Package org.biojava.nbio.structure

Class StructureIO

java.lang.Object

org.biojava.nbio.structure.StructureIO

public class StructureIO
extends Object

A class that provides static access methods for easy lookup of protein structure related components

Since:

3.0.5

Author:

Andreas Prlic

Constructor Summary

Constructors

Constructor	Description
StructureIO()

Method Summary

Modifier and Type	Method	Description
static AtomCache	getAtomCache()
static List<Structure>	getBiologicalAssemblies(String pdbId)	Returns all biological assemblies for the given PDB id, using multiModel=false
static List<Structure>	getBiologicalAssemblies(String pdbId, boolean multiModel)	Returns all biological assemblies for the given PDB id.
static Structure	getBiologicalAssembly(String pdbId)	Returns the first biological assembly that is available for the given PDB id, using multiModel=false
static Structure	getBiologicalAssembly(String pdbId, boolean multiModel)	Returns the first biological assembly that is available for the given PDB id.
static Structure	getBiologicalAssembly(String pdbId, int biolAssemblyNr)	Returns the biological assembly for the given PDB id and bioassembly identifier, using multiModel=false
static Structure	getBiologicalAssembly(String pdbId, int biolAssemblyNr, boolean multiModel)	Returns the biological assembly for the given PDB id and bioassembly identifier.
static Structure	getStructure(String name)	Loads a structure based on a name.
static StructureFiletype	guessFiletype(String filename)	Attempts to guess the type of a structure file based on the extension
static void	setAtomCache(AtomCache c)

Methods inherited from class java.lang.Object

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

Constructor Details

StructureIO

public StructureIO()

Method Details

getStructure

public static Structure getStructure(String name)
                              throws IOException,
StructureException

Loads a structure based on a name. Supported naming conventions are:

                Formal specification for how to specify the name:

                name     := pdbID
                                           | pdbID '.' chainID
                                           | pdbID '.' range
                                           | scopID
                                           | biol
                                           | pdp
                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_]
                biol              := 'BIO:' pdbID [:]? [0-9]+
                resNum        := [-+]?[0-9]+[A-Za-z]?


                Example structures:
                1TIM                #whole structure - asym unit (short format)
                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 - asym unit (extended format)
                PDB_00004HHB.C      #single chain
                PDB_00004GCR.A_1-83 #one domain, by residue number
                PDB_00003AA0.A,B    #two chains treated as one structure
                d2bq6a1     #scop domain
                BIO:1fah   #biological assembly nr 1 for 1fah
                BIO:1fah:0 #asym unit for 1fah
                BIO:1fah:1 #biological assembly nr 1 for 1fah
                BIO:1fah:2 #biological assembly nr 2 for 1fah

 

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
• URLs are accepted as well

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.

setAtomCache

public static void setAtomCache(AtomCache c)

getAtomCache

public static AtomCache getAtomCache()

getBiologicalAssembly

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

Returns the first biological assembly that is available for the given PDB id.

The output Structure will be different depending on the multiModel parameter:

• the symmetry-expanded chains are added as new models, one per transformId. All original models but the first one are discarded.
• as original with symmetry-expanded chains added with renamed chain ids and names (in the form originalAsymId_transformId and originalAuthId_transformId)

For more documentation on quaternary structures see: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies

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:

a Structure object or null if that assembly is not available

Throws:

StructureException

IOException

getBiologicalAssembly

public static Structure getBiologicalAssembly(String pdbId)
                                       throws IOException,
StructureException

Returns the first biological assembly that is available for the given PDB id, using multiModel=false

For more documentation on quaternary structures see: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies

Parameters:

pdbId -

Returns:

a Structure object or null if that assembly is not available

Throws:

StructureException

IOException

getBiologicalAssembly

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

Returns the biological assembly for the given PDB id and bioassembly identifier.

The output Structure will be different depending on the multiModel parameter:

• the symmetry-expanded chains are added as new models, one per transformId. All original models but the first one are discarded.
• as original with symmetry-expanded chains added with renamed chain ids and names (in the form originalAsymId_transformId and originalAuthId_transformId)

Parameters:

pdbId -

biolAssemblyNr - - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym 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 or null if that assembly is not available

Throws:

StructureException - if there is no bioassembly available for given biolAssemblyNr or some other problems encountered while loading it

IOException

getBiologicalAssembly

public static Structure getBiologicalAssembly(String pdbId,
 int biolAssemblyNr)
                                       throws IOException,
StructureException

Returns the biological assembly for the given PDB id and bioassembly identifier, using multiModel=false

Parameters:

pdbId -

biolAssemblyNr - - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).

Returns:

a Structure object or null if that assembly is not available

Throws:

StructureException - if there is no bioassembly available for given biolAssemblyNr or some other problems encountered while loading it

IOException

getBiologicalAssemblies

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

Returns all biological assemblies for the given PDB id.

The output Structure will be different depending on the multiModel parameter:

• the symmetry-expanded chains are added as new models, one per transformId. All original models but the first one are discarded.
• as original with symmetry-expanded chains added with renamed chain ids and names (in the form originalAsymId_transformId and originalAuthId_transformId)

If only one biological assembly is required use getBiologicalAssembly(String) or getBiologicalAssembly(String, int) instead.

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:

IOException

StructureException

Since:

5.0

getBiologicalAssemblies

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

Returns all biological assemblies for the given PDB id, using multiModel=false

If only one biological assembly is required use getBiologicalAssembly(String) or getBiologicalAssembly(String, int) instead.

Parameters:

pdbId -

Returns:

Throws:

IOException

StructureException

Since:

5.0

guessFiletype

public static StructureFiletype guessFiletype(String filename)

Attempts to guess the type of a structure file based on the extension

Parameters:

filename -

Returns: