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

Methods

Modifier and Type	Method and Description
static Structure	getBiologicalAssembly(String pdbId) Returns the first biologicalAssembly that is available for a protein structure.
static Structure	getBiologicalAssembly(String pdbId, int biolAssemblyNr) By default the getStructure method loads asym units.
static Structure	getBiologicalAssembly(String pdbId, int biolAssemblyNr, AtomCache cache)
static Structure	getBiologicalAssembly(String pdbId, int biolAssemblyNr, AtomCache cache, BioUnitDataProvider provider)
static int	getNrBiologicalAssemblies(String pdbId)
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 boolean	hasBiologicalAssembly(String pdbId) Does the provider PDB ID have a biological assembly?
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              := 'BIOL:' 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
                BIOL:1fah   #biological assembly nr 1 for 1fah
                BIOL:1fah:0 #asym unit for 1fah
                BIOL:1fah:1 #biological assembly nr 1 for 1fah
                BIOL: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)

getBiologicalAssembly

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

Returns the first biologicalAssembly that is available for a protein structure. For more documentation on quaternary structures see: http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html

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)
                                       throws IOException,
                                              StructureException

By default the getStructure method loads asym units. This access method allows to recreate the quaternary structure for a protein if it is available.

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

getBiologicalAssembly

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

Throws:

IOException

StructureException

getBiologicalAssembly

public static Structure getBiologicalAssembly(String pdbId,
                              int biolAssemblyNr,
                              AtomCache cache,
                              BioUnitDataProvider provider)
                                       throws IOException,
                                              StructureException

Throws:

IOException

StructureException

hasBiologicalAssembly

public static boolean hasBiologicalAssembly(String pdbId)

Does the provider PDB ID have a biological assembly?

Parameters:

pdbId -

Returns:

flag if one or more biological assemblies are available

getNrBiologicalAssemblies

public static int getNrBiologicalAssemblies(String pdbId)

setPdbPath

public static void setPdbPath(String pathToPDBFiles)

Utility method to set the location where PDB files can be found

Parameters:

pathToPDBFiles -

guessFiletype

public static StructureIO.StructureFiletype guessFiletype(String filename)

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

Parameters:

filename -

Returns: