Class JmolAdapter
- Direct Known Subclasses:
SmarterJmolAdapter
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String[]
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate static final char
canonizeAlphaDigit
(char ch) static final char
canonizeAlternateLocationID
(char altLoc) static final char
canonizeInsertionCode
(char insertionCode) abstract boolean
coordinatesAreFractional
(Object atomSetCollection) Get the boolean whether coordinates are fractional.abstract void
abstract int
getAtomCount
(Object atomSetCollection) Get the estimated number of atoms contained in the file.abstract JmolAdapterAtomIterator
getAtomIterator
(Object atomSetCollection) Get an AtomIterator for retrieval of all atoms in the file.getAtomSetAuxiliaryInfo
(Object atomSetCollection, int atomSetIndex) Get the auxiliary information for a particular atomSet.abstract Object
getAtomSetCollection
(Object atomSetCollectionReader) getAtomSetCollectionAuxiliaryInfo
(Object atomSetCollection) Get the auxiliary information for this atomSetCollection.abstract Object
getAtomSetCollectionFromDOM
(Object DOMNode, Map<String, Object> htParams) abstract Object
getAtomSetCollectionFromReaderType
(String name, String type, Object bufferedReader, Map<String, Object> htParams) all in one -- for TestSmarterJmolAdapterabstract Object
abstract String
getAtomSetCollectionName
(Object atomSetCollection) Get the name of the atom set collection, if known.abstract Object
getAtomSetCollectionReader
(String name, String type, Object bufferedReader, Map<String, Object> htParams) Read an atomSetCollection object from a bufferedReader and close the reader.abstract Object
getAtomSetCollectionReaders
(JmolFilesReaderInterface fileReader, String[] names, String[] types, Map<String, Object> htParams, boolean getReadersOnly) Associate an atomSetCollection object with an array of BufferedReader.abstract int
getAtomSetCount
(Object atomSetCollection) Get number of atomSets in the file.abstract String
getAtomSetName
(Object atomSetCollection, int atomSetIndex) Get the name of an atomSet.abstract int
getAtomSetNumber
(Object atomSetCollection, int atomSetIndex) Get the number identifying each atomSet.static float
getBondingRadius
(int atomicNumberWithIsotope, int charge) abstract JmolAdapterBondIterator
getBondIterator
(Object atomSetCollection) Get a BondIterator for retrieval of all bonds in the file.abstract String[][]
getBondList
(Object atomSetCollection) static int
getElementNumber
(String elementSymbol) static String
getElementSymbol
(int elementNumber) abstract String
getFileTypeName
(Object atomSetCollection) Get the type of this file or molecular model, if known.abstract int
getHydrogenAtomCount
(Object atomSetCollection) Get the hydrogen atom count -- for ligand filesstatic int
getNaturalIsotope
(int elementNumber) abstract JmolAdapterStructureIterator
getStructureIterator
(Object atomSetCollection) Get a StructureIterator.openBufferedReader
(String name, BufferedReader bufferedReader) openBufferedReader
(String name, BufferedReader bufferedReader, Map<String, Object> htParams) openBufferedReader
(String name, String type, BufferedReader bufferedReader)
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Field Details
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ORDER_COVALENT_SINGLE
public static final int ORDER_COVALENT_SINGLE- See Also:
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ORDER_COVALENT_DOUBLE
public static final int ORDER_COVALENT_DOUBLE- See Also:
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ORDER_COVALENT_TRIPLE
public static final int ORDER_COVALENT_TRIPLE- See Also:
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ORDER_COVALENT_QUAD
public static final int ORDER_COVALENT_QUAD- See Also:
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ORDER_COVALENT_QUINT
public static final int ORDER_COVALENT_QUINT- See Also:
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ORDER_COVALENT_HEX
public static final int ORDER_COVALENT_HEX- See Also:
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ORDER_AROMATIC
public static final int ORDER_AROMATIC- See Also:
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ORDER_AROMATIC_SINGLE
public static final int ORDER_AROMATIC_SINGLE- See Also:
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ORDER_AROMATIC_DOUBLE
public static final int ORDER_AROMATIC_DOUBLE- See Also:
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ORDER_HBOND
public static final int ORDER_HBOND- See Also:
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ORDER_STEREO_NEAR
public static final int ORDER_STEREO_NEAR- See Also:
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ORDER_STEREO_FAR
public static final int ORDER_STEREO_FAR- See Also:
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ORDER_PARTIAL01
public static final int ORDER_PARTIAL01- See Also:
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ORDER_PARTIAL12
public static final int ORDER_PARTIAL12- See Also:
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ORDER_PARTIAL23
public static final int ORDER_PARTIAL23- See Also:
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ORDER_PARTIAL32
public static final int ORDER_PARTIAL32- See Also:
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ORDER_UNSPECIFIED
public static final int ORDER_UNSPECIFIED- See Also:
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ORDER_PYMOL_SINGLE
public static final int ORDER_PYMOL_SINGLE- See Also:
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ORDER_PYMOL_MULT
public static final int ORDER_PYMOL_MULT- See Also:
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cellParamNames
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Constructor Details
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JmolAdapter
public JmolAdapter()
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Method Details
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getElementSymbol
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getElementNumber
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getNaturalIsotope
public static int getNaturalIsotope(int elementNumber) -
getBondingRadius
public static float getBondingRadius(int atomicNumberWithIsotope, int charge) -
getAtomSetCollectionReader
public abstract Object getAtomSetCollectionReader(String name, String type, Object bufferedReader, Map<String, Object> htParams) 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.- 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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getAtomSetCollection
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getAtomSetCollectionReaders
public abstract Object getAtomSetCollectionReaders(JmolFilesReaderInterface fileReader, String[] names, String[] types, Map<String, Object> htParams, boolean getReadersOnly) Associate an atomSetCollection 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 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.- Parameters:
fileReader
- the thread requesting a set of files if bufferedReaders is nullnames
- File names, String or URL acting as the source of each readertypes
- File types, if known, or nullhtParams
- The input parameters for each file to loadgetReadersOnly
-- Returns:
- The atomSetCollection or String with an error message
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getAtomSetCollectionFromSet
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getAtomSetCollectionFromReader
public abstract Object getAtomSetCollectionFromReader(String fname, Object reader, Map<String, Object> htParams) throws Exception- Throws:
Exception
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getAtomSetCollectionFromReaderType
public Object getAtomSetCollectionFromReaderType(String name, String type, Object bufferedReader, Map<String, Object> htParams) all in one -- for TestSmarterJmolAdapter- Parameters:
name
-type
-bufferedReader
-htParams
-- Returns:
- AtomSetCollection or error string
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openBufferedReader
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openBufferedReader
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openBufferedReader
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getAtomSetCollectionFromDOM
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finish
- Parameters:
atomSetCollection
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getFileTypeName
Get the type of this file or molecular model, if known.- Parameters:
atomSetCollection
- The client file- Returns:
- The type of this file or molecular model, default
"unknown"
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getAtomSetCollectionName
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:
atomSetCollection
-- Returns:
- The atom set collection name or
null
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getAtomSetCollectionAuxiliaryInfo
Get the auxiliary information for this atomSetCollection.Via the smarterJmolAdapter
- Parameters:
atomSetCollection
- The client file- Returns:
- The auxiliaryInfo Hashtable that may be available for particular
filetypes for this atomSetCollection or
null
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getAtomSetCount
Get number of atomSets in the file.NOTE WARNING:
Not yet implemented everywhere, it is in the smarterJmolAdapter- Parameters:
atomSetCollection
- The client file- Returns:
- The number of atomSets in the file
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getAtomSetNumber
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:
atomSetCollection
- 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
Get the name of an atomSet.- Parameters:
atomSetCollection
- 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
public abstract Map<String,Object> getAtomSetAuxiliaryInfo(Object atomSetCollection, int atomSetIndex) Get the auxiliary information for a particular atomSet.Via the smarterJmolAdapter
- Parameters:
atomSetCollection
- 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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getAtomCount
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:
atomSetCollection
- The client file- Returns:
- The estimated number of atoms in the file
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getHydrogenAtomCount
Get the hydrogen atom count -- for ligand files- Parameters:
atomSetCollection
-- Returns:
- number of hydrogen atoms in this model
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getBondList
- Parameters:
atomSetCollection
-- Returns:
- [ [atomName1 atomName2 order] ...]
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coordinatesAreFractional
Get the boolean whether coordinates are fractional.- Parameters:
atomSetCollection
- The client file- Returns:
- true if the coordinates are fractional, default
false
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getAtomIterator
Get an AtomIterator for retrieval of all atoms in the file.This method may not return
null
.- Parameters:
atomSetCollection
- The client file- Returns:
- An AtomIterator
- See Also:
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getBondIterator
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:
atomSetCollection
- The client file- Returns:
- A BondIterator or
null
- See Also:
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getStructureIterator
Get a StructureIterator.- Parameters:
atomSetCollection
- The client file- Returns:
- A StructureIterator or
null
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canonizeAlphaDigit
private static final char canonizeAlphaDigit(char ch) -
canonizeInsertionCode
public static final char canonizeInsertionCode(char insertionCode) -
canonizeAlternateLocationID
public static final char canonizeAlternateLocationID(char altLoc)
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