org.biojava.nbio.structure.symmetry.core

Class Subunits

java.lang.Object

org.biojava.nbio.structure.symmetry.core.Subunits

public class Subunits
extends Object

A bean to represent information about the set of Subunit being considered for symmetry detection. This class is a helper for the QuatSymmetryDetector algorithm, since it calculates the MomentsOfInertia and the centroids of each Subunit.

Delete public modifier when finished.

Author:

Peter Rose, Aleix Lafita

Constructor Summary

Constructors

Constructor and Description
Subunits(List<javax.vecmath.Point3d[]> caCoords, List<Integer> sequenceClusterIds, List<Boolean> pseudoStoichiometry, List<Double> minSequenceIdentity, List<Double> maxSequenceIdentity, List<Integer> folds, List<String> chainIds, List<Integer> modelNumbers) Deprecated.
Subunits(List<SubunitCluster> clusters) Converts the List of SubunitCluster to a Subunit object.

Method Summary

Modifier and Type	Method and Description
boolean	contains(Subunits subunits)
int	getCalphaCount()
List<javax.vecmath.Point3d>	getCenters()
javax.vecmath.Point3d	getCentroid()
List<String>	getChainIds()
List<Integer>	getFolds()
int	getLargestSubunit()
javax.vecmath.Point3d	getLowerBound()
double	getMaxSequenceIdentity()
double	getMinSequenceIdentity()
List<Integer>	getModelNumbers()
MomentsOfInertia	getMomentsOfInertia()
int	getNucleicAcidChainCount()
List<javax.vecmath.Point3d>	getOriginalCenters()
List<Integer>	getSequenceClusterIds()
String	getStoichiometry()
int	getSubunitCount()
List<javax.vecmath.Point3d[]>	getTraces()
List<javax.vecmath.Vector3d>	getUnitVectors()
javax.vecmath.Point3d	getUpperBound()
static List<Integer>	getValidFolds(List<Integer> stoichiometry) Find valid symmetry orders for a given stoichiometry.
boolean	isPseudoStoichiometric()
boolean	isPseudoSymmetric()
boolean	overlaps(Subunits subunits)
void	setNucleicAcidChainCount(int nucleicAcidChainCount)
void	setPseudoSymmetric(boolean pseudoSymmetric)

Methods inherited from class java.lang.Object

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

Constructor Detail

Subunits

@Deprecated
public Subunits(List<javax.vecmath.Point3d[]> caCoords,
                            List<Integer> sequenceClusterIds,
                            List<Boolean> pseudoStoichiometry,
                            List<Double> minSequenceIdentity,
                            List<Double> maxSequenceIdentity,
                            List<Integer> folds,
                            List<String> chainIds,
                            List<Integer> modelNumbers)

Deprecated.

All input Lists should contain one element per subunit.

Parameters:

caCoords - CA coordinates of all subunits

sequenceClusterIds - ID of the cluster that each subunit belongs to

pseudoStoichiometry - Whether pseudosymmetry was used when clustering the subunit

minSequenceIdentity - Minimum sequence identity to other cluster members

maxSequenceIdentity - Maximum sequence identity to other cluster members

folds - Valid symmetry orders for this stoichiometry

chainIds - Chain ID for the subunit

modelNumbers - Model number for the subunit

Subunits

public Subunits(List<SubunitCluster> clusters)

Converts the List of SubunitCluster to a Subunit object.

Parameters:

clusters - List of SubunitCluster

Method Detail

getTraces

public List<javax.vecmath.Point3d[]> getTraces()

getSubunitCount

public int getSubunitCount()

getSequenceClusterIds

public List<Integer> getSequenceClusterIds()

isPseudoStoichiometric

public boolean isPseudoStoichiometric()

isPseudoSymmetric

public boolean isPseudoSymmetric()

setPseudoSymmetric

public void setPseudoSymmetric(boolean pseudoSymmetric)

getMinSequenceIdentity

public double getMinSequenceIdentity()

getMaxSequenceIdentity

public double getMaxSequenceIdentity()

getChainIds

public List<String> getChainIds()

getModelNumbers

public List<Integer> getModelNumbers()

getFolds

public List<Integer> getFolds()

getStoichiometry

public String getStoichiometry()

getCalphaCount

public int getCalphaCount()

getLargestSubunit

public int getLargestSubunit()

getCenters

public List<javax.vecmath.Point3d> getCenters()

getUnitVectors

public List<javax.vecmath.Vector3d> getUnitVectors()

getOriginalCenters

public List<javax.vecmath.Point3d> getOriginalCenters()

getCentroid

public javax.vecmath.Point3d getCentroid()

getMomentsOfInertia

public MomentsOfInertia getMomentsOfInertia()

getNucleicAcidChainCount

public int getNucleicAcidChainCount()

Returns:

the nucleicAcidChainCount

setNucleicAcidChainCount

public void setNucleicAcidChainCount(int nucleicAcidChainCount)

Parameters:

nucleicAcidChainCount - the nucleicAcidChainCount to set

overlaps

public boolean overlaps(Subunits subunits)

contains

public boolean contains(Subunits subunits)

getLowerBound

public javax.vecmath.Point3d getLowerBound()

getUpperBound

public javax.vecmath.Point3d getUpperBound()

getValidFolds

public static List<Integer> getValidFolds(List<Integer> stoichiometry)

Find valid symmetry orders for a given stoichiometry. For instance, an A6B4 protein would give [1,2] because (A6B4)1 and (A3B2)2 are valid decompositions.

Parameters:

stoichiometry - List giving the number of copies in each chain cluster

Returns:

The common factors of the stoichiometry