Class RemoteRawBioUnitDataProvider
- java.lang.Object
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- org.biojava.nbio.structure.quaternary.io.RemoteRawBioUnitDataProvider
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- All Implemented Interfaces:
RawBioUnitDataProvider
public class RemoteRawBioUnitDataProvider extends java.lang.Object implements RawBioUnitDataProvider
A BioUnitDataProvider that fetches the symmetry operations via remote calls to servers from RCSB PDB- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
DEFAULT_SERVERNAME
static java.lang.String
GET_ASSEMBLY
static java.lang.String
GET_ASSEMBLY_GENS
static java.lang.String
GET_STRUCT_OPER
static java.lang.String
NR_BIOL_APPEND
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Constructor Summary
Constructors Constructor Description RemoteRawBioUnitDataProvider()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getNrBiolAssemblies()
Returns the number of available biological assemblies.java.util.List<PdbxStructAssembly>
getPdbxStructAssemblies()
Data access method for list describing all assembliesPdbxStructAssembly
getPdbxStructAssembly(int biolAssemblyNr)
get the data for a particular pdbxStructAssembly.java.util.List<PdbxStructAssemblyGen>
getPdbxStructAssemblyGen(int biolAssemblyNr)
get the data for a particular pdbxStructAssemblyGen.java.util.List<PdbxStructAssemblyGen>
getPdbxStructAssemblyGens()
Data access method for list describing all assembliesjava.util.List<PdbxStructOperList>
getPdbxStructOperList()
Get all the possible operatorsint
getTimeout()
boolean
hasBiolAssembly()
Does the PDB ID have biological assembly information?static void
main(java.lang.String[] args)
void
setPdbId(java.lang.String pdbId)
Tell the provider for which PDB ID the quaternary structure should be returned.void
setTimeout(int timeout)
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Field Detail
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DEFAULT_SERVERNAME
public static java.lang.String DEFAULT_SERVERNAME
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NR_BIOL_APPEND
public static java.lang.String NR_BIOL_APPEND
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GET_ASSEMBLY
public static java.lang.String GET_ASSEMBLY
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GET_ASSEMBLY_GENS
public static java.lang.String GET_ASSEMBLY_GENS
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GET_STRUCT_OPER
public static java.lang.String GET_STRUCT_OPER
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Method Detail
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main
public static void main(java.lang.String[] args)
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getTimeout
public int getTimeout()
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setTimeout
public void setTimeout(int timeout)
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setPdbId
public void setPdbId(java.lang.String pdbId)
Description copied from interface:RawBioUnitDataProvider
Tell the provider for which PDB ID the quaternary structure should be returned.- Specified by:
setPdbId
in interfaceRawBioUnitDataProvider
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getNrBiolAssemblies
public int getNrBiolAssemblies()
Description copied from interface:RawBioUnitDataProvider
Returns the number of available biological assemblies.- Specified by:
getNrBiolAssemblies
in interfaceRawBioUnitDataProvider
- Returns:
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hasBiolAssembly
public boolean hasBiolAssembly()
Description copied from interface:RawBioUnitDataProvider
Does the PDB ID have biological assembly information?- Specified by:
hasBiolAssembly
in interfaceRawBioUnitDataProvider
- Returns:
- boolean flag
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getPdbxStructAssembly
public PdbxStructAssembly getPdbxStructAssembly(int biolAssemblyNr)
Description copied from interface:RawBioUnitDataProvider
get the data for a particular pdbxStructAssembly. We start counting at 0.- Specified by:
getPdbxStructAssembly
in interfaceRawBioUnitDataProvider
- Returns:
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getPdbxStructAssemblyGen
public java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGen(int biolAssemblyNr)
Description copied from interface:RawBioUnitDataProvider
get the data for a particular pdbxStructAssemblyGen. We start counting at 0.- Specified by:
getPdbxStructAssemblyGen
in interfaceRawBioUnitDataProvider
- Returns:
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getPdbxStructAssemblies
public java.util.List<PdbxStructAssembly> getPdbxStructAssemblies()
Description copied from interface:RawBioUnitDataProvider
Data access method for list describing all assemblies- Specified by:
getPdbxStructAssemblies
in interfaceRawBioUnitDataProvider
- Returns:
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getPdbxStructAssemblyGens
public java.util.List<PdbxStructAssemblyGen> getPdbxStructAssemblyGens()
Description copied from interface:RawBioUnitDataProvider
Data access method for list describing all assemblies- Specified by:
getPdbxStructAssemblyGens
in interfaceRawBioUnitDataProvider
- Returns:
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getPdbxStructOperList
public java.util.List<PdbxStructOperList> getPdbxStructOperList()
Description copied from interface:RawBioUnitDataProvider
Get all the possible operators- Specified by:
getPdbxStructOperList
in interfaceRawBioUnitDataProvider
- Returns:
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