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java.lang.Objectorg.biojava.bio.structure.PDBStatus
public class PDBStatus
Methods for getting the status of a PDB file (current, obsolete, etc) and for accessing different versions of the structure.
All methods query the PDB website.
PDB supersessions form a directed acyclic graph, where edges point from an
obsolete ID to the entry that directly superseded it. For example, here are
edges from one portion of the graph:
1CAT -> 3CAT
3CAT -> 7CAT
3CAT -> 8CAT
The methods getReplaces(pdbId, false)
/
getReplacement(pdbId, false, true)
just get the incoming/outgoing edges for a single node. The recursive versions
(getReplaces(pdbId, true)
,
getReplacement(pdbId, true, false)
)
will do a depth-first search up/down the tree and return a list of all nodes ]
reached.
Finally, the getCurrent() method returns a single PDB ID from among the
results of
getReplacement(pdbId, true)
.
To be consistent with the old REST ordering, this is the PDB ID that occurs
last alphabetically.
Results are cached to reduce server load.
Nested Class Summary | |
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static class |
PDBStatus.Status
Represents the status of PDB IDs. |
Field Summary | |
---|---|
static String |
DEFAULT_PDB_SERVER
|
static String |
PDB_SERVER_PROPERTY
|
Constructor Summary | |
---|---|
PDBStatus()
|
Method Summary | |
---|---|
static void |
clearCache()
The status of PDB IDs are cached to reduce server overload. |
static String |
getCurrent(String oldPdbId)
Gets the current version of a PDB ID. |
static List<String> |
getReplacement(String oldPdbId,
boolean recurse,
boolean includeObsolete)
Gets the PDB which superseded oldPdbId. |
static List<String> |
getReplaces(String newPdbId,
boolean recurse)
Get the ID of the protein which was made obsolete by newPdbId. |
static PDBStatus.Status |
getStatus(String pdbId)
Get the status of the PDB in question. |
static PDBStatus.Status[] |
getStatus(String[] pdbIds)
Get the status of the a collection of PDBs in question in a single query. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String DEFAULT_PDB_SERVER
public static final String PDB_SERVER_PROPERTY
Constructor Detail |
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public PDBStatus()
Method Detail |
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public static PDBStatus.Status getStatus(String pdbId)
pdbId
-
public static PDBStatus.Status[] getStatus(String[] pdbIds)
pdbIds
-
getStatus(String)
public static String getCurrent(String oldPdbId)
getReplacement(oldPdbId,true,false)
oldPdbId
-
public static List<String> getReplacement(String oldPdbId, boolean recurse, boolean includeObsolete)
oldPdbId
- A pdb IDrecurse
- Indicates whether the replacements for obsolete records
should be fetched.includeObsolete
- Indicates whether obsolete records should be
included in the results.
public static List<String> getReplaces(String newPdbId, boolean recurse)
newPdbId
- PDB ID of the newer structurerecurse
- If true, return all ancestors of newPdbId.
Otherwise, just go one step newer than oldPdbId.
public static void clearCache()
|
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