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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StructureIO.StructureFiletype

Constructor Summary

Constructors

Constructor and Description
StructureIO()

Method Summary

Modifier and Type	Method and Description
static AtomCache	getAtomCache()
static List<Structure>	getBiologicalAssemblies(String pdbId) Returns all biological assemblies for the given PDB id, using multiModel= If only one biological assembly is required use getBiologicalAssembly(String) or getBiologicalAssembly(String, int) instead.
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= For more documentation on quaternary structures see: http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies
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=
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 StructureIO.StructureFiletype	guessFiletype(String filename) Attempts to guess the type of a structure file based on the extension
static void	setAtomCache(AtomCache c)
static void	setPdbPath(String pathToPDBFiles) Utility method to set the location where PDB files can be found

Methods inherited from class java.lang.Object

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

Constructor Detail

StructureIO

public StructureIO()

Method Detail

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         := [0-9][a-zA-Z0-9]{3}
                chainID       := [a-zA-Z0-9]
                scopID        := 'd' pdbID [a-z_][0-9_]
                biol              := 'BIO:' pdbID [:]? [0-9]+
                pdp                       := 'PDP:' pdbID[A-Za-z0-9_]+
                resNum        := [-+]?[0-9]+[A-Za-z]?


                Example structures:
                1TIM            #whole structure - asym unit
                4HHB.C          #single chain
                4GCR.A_1-83 #one domain, by residue number
                3AA0.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. Some flexibility can be allowed in SCOP domain names, see #setStrictSCOP(boolean)
• 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=

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)