Package org.biojava.nbio.structure.quaternary

Class BiologicalAssemblyBuilder

java.lang.Object

org.biojava.nbio.structure.quaternary.BiologicalAssemblyBuilder

public class BiologicalAssemblyBuilder
extends Object

Reconstructs the quaternary structure of a protein from an asymmetric unit

Author:

Peter Rose, Andreas Prlic, Jose Duarte

Field Summary

Fields

Modifier and Type	Field	Description
static final String	COMPOSED_OPERATOR_SEPARATOR	The character separating operator ids that are composed.
static final String	SYM_CHAIN_ID_SEPARATOR	The character separating the original chain identifier from the operator id.

Constructor Summary

Constructors

Constructor	Description
BiologicalAssemblyBuilder()

Method Summary

Modifier and Type	Method	Description
List<BiologicalAssemblyTransformation>	getBioUnitTransformationList(org.rcsb.cif.schema.mm.PdbxStructAssembly pdbxStructAssembly, int assemblyIndex, org.rcsb.cif.schema.mm.PdbxStructAssemblyGen pdbxStructAssemblyGen, org.rcsb.cif.schema.mm.PdbxStructOperList pdbxStructOperList)	Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.
Structure	rebuildQuaternaryStructure(Structure asymUnit, List<BiologicalAssemblyTransformation> transformations, boolean useAsymIds, boolean multiModel)	Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models.

Methods inherited from class java.lang.Object

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

Field Details

SYM_CHAIN_ID_SEPARATOR

public static final String SYM_CHAIN_ID_SEPARATOR

The character separating the original chain identifier from the operator id.

See Also:

• Constant Field Values

COMPOSED_OPERATOR_SEPARATOR

public static final String COMPOSED_OPERATOR_SEPARATOR

The character separating operator ids that are composed.

See Also:

• Constant Field Values

Constructor Details

BiologicalAssemblyBuilder

public BiologicalAssemblyBuilder()

Method Details

rebuildQuaternaryStructure

public Structure rebuildQuaternaryStructure(Structure asymUnit,
 List<BiologicalAssemblyTransformation> transformations,
 boolean useAsymIds,
 boolean multiModel)

Builds a Structure object containing the quaternary structure built from given asymUnit and transformations, by adding symmetry partners as new models. 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:

asymUnit -

transformations -

useAsymIds - if true use Chain.getId() to match the ids in the BiologicalAssemblyTransformation (needed if data read from mmCIF), if false use Chain.getName() for the chain matching (needed if data read from PDB).

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:

getBioUnitTransformationList

public List<BiologicalAssemblyTransformation> getBioUnitTransformationList(org.rcsb.cif.schema.mm.PdbxStructAssembly pdbxStructAssembly,
 int assemblyIndex,
 org.rcsb.cif.schema.mm.PdbxStructAssemblyGen pdbxStructAssemblyGen,
 org.rcsb.cif.schema.mm.PdbxStructOperList pdbxStructOperList)

Returns a list of transformation matrices for the generation of a macromolecular assembly for the specified assembly Id.

Parameters:

pdbxStructAssembly -

assemblyIndex -

pdbxStructAssemblyGen -

pdbxStructOperList -

Returns:

list of transformation matrices to generate macromolecular assembly