de.bioforscher.singa.structure.model.interfaces

Interface LeafSubstructureContainer

All Superinterfaces:

AtomContainer

All Known Subinterfaces:

Chain, Model, Structure

All Known Implementing Classes:

MmtfChain, MmtfModel, MmtfStructure, OakChain, OakModel, OakStructure, StructuralMotif

public interface LeafSubstructureContainer
extends AtomContainer

Everything that contains leaf substructures. Provides default methods to retrieve AminoAcids, Nucleotides, and Ligands.

Author:

cl

Method Summary

Modifier and Type	Method and Description
default List<AminoAcid>	getAllAminoAcids() Returns all AminoAcids.
default List<Atom>	getAllAtoms() Returns all Atoms.
List<LeafSubstructure<?>>	getAllLeafSubstructures() Returns all LeafSubstructures.
default List<Ligand>	getAllLigands() Returns all Ligands.
default List<Nucleotide>	getAllNucleotides() Returns all Nucleotides.
default Optional<AminoAcid>	getAminoAcid(LeafIdentifier leafIdentifier) Returns an Optional of the AminoAcid with the given identifier.
default Optional<Atom>	getAtom(int atomIdentifier) Returns an Optional of the Atom with the given identifier.
<ContainerType extends LeafSubstructureContainer> ContainerType	getCopy()
LeafSubstructure<?>	getFirstLeafSubstructure()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
default Optional<Ligand>	getLigand(LeafIdentifier leafIdentifier) Returns an Optional of the Ligand with the given identifier.
default Optional<Nucleotide>	getNucleotide(LeafIdentifier leafIdentifier) Returns an Optional of the Nucleotide with the given identifier.
default int	getNumberOfLeafSubstructures()
boolean	removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.
default boolean	removeLeafSubstructure(LeafSubstructure leafSubstructure)
default void	removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep) Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer.

Methods inherited from interface de.bioforscher.singa.structure.model.interfaces.AtomContainer

getAtom, removeAtom

Method Detail

getAllLeafSubstructures

List<LeafSubstructure<?>> getAllLeafSubstructures()

Returns all LeafSubstructures.

Returns:

All LeafSubstructures.

getLeafSubstructure

Optional<LeafSubstructure<?>> getLeafSubstructure(LeafIdentifier leafIdentifier)

Returns an Optional of the LeafSubstructure with the given identifier. If no LeafSubstructure with the identifier could be found, an empty optional is returned.

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

An Optional encapsulating the LeafSubstructure.

getFirstLeafSubstructure

LeafSubstructure<?> getFirstLeafSubstructure()

removeLeafSubstructure

boolean removeLeafSubstructure(LeafIdentifier leafIdentifier)

Removes a LeafSubstructure from this container.

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

True if the LeafSubstructure was removed.

removeLeafSubstructure

default boolean removeLeafSubstructure(LeafSubstructure leafSubstructure)

removeLeafSubstructuresNotRelevantFor

default void removeLeafSubstructuresNotRelevantFor(LeafSubstructureContainer leafSubstructuresToKeep)

Removes all LeafSubstructures from this container that are not referenced in the given LeafSubstructureContainer. Basically all LeafSubstructures are removed that do not match any of the given containers families. This method also keeps exchangeable families if any are defined.

Parameters:

leafSubstructuresToKeep - The leaf structures that are kept.

getNumberOfLeafSubstructures

default int getNumberOfLeafSubstructures()

getAllAminoAcids

default List<AminoAcid> getAllAminoAcids()

Returns all AminoAcids.

Returns:

All AminoAcids.

getAminoAcid

default Optional<AminoAcid> getAminoAcid(LeafIdentifier leafIdentifier)

Returns an Optional of the AminoAcid with the given identifier. If no LeafSubstructure with the identifier could be found or the LeafSubstructure is no AminoAcid, an empty optional is returned.

Parameters:

leafIdentifier - The identifier of the amino acid.

Returns:

An Optional encapsulating the AminoAcid.

getAllNucleotides

default List<Nucleotide> getAllNucleotides()

Returns all Nucleotides.

Returns:

All Nucleotides.

getNucleotide

default Optional<Nucleotide> getNucleotide(LeafIdentifier leafIdentifier)

Returns an Optional of the Nucleotide with the given identifier. If no LeafSubstructure with the identifier could be found or the LeafSubstructure is no Nucleotide, an empty optional is returned.

Parameters:

leafIdentifier - The identifier of the nucleotide.

Returns:

An Optional encapsulating the Nucleotide.

getAllLigands

default List<Ligand> getAllLigands()

Returns all Ligands.

Returns:

All Ligands.

getLigand

default Optional<Ligand> getLigand(LeafIdentifier leafIdentifier)

Returns an Optional of the Ligand with the given identifier. If no LeafSubstructure with the identifier could be found or the LeafSubstructure is no Ligand, an empty optional is returned.

Parameters:

leafIdentifier - The identifier of the ligand.

Returns:

An Optional encapsulating the Ligand.

getAllAtoms

default List<Atom> getAllAtoms()

Returns all Atoms.

Specified by:

getAllAtoms in interface AtomContainer

Returns:

All Atoms.

getAtom

default Optional<Atom> getAtom(int atomIdentifier)

Returns an Optional of the Atom with the given identifier. If no Atom with the identifier could be found an empty optional is returned.

Parameters:

atomIdentifier - The identifier of the atom.

Returns:

An Optional encapsulating the Atom.

getCopy

<ContainerType extends LeafSubstructureContainer> ContainerType getCopy()