Get a BondIterator for retrieval of all bonds in the file.String[][]
getBondList
(Object asc) getFileTypeName
(Object ascOrReader) Just get the resolved file type; if a file, does NOT close the readerint
Get the hydrogen atom count -- for ligand filesGet a StructureIterator.static Object
static Object
staticGetAtomSetCollectionReader
(String name, String type, Object bufferedReader, Map<String, Object> htParams) The primary file or string reader -- returns just the reader nowMethods inherited from class org.jmol.api.JmolAdapter
canonizeAlternateLocationID, canonizeInsertionCode, getAtomSetCollectionFromReaderType, getBondingRadius, getElementNumber, getElementSymbol, getNaturalIsotope, openBufferedReader, openBufferedReader, openBufferedReader
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Field Details
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PATH_KEY
AtomSetCollectionReader.readData() will close any BufferedReader- See Also:
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PATH_SEPARATOR
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Constructor Details
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SmarterJmolAdapter
public SmarterJmolAdapter()
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Method Details
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getFileTypeName
Just get the resolved file type; if a file, does NOT close the reader- Specified by:
getFileTypeName
in classJmolAdapter
- Parameters:
ascOrReader
-- Returns:
- a file type or null
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getAtomSetCollectionReader
public Object getAtomSetCollectionReader(String name, String type, Object bufferedReader, Map<String, 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 thename
parameter. The return value is an object which represents aatomSetCollection
. ThisatomSetCollection
will be passed back in to other methods. If the return value isinstanceof String
then it is considered an error condition and the returned String is the error message.- Specified by:
getAtomSetCollectionReader
in classJmolAdapter
- Parameters:
name
- File name, String or URL acting as the source of the readertype
- File type, if known, or nullbufferedReader
- The BufferedReaderhtParams
- a hash table containing parameter information- Returns:
- The atomSetCollection or String with an error message
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staticGetAtomSetCollectionReader
public static Object staticGetAtomSetCollectionReader(String name, String type, Object bufferedReader, Map<String, 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
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getAtomSetCollectionFromReader
public Object getAtomSetCollectionFromReader(String fname, Object readerOrDocument, Map<String, Object> htParams) throws Exception- Specified by:
getAtomSetCollectionFromReader
in classJmolAdapter
- Throws:
Exception
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getAtomSetCollection
Create the AtomSetCollection and return it- Specified by:
getAtomSetCollection
in classJmolAdapter
- Parameters:
ascReader
-- Returns:
- an AtomSetCollection or an error string
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staticGetAtomSetCollection
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getAtomSetCollectionReaders
public Object getAtomSetCollectionReaders(JmolFilesReaderInterface filesReader, String[] names, String[] types, Map<String, 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 classJmolAdapter
- 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
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getAtomSetCollectionFromSet
public Object getAtomSetCollectionFromSet(Object readerSet, Object atomsets, Map<String, Object> htParams) needed to consolidate a set of models into one model; could start with AtomSetCollectionReader[] or with AtomSetCollection[]- Specified by:
getAtomSetCollectionFromSet
in classJmolAdapter
- Parameters:
readerSet
-atomsets
-htParams
-- Returns:
- a single AtomSetCollection or an error string
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getAtomSetCollectionFromDOM
Direct DOM HTML4 page reading; Egon was interested in this at one point.- Specified by:
getAtomSetCollectionFromDOM
in classJmolAdapter
- Parameters:
DOMNode
-htParams
-- Returns:
- a single AtomSetCollection or an error string
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finish
- Specified by:
finish
in classJmolAdapter
- Parameters:
asc
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getAtomSetCollectionName
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 classJmolAdapter
- Parameters:
asc
-- Returns:
- The atom set collection name or
null
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getAtomSetCollectionAuxiliaryInfo
Description copied from class:JmolAdapter
Get the auxiliary information for this atomSetCollection.Via the smarterJmolAdapter
- Specified by:
getAtomSetCollectionAuxiliaryInfo
in classJmolAdapter
- Parameters:
asc
- The client file- Returns:
- The auxiliaryInfo Hashtable that may be available for particular
filetypes for this atomSetCollection or
null
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getAtomSetCount
Description copied from class:JmolAdapter
Get number of atomSets in the file or specific model index in fileNOTE WARNING:
Not yet implemented everywhere, it is in the smarterJmolAdapter- Specified by:
getAtomSetCount
in classJmolAdapter
- Parameters:
asc
- The client file- Returns:
- The number of atomSets in the file
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getAtomSetNumber
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 classJmolAdapter
- Parameters:
asc
- The client fileatomSetIndex
- The atom set's index for which to get the atom set number- Returns:
- The number identifying each atom set.
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getAtomSetName
Description copied from class:JmolAdapter
Get the name of an atomSet.- Specified by:
getAtomSetName
in classJmolAdapter
- Parameters:
asc
- The client fileatomSetIndex
- The atom set index- Returns:
- The name of the atom set, default the string representation of atomSetIndex
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getAtomSetAuxiliaryInfo
Description copied from class:JmolAdapter
Get the auxiliary information for a particular atomSet.Via the smarterJmolAdapter
- Specified by:
getAtomSetAuxiliaryInfo
in classJmolAdapter
- Parameters:
asc
- The client fileatomSetIndex
- The atom set index- Returns:
- The auxiliaryInfo Hashtable that may be available for particular
filetypes for this atomSet or
null
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getHydrogenAtomCount
Description copied from class:JmolAdapter
Get the hydrogen atom count -- for ligand files- Specified by:
getHydrogenAtomCount
in classJmolAdapter
- Parameters:
asc
-- Returns:
- number of hydrogen atoms in this model
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getBondList
- Specified by:
getBondList
in classJmolAdapter
- Parameters:
asc
-- Returns:
- [ [atomName1 atomName2 order] ...]
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getAtomCount
Description copied from class:JmolAdapter
Get the number of atoms contained in the file.- Specified by:
getAtomCount
in classJmolAdapter
- Parameters:
asc
- The client fileatomSetIndex
- if -1, then count for the whole collection, else for this set- Returns:
- The estimated number of atoms in the file
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coordinatesAreFractional
Description copied from class:JmolAdapter
Get the boolean whether coordinates are fractional.- Specified by:
coordinatesAreFractional
in classJmolAdapter
- Parameters:
asc
- The client file- Returns:
- true if the coordinates are fractional, default
false
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getAtomIterator
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 classJmolAdapter
- Parameters:
asc
- The client file- Returns:
- An AtomIterator
- See Also:
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getBondIterator
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 classJmolAdapter
- Parameters:
asc
- The client file- Returns:
- A BondIterator or
null
- See Also:
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getStructureIterator
Description copied from class:JmolAdapter
Get a StructureIterator.- Specified by:
getStructureIterator
in classJmolAdapter
- Parameters:
asc
- The client file- Returns:
- A StructureIterator or
null
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close
- Throws:
IOException
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