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

Class Stoichiometry

java.lang.Object

org.biojava.nbio.structure.symmetry.core.Stoichiometry

public class Stoichiometry
extends Object

A utility object that describes Stoichiometry (composition of a protein assembly), determined via clustering procedure SubunitClusterer, and implements human-readable representation using various strategies.

Since:

5.0.0

Author:

Dmytro Guzenko

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	Stoichiometry.StringOverflowStrategy	What to do when the number of SubunitCluster exceeds the length of the alphabet.

Constructor Summary

Constructors

Constructor	Description
Stoichiometry(List<SubunitCluster> clusters)	Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, boolean resetAlphas)	Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Function<List<SubunitCluster>,String> customStringGenerator)	Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Stoichiometry.StringOverflowStrategy strategy)	Constructor for Stoichiometry.
Stoichiometry(List<SubunitCluster> clusters, Stoichiometry.StringOverflowStrategy strategy, boolean resetAlphas)	Constructor for Stoichiometry.

Method Summary

Modifier and Type	Method	Description
Stoichiometry	combineWith(Stoichiometry other)	Make a combined Stoichiometry object of this and the other.
String	getAlphabet()
List<SubunitCluster>	getClusters()
Stoichiometry	getComponent(int i)	Make a Stoichiometry object that corresponds to a single component.
Stoichiometry.StringOverflowStrategy	getStrategy()
boolean	isPseudoStoichiometric()	A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.
int	numberOfComponents()
void	resetAlphas()	Reassign alpha-strings for each cluster according to the current strategy.
void	setAlphabet(String alphabet)	Change alphabet used for string representation of a stoichiometry.
void	setCustomStringGenerator(Function<List<SubunitCluster>,String> customStringGenerator)	Let a user-defined function handle the entire string representation of a stoichiometry.
void	setStrategy(Stoichiometry.StringOverflowStrategy strategy)	Change string representation of a stoichiometry in case number of clusters exceeds number of letters in the alphabet.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Stoichiometry

public Stoichiometry(List<SubunitCluster> clusters)

Constructor for Stoichiometry. The default strategy is CYCLE, the letters assigned for each cluster will be reset.

Parameters:

clusters - List of SubunitCluster that defines assembly composition.

Stoichiometry

public Stoichiometry(List<SubunitCluster> clusters,
                     boolean resetAlphas)

Constructor for Stoichiometry. The default strategy is CYCLE.

Parameters:

clusters - List of SubunitCluster that defines assembly composition.

resetAlphas - Whether to keep alphas assigned to SubunitCluster object (useful for local symmetry detection) or to generate them anew.

Stoichiometry

public Stoichiometry(List<SubunitCluster> clusters,
                     Stoichiometry.StringOverflowStrategy strategy)

Constructor for Stoichiometry. The alphas assigned to SubunitCluster objects will be reset.

Parameters:

clusters - List of SubunitCluster that defines assembly composition.

strategy - What to do if number of SubunitCluster exceeds the alphabet length.

Stoichiometry

public Stoichiometry(List<SubunitCluster> clusters,
                     Stoichiometry.StringOverflowStrategy strategy,
                     boolean resetAlphas)

Constructor for Stoichiometry.

Parameters:

clusters - List of SubunitCluster that defines assembly composition.

strategy - What to do if number of SubunitCluster exceeds the alphabet length.

resetAlphas - Whether to keep alphas assigned to SubunitCluster object (useful for local symmetry detection) or to generate them anew.

Stoichiometry

public Stoichiometry(List<SubunitCluster> clusters,
                     Function<List<SubunitCluster>,String> customStringGenerator)

Constructor for Stoichiometry.

Parameters:

clusters - List of SubunitCluster that defines assembly composition.

customStringGenerator - A function which produces a string for a composition (list of subunit clusters).

Method Detail

resetAlphas

public void resetAlphas()

Reassign alpha-strings for each cluster according to the current strategy. Has no effect if custom string generator is used.

getClusters

public List<SubunitCluster> getClusters()

Returns:

list of SubunitCluster, ordered by the number of subunits (decreasing).

numberOfComponents

public int numberOfComponents()

Returns:

Number of distinct components in this stoichiometry.

combineWith

public Stoichiometry combineWith(Stoichiometry other)

Make a combined Stoichiometry object of this and the other. The combined list of clusters will be ordered by the number of subunits.

Returns:

new Stoichiometry object.

getComponent

public Stoichiometry getComponent(int i)

Make a Stoichiometry object that corresponds to a single component.

Parameters:

i - component index

Returns:

new Stoichiometry object.

getStrategy

public Stoichiometry.StringOverflowStrategy getStrategy()

Returns:

Stoichiometry.StringOverflowStrategy used in this stoichiometry to construct human-readable representation in case number of clusters exceeds number of letters in the alphabet.

setStrategy

public void setStrategy(Stoichiometry.StringOverflowStrategy strategy)

Change string representation of a stoichiometry in case number of clusters exceeds number of letters in the alphabet. This action may invalidate alphas already assigned to the clusters.

Parameters:

strategy - Stoichiometry.StringOverflowStrategy used in this stoichiometry to construct human-readable representation in case number of clusters exceeds number of letters in the alphabet.

setCustomStringGenerator

public void setCustomStringGenerator(Function<List<SubunitCluster>,String> customStringGenerator)

Let a user-defined function handle the entire string representation of a stoichiometry.

Parameters:

customStringGenerator - A function which accepts a list of subunit clusters and returns a string.

getAlphabet

public String getAlphabet()

Returns:

Alphabet (a sequence of characters) used in this stoichiometry to construct human-readable representation.

setAlphabet

public void setAlphabet(String alphabet)

Change alphabet used for string representation of a stoichiometry. This action invalidates alphas already assigned to the clusters.

Parameters:

alphabet - a sequence of characters used in this stoichiometry to construct human-readable representation.

toString

public String toString()

Overrides:

toString in class Object

Returns:

Human-readable representation of this stoichiometry.

isPseudoStoichiometric

public boolean isPseudoStoichiometric()

A pseudostoichiometric SubunitCluster was obtained using the SubunitClustererMethod.STRUCTURE similarity, or SubunitClustererMethod.SEQUENCE similarity with low scores.

Returns:

true if any of the clusters is pseudostoichiometric, false otherwise