public class SmarterJmolAdapter extends JmolAdapter
Modifier and Type | Field and Description |
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static java.lang.String |
PATH_KEY
AtomSetCollectionReader.readData() will close any BufferedReader
|
static java.lang.String |
PATH_SEPARATOR |
cellParamNames, ORDER_AROMATIC, ORDER_AROMATIC_DOUBLE, ORDER_AROMATIC_SINGLE, ORDER_COVALENT_DOUBLE, ORDER_COVALENT_SINGLE, ORDER_COVALENT_TRIPLE, ORDER_HBOND, ORDER_PARTIAL01, ORDER_PARTIAL12, ORDER_PARTIAL23, ORDER_PARTIAL32, ORDER_PYMOL_MULT, ORDER_PYMOL_SINGLE, ORDER_STEREO_FAR, ORDER_STEREO_NEAR, ORDER_UNSPECIFIED
Constructor and Description |
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SmarterJmolAdapter() |
Modifier and Type | Method and Description |
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static void |
close(java.lang.Object bufferedReader) |
boolean |
coordinatesAreFractional(java.lang.Object asc)
Get the boolean whether coordinates are fractional.
|
void |
finish(java.lang.Object asc) |
int |
getAtomCount(java.lang.Object asc)
Get the estimated number of atoms contained in the file.
|
JmolAdapterAtomIterator |
getAtomIterator(java.lang.Object asc)
Get an AtomIterator for retrieval of all atoms in the file.
|
java.util.Map<java.lang.String,java.lang.Object> |
getAtomSetAuxiliaryInfo(java.lang.Object asc,
int atomSetIndex)
Get the auxiliary information for a particular atomSet.
|
java.lang.Object |
getAtomSetCollection(java.lang.Object ascReader)
Create the AtomSetCollection and return it
|
java.util.Map<java.lang.String,java.lang.Object> |
getAtomSetCollectionAuxiliaryInfo(java.lang.Object asc)
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 asc)
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 asc)
Get number of atomSets in the file.
|
java.lang.String |
getAtomSetName(java.lang.Object asc,
int atomSetIndex)
Get the name of an atomSet.
|
int |
getAtomSetNumber(java.lang.Object asc,
int atomSetIndex)
Get the number identifying each atomSet.
|
JmolAdapterBondIterator |
getBondIterator(java.lang.Object asc)
Get a BondIterator for retrieval of all bonds in the file.
|
java.lang.String[][] |
getBondList(java.lang.Object asc) |
java.lang.String |
getFileTypeName(java.lang.Object ascOrReader)
Just get the resolved file type; if a file, does NOT close the reader
|
int |
getHydrogenAtomCount(java.lang.Object asc)
Get the hydrogen atom count -- for ligand files
|
JmolAdapterStructureIterator |
getStructureIterator(java.lang.Object asc)
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
|
canonizeAlternateLocationID, canonizeInsertionCode, getAtomSetCollectionFromReaderType, getBondingRadius, getElementNumber, getElementSymbol, getNaturalIsotope, openBufferedReader, openBufferedReader, openBufferedReader
public static final java.lang.String PATH_KEY
public static final java.lang.String PATH_SEPARATOR
public java.lang.String getFileTypeName(java.lang.Object ascOrReader)
getFileTypeName
in class JmolAdapter
ascOrReader
- 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)
JmolAdapter
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.
getAtomSetCollectionReader
in class JmolAdapter
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 informationpublic 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)
name
- type
- bufferedReader
- htParams
- 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
getAtomSetCollectionFromReader
in class JmolAdapter
java.lang.Exception
public java.lang.Object getAtomSetCollection(java.lang.Object ascReader)
getAtomSetCollection
in class JmolAdapter
ascReader
- public static java.lang.Object staticGetAtomSetCollection(AtomSetCollectionReader a)
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)
getAtomSetCollectionReaders
in class JmolAdapter
filesReader
- names
- types
- htParams
- getReadersOnly
- TRUE for a set of readers; FALSE for one ascpublic java.lang.Object getAtomSetCollectionFromSet(java.lang.Object readerSet, java.lang.Object atomsets, java.util.Map<java.lang.String,java.lang.Object> htParams)
getAtomSetCollectionFromSet
in class JmolAdapter
readerSet
- atomsets
- htParams
- public java.lang.Object getAtomSetCollectionFromDOM(java.lang.Object DOMNode, java.util.Map<java.lang.String,java.lang.Object> htParams)
getAtomSetCollectionFromDOM
in class JmolAdapter
DOMNode
- htParams
- public void finish(java.lang.Object asc)
finish
in class JmolAdapter
public java.lang.String getAtomSetCollectionName(java.lang.Object asc)
JmolAdapter
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.
getAtomSetCollectionName
in class JmolAdapter
null
public java.util.Map<java.lang.String,java.lang.Object> getAtomSetCollectionAuxiliaryInfo(java.lang.Object asc)
JmolAdapter
Via the smarterJmolAdapter
getAtomSetCollectionAuxiliaryInfo
in class JmolAdapter
asc
- The client filenull
public int getAtomSetCount(java.lang.Object asc)
JmolAdapter
NOTE WARNING:
Not yet implemented everywhere, it is in the smarterJmolAdapter
getAtomSetCount
in class JmolAdapter
asc
- The client filepublic int getAtomSetNumber(java.lang.Object asc, int atomSetIndex)
JmolAdapter
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
getAtomSetNumber
in class JmolAdapter
asc
- The client fileatomSetIndex
- The atom set's index for which to get
the atom set numberpublic java.lang.String getAtomSetName(java.lang.Object asc, int atomSetIndex)
JmolAdapter
getAtomSetName
in class JmolAdapter
asc
- The client fileatomSetIndex
- The atom set indexpublic java.util.Map<java.lang.String,java.lang.Object> getAtomSetAuxiliaryInfo(java.lang.Object asc, int atomSetIndex)
JmolAdapter
Via the smarterJmolAdapter
getAtomSetAuxiliaryInfo
in class JmolAdapter
asc
- The client fileatomSetIndex
- The atom set indexnull
public int getHydrogenAtomCount(java.lang.Object asc)
JmolAdapter
getHydrogenAtomCount
in class JmolAdapter
public java.lang.String[][] getBondList(java.lang.Object asc)
getBondList
in class JmolAdapter
public int getAtomCount(java.lang.Object asc)
JmolAdapter
Just return -1 if you don't know (or don't want to figure it out)
getAtomCount
in class JmolAdapter
asc
- The client filepublic boolean coordinatesAreFractional(java.lang.Object asc)
JmolAdapter
coordinatesAreFractional
in class JmolAdapter
asc
- The client filefalse
public JmolAdapterAtomIterator getAtomIterator(java.lang.Object asc)
JmolAdapter
This method may not return null
.
getAtomIterator
in class JmolAdapter
asc
- The client fileJmolAdapterAtomIterator
public JmolAdapterBondIterator getBondIterator(java.lang.Object asc)
JmolAdapter
If this method returns null
and no
bonds are defined then the JmolViewer will automatically apply its
rebonding code to build bonds between atoms.
getBondIterator
in class JmolAdapter
asc
- The client filenull
JmolAdapterBondIterator
public JmolAdapterStructureIterator getStructureIterator(java.lang.Object asc)
JmolAdapter
getStructureIterator
in class JmolAdapter
asc
- The client filenull
public static void close(java.lang.Object bufferedReader) throws java.io.IOException
java.io.IOException