de.bioforscher.singa.structure.algorithms.superimposition

Class FragmentSubstructureSuperimposer

java.lang.Object

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

de.bioforscher.singa.structure.algorithms.superimposition.FragmentSubstructureSuperimposer

public class FragmentSubstructureSuperimposer
extends SubstructureSuperimposer

A special version of the SubstructureSuperimposer that uses subgraph isomorphism to align a candidate against a given reference fragment. This is useful if one wants to align, for example, ligands where no consistent atom names are guaranteed.

Author:

fk

Field Summary

Fields inherited from class de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer

candidate, reference

Method Summary

Modifier and Type	Method and Description
static SubstructureSuperimposition	calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate)
static SubstructureSuperimposition	calculateSubstructureSuperimposition(List<LeafSubstructure<?>> reference, List<LeafSubstructure<?>> candidate, BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition, BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)
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 de.bioforscher.singa.structure.algorithms.superimposition.SubstructureSuperimposer

calculateIdealSubstructureSuperimposition, calculateIdealSubstructureSuperimposition, calculateIdealSubstructureSuperimposition, calculateIdealSubstructureSuperimposition, calculateIdealSubstructureSuperimposition, calculateIdealSubstructureSuperimposition, calculateKuhnMunkresSubstructureSuperimposition, calculateKuhnMunkresSubstructureSuperimposition, calculateKuhnMunkresSubstructureSuperimposition, calculateKuhnMunkresSubstructureSuperimposition, calculateKuhnMunkresSubstructureSuperimposition, calculateKuhnMunkresSubstructureSuperimposition, calculateSubstructureSuperimposition, calculateSubstructureSuperimposition, calculateSubstructureSuperimposition, calculateSubstructureSuperimposition, calculateSubstructureSuperimposition, calculateSuperimposition

Methods inherited from class java.lang.Object

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

Method Detail

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,
                                                                               BiFunction<MoleculeAtom,MoleculeAtom,Boolean> atomCondition,
                                                                               BiFunction<MoleculeBond,MoleculeBond,Boolean> bondCondition)
                                                                        throws SubstructureSuperimpositionException

Throws:

SubstructureSuperimpositionException

defineAtoms

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

Description copied from class: SubstructureSuperimposer

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.

Overrides:

defineAtoms in class SubstructureSuperimposer

Returns:

The paired Atoms that constitute the alignment.