Package org.biojava.nbio.structure.align.util

Class AtomCache

java.lang.Object

org.biojava.nbio.structure.align.util.AtomCache

public class AtomCache
extends Object

A utility class that provides easy access to Structure objects. If you are running a script that is frequently re-using the same PDB structures, the AtomCache keeps an in-memory cache of the files for quicker access. The cache is a soft-cache, this means it won't cause out of memory exceptions, but garbage collects the data if the Java virtual machine needs to free up space. The AtomCache is thread-safe.

Since:

3.0

Author:

Andreas Prlic, Spencer Bliven, Peter Rose

Field Summary

Fields

Modifier and Type	Field	Description
static String	BIOL_ASSEMBLY_IDENTIFIER
static String	CHAIN_NR_SYMBOL
static String	CHAIN_SPLIT_SYMBOL
static boolean	DEFAULT_BIOASSEMBLY_STYLE	The default output bioassembly style: if true the bioassemblies are multimodel, if false the bioassemblies are flat with renamed chains for symmetry-partners.
protected FileParsingParameters	params
static String	UNDERSCORE

Constructor Summary

Constructors

Constructor	Description
AtomCache()	Default AtomCache constructor.
AtomCache(String pdbFilePath)	Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(String pdbFilePath, String cachePath)	Creates an instance of an AtomCache that is pointed to the a particular path in the file system.
AtomCache(UserConfiguration config)	Creates a new AtomCache object based on the provided UserConfiguration.

Method Summary

Modifier and Type	Method	Description
protected void	flagLoading(PdbId pdbId)
protected void	flagLoadingFinished(PdbId pdbId)
Atom[]	getAtoms(String name)	Returns the CA atoms for the provided name.
Atom[]	getAtoms(StructureIdentifier name)
List<Structure>	getBiologicalAssemblies(String pdbId, boolean multiModel)	Returns all biological assemblies for given PDB id.
Structure	getBiologicalAssembly(String pdbId, boolean multiModel)	Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz).
Structure	getBiologicalAssembly(String pdbId, int bioAssemblyId, boolean multiModel)	Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
Structure	getBiologicalAssembly(PdbId pdbId, int bioAssemblyId, boolean multiModel)	Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()
String	getCachePath()	Returns the path that contains the caching file for utility data, such as domain definitions.
LocalPDBDirectory.FetchBehavior	getFetchBehavior()	Get the behavior for fetching files from the server
FileParsingParameters	getFileParsingParams()
StructureFiletype	getFiletype()	Returns the currently active file type that will be parsed.
LocalPDBDirectory.ObsoleteBehavior	getObsoleteBehavior()	Returns how this instance deals with obsolete entries.
String	getPath()	Get the path that is used to cache PDB files.
Atom[]	getRepresentativeAtoms(String name)	Returns the representative atoms for the provided name.
Atom[]	getRepresentativeAtoms(StructureIdentifier name)
Structure	getStructure(String name)	Request a Structure based on a name.
Structure	getStructure(StructureIdentifier strucId)	Get the structure corresponding to the given StructureIdentifier.
Structure	getStructureForCathDomain(StructureName structureName)	Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().
Structure	getStructureForCathDomain(StructureName structureName, CathDatabase cathInstall)	Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.
Structure	getStructureForDomain(String scopId)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	getStructureForDomain(String scopId, ScopDatabase scopDatabase)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	getStructureForDomain(ScopDomain domain)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	getStructureForDomain(ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)	Returns the representation of a ScopDomain as a BioJava Structure object.
Structure	getStructureForPdbId(String id)	Loads a structure directly by PDB ID
Structure	getStructureForPdbId(PdbId pdbId)	Loads a structure directly by PDB ID
protected Structure	loadStructureFromBcifByPdbId(String pdbId)
protected Structure	loadStructureFromBcifByPdbId(PdbId pdbId)
protected Structure	loadStructureFromCifByPdbId(String pdbId)
protected Structure	loadStructureFromCifByPdbId(PdbId pdbId)
protected Structure	loadStructureFromMmtfByPdbId(String pdbId)
protected Structure	loadStructureFromMmtfByPdbId(PdbId pdbId)	Load a Structure from MMTF either from the local file system.
protected Structure	loadStructureFromPdbByPdbId(String pdbId)
protected Structure	loadStructureFromPdbByPdbId(PdbId pdbId)
void	setCachePath(String cachePath)	set the location at which utility data should be cached.
void	setFetchBehavior(LocalPDBDirectory.FetchBehavior fetchBehavior)	Set the behavior for fetching files from the server
void	setFileParsingParams(FileParsingParameters params)
void	setFiletype(StructureFiletype filetype)	Set the file type that will be parsed.
void	setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior behavior)	[Optional] This method changes the behavior when obsolete entries are requested.
void	setPath(String path)	Set the path that is used to cache PDB files.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_BIOASSEMBLY_STYLE

public static final boolean DEFAULT_BIOASSEMBLY_STYLE

The default output bioassembly style: if true the bioassemblies are multimodel, if false the bioassemblies are flat with renamed chains for symmetry-partners.

See Also:

Constant Field Values

BIOL_ASSEMBLY_IDENTIFIER

public static final String BIOL_ASSEMBLY_IDENTIFIER

See Also:

Constant Field Values

CHAIN_NR_SYMBOL

public static final String CHAIN_NR_SYMBOL

See Also:

Constant Field Values

CHAIN_SPLIT_SYMBOL

public static final String CHAIN_SPLIT_SYMBOL

See Also:

Constant Field Values

UNDERSCORE

public static final String UNDERSCORE

See Also:

Constant Field Values

params

protected FileParsingParameters params

Constructor Detail

AtomCache

public AtomCache()

Default AtomCache constructor. Usually stores files in a temp directory, but this can be overriden by setting the PDB_DIR variable at runtime.

See Also:

UserConfiguration()

AtomCache

public AtomCache(String pdbFilePath)

Creates an instance of an AtomCache that is pointed to the a particular path in the file system. It will use the same value for pdbFilePath and cachePath.

Parameters:

pdbFilePath - a directory in the file system to use as a location to cache files.

AtomCache

public AtomCache(String pdbFilePath,
                 String cachePath)

Creates an instance of an AtomCache that is pointed to the a particular path in the file system.

Parameters:

pdbFilePath - a directory in the file system to use as a location to cache files.

cachePath -

AtomCache

public AtomCache(UserConfiguration config)

Creates a new AtomCache object based on the provided UserConfiguration.

Parameters:

config - the UserConfiguration to use for this cache.

Method Detail

getAtoms

public Atom[] getAtoms(String name)
                throws IOException,
                       StructureException

Returns the CA atoms for the provided name. See getStructure(String) for supported naming conventions.

This method only works with protein chains. Use getRepresentativeAtoms(String) for a more general solution.

Parameters:

name -

Returns:

an array of Atoms.

Throws:

IOException

StructureException

getAtoms

public Atom[] getAtoms(StructureIdentifier name)
                throws IOException,
                       StructureException

Throws:

IOException

StructureException

getRepresentativeAtoms

public Atom[] getRepresentativeAtoms(String name)
                              throws IOException,
                                     StructureException

Returns the representative atoms for the provided name. See getStructure(String) for supported naming conventions.

Parameters:

name -

Returns:

an array of Atoms.

Throws:

IOException

StructureException

getRepresentativeAtoms

public Atom[] getRepresentativeAtoms(StructureIdentifier name)
                              throws IOException,
                                     StructureException

Throws:

IOException

StructureException

getBiologicalAssembly

public Structure getBiologicalAssembly(String pdbId,
                                       int bioAssemblyId,
                                       boolean multiModel)
                                throws StructureException,
                                       IOException

Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()

Note, the number of available biological unit files varies. Many entries don't have a biological assembly specified (e.g. NMR structures), many entries have only one biological assembly (bioAssemblyId=1), and some structures have multiple biological assemblies.

Parameters:

pdbId - the PDB ID

bioAssemblyId - the 1-based index of the biological assembly (0 gets the asymmetric unit)

multiModel - if true the output Structure will be a multi-model one with one transformId per model, if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).

Returns:

a structure object

Throws:

IOException

StructureException - if biassemblyId < 0 or other problems while loading structure

Since:

3.2

getBiologicalAssembly

public Structure getBiologicalAssembly(PdbId pdbId,
                                       int bioAssemblyId,
                                       boolean multiModel)
                                throws StructureException,
                                       IOException

Returns the biological assembly for a given PDB ID and bioAssemblyId, by building the assembly from the biounit annotations found in Structure.getPDBHeader()

Note, the number of available biological unit files varies. Many entries don't have a biological assembly specified (e.g. NMR structures), many entries have only one biological assembly (bioAssemblyId=1), and some structures have multiple biological assemblies.

Parameters:

pdbId - the PDB ID

bioAssemblyId - the 1-based index of the biological assembly (0 gets the asymmetric unit)

multiModel - if true the output Structure will be a multi-model one with one transformId per model, if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).

Returns:

a structure object

Throws:

IOException

StructureException - if biassemblyId < 0 or other problems while loading structure

Since:

6.0.0

getBiologicalAssembly

public Structure getBiologicalAssembly(String pdbId,
                                       boolean multiModel)
                                throws StructureException,
                                       IOException

Returns the default biological unit (bioassemblyId=1, known in PDB as pdb1.gz). If it is not available, the asymmetric unit will be returned, e.g. for NMR structures.

Biological assemblies can also be accessed using getStructure("BIO:[pdbId]")

Parameters:

pdbId - the PDB id

multiModel - if true the output Structure will be a multi-model one with one transformId per model, if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).

Returns:

a structure object

Throws:

IOException

StructureException

Since:

4.2

getBiologicalAssemblies

public List<Structure> getBiologicalAssemblies(String pdbId,
                                               boolean multiModel)
                                        throws StructureException,
                                               IOException

Returns all biological assemblies for given PDB id.

Parameters:

pdbId -

multiModel - if true the output Structure will be a multi-model one with one transformId per model, if false the outputStructure will be as the original with added chains with renamed asymIds (in the form originalAsymId_transformId and originalAuthId_transformId).

Returns:

Throws:

StructureException

IOException

Since:

5.0

getCachePath

public String getCachePath()

Returns the path that contains the caching file for utility data, such as domain definitions.

Returns:

getFileParsingParams

public FileParsingParameters getFileParsingParams()

getPath

public String getPath()

Get the path that is used to cache PDB files.

Returns:

path to a directory

getStructure

public Structure getStructure(String name)
                       throws IOException,
                              StructureException

Request a Structure based on a name.

                Formal specification for how to specify the name:

                name     := pdbID
                               | pdbID '.' chainID
                               | pdbID '.' range
                               | scopID
                range         := '('? range (',' range)? ')'?
                               | chainID
                               | chainID '_' resNum '-' resNum
                pdbID         := [1-9][a-zA-Z0-9]{3}
                               | PDB_[a-zA-Z0-9]{8}
                chainID       := [a-zA-Z0-9]
                scopID        := 'd' pdbID [a-z_][0-9_]
                resNum        := [-+]?[0-9]+[A-Za-z]?


                Example structures:
                1TIM                 #whole structure
                4HHB.C               #single chain
                4GCR.A_1-83          #one domain, by residue number
                3AA0.A,B             #two chains treated as one structure
                PDB_00001TIM         #whole structure (extended format)
                PDB_00004HHB.C       #single chain (extended format)
                PDB_00004GCR.A_1-83  #one domain, by residue number (extended format)
                PDB_00003AA0.A,B     #two chains treated as one structure (extended format)
                d2bq6a1              #scop domain
 

With the additional set of rules:

• If only a PDB code is provided, the whole structure will be return including ligands, but the first model only (for NMR).
• Chain IDs are case sensitive, PDB ids are not. To specify a particular chain write as: 4hhb.A or 4HHB.A
• To specify a SCOP domain write a scopId e.g. d2bq6a1. Some flexibility can be allowed in SCOP domain names, see #setStrictSCOP(boolean)
• URLs are accepted as well

Note that this method should not be used in StructureIdentifier implementations to avoid circular calls.

Parameters:

name -

Returns:

a Structure object, or null if name appears improperly formated (eg too short, etc)

Throws:

IOException - The PDB file cannot be cached due to IO errors

StructureException - The name appeared valid but did not correspond to a structure. Also thrown by some submethods upon errors, eg for poorly formatted subranges.

getStructure

public Structure getStructure(StructureIdentifier strucId)
                       throws IOException,
                              StructureException

Get the structure corresponding to the given StructureIdentifier. Equivalent to calling StructureIdentifier.loadStructure(AtomCache) followed by StructureIdentifier.reduce(Structure).

Note that this method should not be used in StructureIdentifier implementations to avoid circular calls.

Parameters:

strucId -

Returns:

Throws:

IOException

StructureException

getStructureForDomain

public Structure getStructureForDomain(ScopDomain domain)
                                throws IOException,
                                       StructureException

Returns the representation of a ScopDomain as a BioJava Structure object.

Parameters:

domain - a SCOP domain

Returns:

a Structure object

Throws:

IOException

StructureException

getStructureForDomain

public Structure getStructureForDomain(ScopDomain domain,
                                       ScopDatabase scopDatabase)
                                throws IOException,
                                       StructureException

Returns the representation of a ScopDomain as a BioJava Structure object.

Parameters:

domain - a SCOP domain

scopDatabase - A ScopDatabase to use

Returns:

a Structure object

Throws:

IOException

StructureException

getStructureForDomain

public Structure getStructureForDomain(ScopDomain domain,
                                       ScopDatabase scopDatabase,
                                       boolean strictLigandHandling)
                                throws IOException,
                                       StructureException

Returns the representation of a ScopDomain as a BioJava Structure object.

Parameters:

domain - a SCOP domain

scopDatabase - A ScopDatabase to use

strictLigandHandling - If set to false, hetero-atoms are included if and only if they belong to a chain to which the SCOP domain belongs; if set to true, hetero-atoms are included if and only if they are strictly within the definition (residue numbers) of the SCOP domain

Returns:

a Structure object

Throws:

IOException

StructureException

getStructureForDomain

public Structure getStructureForDomain(String scopId)
                                throws IOException,
                                       StructureException

Returns the representation of a ScopDomain as a BioJava Structure object.

Parameters:

scopId - a SCOP Id

Returns:

a Structure object

Throws:

IOException

StructureException

getStructureForDomain

public Structure getStructureForDomain(String scopId,
                                       ScopDatabase scopDatabase)
                                throws IOException,
                                       StructureException

Returns the representation of a ScopDomain as a BioJava Structure object.

Parameters:

scopId - a SCOP Id

scopDatabase - A ScopDatabase to use

Returns:

a Structure object

Throws:

IOException

StructureException

setCachePath

public void setCachePath(String cachePath)

set the location at which utility data should be cached.

Parameters:

cachePath -

setFileParsingParams

public void setFileParsingParams(FileParsingParameters params)

setObsoleteBehavior

public void setObsoleteBehavior(LocalPDBDirectory.ObsoleteBehavior behavior)

[Optional] This method changes the behavior when obsolete entries are requested. Current behaviors are:

• THROW_EXCEPTION Throw a StructureException (the default)
• FETCH_OBSOLETE Load the requested ID from the PDB's obsolete repository
• FETCH_CURRENT Load the most recent version of the requested structure

  This setting may be silently ignored by implementations which do not have access to the server to determine whether an entry is obsolete, such as if #isAutoFetch() is false. Note that an obsolete entry may still be returned even this is FETCH_CURRENT if the entry is found locally.

Parameters:

fetchFileEvenIfObsolete - Whether to fetch obsolete records

Since:

4.0.0

See Also:

#setFetchCurrent(boolean)

getObsoleteBehavior

public LocalPDBDirectory.ObsoleteBehavior getObsoleteBehavior()

Returns how this instance deals with obsolete entries. Note that this setting may be ignored by some implementations or in some situations, such as when #isAutoFetch() is false.

For most implementations, the default value is THROW_EXCEPTION.

Returns:

The ObsoleteBehavior

Since:

4.0.0

getFetchBehavior

public LocalPDBDirectory.FetchBehavior getFetchBehavior()

Get the behavior for fetching files from the server

Returns:

setFetchBehavior

public void setFetchBehavior(LocalPDBDirectory.FetchBehavior fetchBehavior)

Set the behavior for fetching files from the server

Parameters:

fetchBehavior -

setPath

public void setPath(String path)

Set the path that is used to cache PDB files.

Parameters:

path - to a directory

getFiletype

public StructureFiletype getFiletype()

Returns the currently active file type that will be parsed.

Returns:

a StructureFiletype

setFiletype

public void setFiletype(StructureFiletype filetype)

Set the file type that will be parsed.

Parameters:

filetype - a StructureFiletype

getStructureForCathDomain

public Structure getStructureForCathDomain(StructureName structureName)
                                    throws IOException,
                                           StructureException

Returns a Structure corresponding to the CATH identifier supplied in structureName, using the the CathDatabase at CathFactory.getCathDatabase().

Throws:

IOException

StructureException

getStructureForCathDomain

public Structure getStructureForCathDomain(StructureName structureName,
                                           CathDatabase cathInstall)
                                    throws IOException,
                                           StructureException

Returns a Structure corresponding to the CATH identifier supplied in structureName, using the specified CathDatabase.

Throws:

IOException

StructureException

flagLoading

protected void flagLoading(PdbId pdbId)

flagLoadingFinished

protected void flagLoadingFinished(PdbId pdbId)

getStructureForPdbId

public Structure getStructureForPdbId(String id)
                               throws IOException,
                                      StructureException

Loads a structure directly by PDB ID

Parameters:

pdbId -

Returns:

Throws:

IOException

StructureException

getStructureForPdbId

public Structure getStructureForPdbId(PdbId pdbId)
                               throws IOException

Loads a structure directly by PDB ID

Parameters:

pdbId -

Returns:

Throws:

IOException

StructureException

loadStructureFromMmtfByPdbId

protected Structure loadStructureFromMmtfByPdbId(String pdbId)
                                          throws IOException

Throws:

IOException

loadStructureFromMmtfByPdbId

protected Structure loadStructureFromMmtfByPdbId(PdbId pdbId)
                                          throws IOException

Load a Structure from MMTF either from the local file system.

Parameters:

pdbId - the input PDB id

Returns:

the Structure object of the parsed structure

Throws:

IOException - error reading from Web or file system

loadStructureFromCifByPdbId

protected Structure loadStructureFromCifByPdbId(String pdbId)
                                         throws IOException

Throws:

IOException

loadStructureFromCifByPdbId

protected Structure loadStructureFromCifByPdbId(PdbId pdbId)
                                         throws IOException

Throws:

IOException

loadStructureFromBcifByPdbId

protected Structure loadStructureFromBcifByPdbId(String pdbId)
                                          throws IOException

Throws:

IOException

loadStructureFromBcifByPdbId

protected Structure loadStructureFromBcifByPdbId(PdbId pdbId)
                                          throws IOException

Throws:

IOException

loadStructureFromPdbByPdbId

protected Structure loadStructureFromPdbByPdbId(String pdbId)
                                         throws IOException

Throws:

IOException

loadStructureFromPdbByPdbId

protected Structure loadStructureFromPdbByPdbId(PdbId pdbId)
                                         throws IOException

Throws:

IOException