de.bioforscher.singa.structure.algorithms.superimposition

Class SubstructureSuperimposer

java.lang.Object

de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer

Direct Known Subclasses:

FragmentSubstructureSuperimposer

public class SubstructureSuperimposer
extends Object

Calculates the various Superimpositions for structures. TODO migrate to builder pattern to avoid overloaded constructor

Author:

fk

Field Summary

Fields

Modifier and Type	Field and Description
protected List<LeafSubstructure<?>>	candidate
protected List<LeafSubstructure<?>>	reference

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SubstructureSuperimposer(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)

Method Summary

Modifier and Type	Method and Description
static SubstructureSuperimposition	calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
static SubstructureSuperimposition	calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, RepresentationScheme representationScheme)
static SubstructureSuperimposition	calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
static SubstructureSuperimposition	calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, RepresentationScheme representationScheme)
static SubstructureSuperimposition	calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, RepresentationScheme representationScheme, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, RepresentationScheme representationScheme, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, SubstitutionMatrix substitutionMatrix, boolean considerExchanges)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(LeafSubstructureContainer reference, LeafSubstructureContainer candidate, RepresentationScheme representationScheme)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, Predicate<Atom> atomFilter)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, RepresentationScheme representationScheme)
protected SubstructureSuperimposition	calculateSuperimposition() Finds the superimposition for a list of LeafSubstructure according to their input order
protected de.bioforscher.singa.core.utility.Pair<List<Atom>>	defineAtoms() Method to define the intersecting Atoms that should be used for the alignment.

Methods inherited from class java.lang.Object

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

Field Detail

reference

protected final List<LeafSubstructure<?>> reference

candidate

protected final List<LeafSubstructure<?>> candidate

Constructor Detail

SubstructureSuperimposer

protected SubstructureSuperimposer(List<LeafSubstructure<?>> reference,
                                   List<LeafSubstructure<?>> candidate)

Method Detail

calculateIdealSubstructureSuperimposition

public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                    List<LeafSubstructure<?>> candidate)

calculateIdealSubstructureSuperimposition

public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                    List<LeafSubstructure<?>> candidate,
                                                                                    Predicate<Atom> atomFilter)

calculateIdealSubstructureSuperimposition

public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                    List<LeafSubstructure<?>> candidate,
                                                                                    RepresentationScheme representationScheme)

calculateIdealSubstructureSuperimposition

public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                    LeafSubstructureContainer candidate)

calculateIdealSubstructureSuperimposition

public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                    LeafSubstructureContainer candidate,
                                                                                    Predicate<Atom> atomFilter)

calculateIdealSubstructureSuperimposition

public static SubstructureSuperimposition calculateIdealSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                    LeafSubstructureContainer candidate,
                                                                                    RepresentationScheme representationScheme)

calculateKuhnMunkresSubstructureSuperimposition

public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          SubstitutionMatrix substitutionMatrix,
                                                                                          boolean considerExchanges)

calculateKuhnMunkresSubstructureSuperimposition

public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          Predicate<Atom> atomFilter,
                                                                                          SubstitutionMatrix substitutionMatrix,
                                                                                          boolean considerExchanges)

calculateKuhnMunkresSubstructureSuperimposition

public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                                          List<LeafSubstructure<?>> candidate,
                                                                                          RepresentationScheme representationScheme,
                                                                                          SubstitutionMatrix substitutionMatrix,
                                                                                          boolean considerExchanges)

calculateKuhnMunkresSubstructureSuperimposition

public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          SubstitutionMatrix substitutionMatrix,
                                                                                          boolean considerExchanges)

calculateKuhnMunkresSubstructureSuperimposition

public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          Predicate<Atom> atomFilter,
                                                                                          SubstitutionMatrix substitutionMatrix,
                                                                                          boolean considerExchanges)

calculateKuhnMunkresSubstructureSuperimposition

public static SubstructureSuperimposition calculateKuhnMunkresSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                                          LeafSubstructureContainer candidate,
                                                                                          RepresentationScheme representationScheme,
                                                                                          SubstitutionMatrix substitutionMatrix,
                                                                                          boolean considerExchanges)

calculateSubstructureSuperimposition

public static SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                               List<LeafSubstructure<?>> candidate)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

calculateSubstructureSuperimposition

public static SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                               List<LeafSubstructure<?>> candidate,
                                                                               Predicate<Atom> atomFilter)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

calculateSubstructureSuperimposition

public static SubstructureSuperimposition calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference,
                                                                               List<LeafSubstructure<?>> candidate,
                                                                               RepresentationScheme representationScheme)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

calculateSubstructureSuperimposition

public static SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                               LeafSubstructureContainer candidate)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

calculateSubstructureSuperimposition

public static SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                               LeafSubstructureContainer candidate,
                                                                               Predicate<Atom> atomFilter)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

calculateSubstructureSuperimposition

public static SubstructureSuperimposition calculateSubstructureSuperimposition(LeafSubstructureContainer reference,
                                                                               LeafSubstructureContainer candidate,
                                                                               RepresentationScheme representationScheme)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

calculateSuperimposition

protected SubstructureSuperimposition calculateSuperimposition()
                                                        throws SubstructureSuperimpositionException

Finds the superimposition for a list of LeafSubstructure according to their input order

Returns:

the superimposition according to their order

Throws:

SubstructureSuperimpositionException

defineAtoms

protected de.bioforscher.singa.core.utility.Pair<List<Atom>> defineAtoms()

Method to define the intersecting Atoms that should be used for the alignment. If this is not a fragment-based superimposition, the pairing is made based on atom names.

Returns:

The paired Atoms that constitute the alignment.