Package org.biojava.nbio.structure.symmetry.core

Class QuatSymmetryDetector

java.lang.Object

org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector

public class QuatSymmetryDetector
extends Object

Detects the symmetry (global, pseudo, internal and local) of protein structures.

The SubunitClustererParameters determine the subunit definition and clustering, while the QuatSymmetryParameters determine the calculated symmetry results (point group and axes).

Author:

Peter Rose, Aleix Lafita

Method Summary

Modifier and Type	Method	Description
static QuatSymmetryResults	calcGlobalSymmetry(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)	Calculate GLOBAL symmetry results.
static QuatSymmetryResults	calcGlobalSymmetry(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)	Calculate GLOBAL symmetry results.
static QuatSymmetryResults	calcGlobalSymmetry(Stoichiometry composition, QuatSymmetryParameters symmParams)	Calculate GLOBAL symmetry results.
static List<QuatSymmetryResults>	calcLocalSymmetries(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)	Returns a List of LOCAL symmetry results.
static List<QuatSymmetryResults>	calcLocalSymmetries(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)	Returns a List of LOCAL symmetry results.
static List<QuatSymmetryResults>	calcLocalSymmetries(Stoichiometry globalComposition, QuatSymmetryParameters symmParams)	Returns a List of LOCAL symmetry results.

Methods inherited from class java.lang.Object

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

Method Detail

calcGlobalSymmetry

public static QuatSymmetryResults calcGlobalSymmetry(Structure structure,
                                                     QuatSymmetryParameters symmParams,
                                                     SubunitClustererParameters clusterParams)

Calculate GLOBAL symmetry results. This means that all Subunit are included in the symmetry.

Parameters:

structure - protein chains will be extracted as Subunit

symmParams - quaternary symmetry parameters

clusterParams - subunit clustering parameters

Returns:

GLOBAL quaternary structure symmetry results

calcGlobalSymmetry

public static QuatSymmetryResults calcGlobalSymmetry(List<Subunit> subunits,
                                                     QuatSymmetryParameters symmParams,
                                                     SubunitClustererParameters clusterParams)

Calculate GLOBAL symmetry results. This means that all Subunit are included in the symmetry.

Parameters:

subunits - list of Subunit

symmParams - quaternary symmetry parameters

clusterParams - subunit clustering parameters

Returns:

GLOBAL quaternary structure symmetry results

calcGlobalSymmetry

public static QuatSymmetryResults calcGlobalSymmetry(Stoichiometry composition,
                                                     QuatSymmetryParameters symmParams)

Calculate GLOBAL symmetry results. This means that all Subunit are included in the symmetry.

Parameters:

composition - Stoichiometry object that contains clustering results

symmParams - quaternary symmetry parameters

Returns:

GLOBAL quaternary structure symmetry results

calcLocalSymmetries

public static List<QuatSymmetryResults> calcLocalSymmetries(Structure structure,
                                                            QuatSymmetryParameters symmParams,
                                                            SubunitClustererParameters clusterParams)

Returns a List of LOCAL symmetry results. This means that a subset of the SubunitCluster is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.

Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)

Parameters:

structure - protein chains will be extracted as Subunit

symmParams - quaternary symmetry parameters

clusterParams - subunit clustering parameters

Returns:

List of LOCAL quaternary structure symmetry results. Empty if none.

calcLocalSymmetries

public static List<QuatSymmetryResults> calcLocalSymmetries(List<Subunit> subunits,
                                                            QuatSymmetryParameters symmParams,
                                                            SubunitClustererParameters clusterParams)

Returns a List of LOCAL symmetry results. This means that a subset of the SubunitCluster is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.

Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)

Parameters:

subunits - list of Subunit

symmParams - quaternary symmetry parameters

clusterParams - subunit clustering parameters

Returns:

List of LOCAL quaternary structure symmetry results. Empty if none.

calcLocalSymmetries

public static List<QuatSymmetryResults> calcLocalSymmetries(Stoichiometry globalComposition,
                                                            QuatSymmetryParameters symmParams)

Returns a List of LOCAL symmetry results. This means that a subset of the SubunitCluster is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.

Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)

Parameters:

globalComposition - Stoichiometry object that contains global clustering results

symmParams - quaternary symmetry parameters

Returns:

List of LOCAL quaternary structure symmetry results. Empty if none.