de.bioforscher.singa.structure.model.oak

Class StructuralMotif

java.lang.Object

de.bioforscher.singa.structure.model.oak.StructuralMotif

All Implemented Interfaces:

AtomContainer, LeafSubstructureContainer

public class StructuralMotif
extends Object
implements LeafSubstructureContainer

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StructuralMotif.Type The type of a StructuralMotif, representing inter (across multiple protein chains) and intra (within one protein chain) StructuralMotifs.

Field Summary

Fields

Modifier and Type	Field and Description
LinkedHashMap<LeafIdentifier,LeafSubstructure<?>>	leafSubstructures

Method Summary

Modifier and Type	Method and Description
void	addExchangeableFamily(LeafIdentifier leafIdentifier, AminoAcidFamily aminoAcidFamily) For a given LeafIdentifier a possible exchange is added.
void	addExchangeableFamily(LeafIdentifier leafIdentifier, MatcherFamily matcherFamily) For a given LeafIdentifier a possible exchange is added.
void	addExchangeableFamily(LeafIdentifier leafIdentifier, NucleotideFamily nucleotideFamily) For a given LeafIdentifier a possible exchange is added.
void	addExchangeableFamilyToAll(AminoAcidFamily aminoAcidFamily) Assigns an AminoAcidFamily to all members of this motif as exchange.
void	addExchangeableFamilyToAll(MatcherFamily matcherFamily) Assigns each member of a MatcherFamily to all members of this motif as exchange.
void	addExchangeableFamilyToAll(NucleotideFamily nucleotideFamily) Assigns an NucleotideFamily to all members of this motif as exchange.
void	addLeafSubstructure(LeafSubstructure leafSubstructure)
static StructuralMotif	fromLeafIdentifiers(Structure structure, List<LeafIdentifier> leafIdentifiers) Creates a StructuralMotif by extracting the given residues identified by a list of LeafIdentifiers.
static StructuralMotif	fromLeafSubstructures(List<LeafSubstructure<?>> leafSubstructures) Forms a StructuralMotif out of the given LeafSubstructures.
List<LeafSubstructure<?>>	getAllLeafSubstructures() Returns all LeafSubstructures.
Optional<Atom>	getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
StructuralMotif	getCopy()
LeafSubstructure<?>	getFirstLeafSubstructure()
Optional<LeafSubstructure<?>>	getLeafSubstructure(LeafIdentifier leafIdentifier) Returns an Optional of the LeafSubstructure with the given identifier.
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
boolean	removeLeafSubstructure(LeafIdentifier leafIdentifier) Removes a LeafSubstructure from this container.
int	size() Returns the size of the structural motif (the number of contained LeafSubstructures).
String	toString()

Methods inherited from class java.lang.Object

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

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

getAllAminoAcids, getAllAtoms, getAllLigands, getAllNucleotides, getAminoAcid, getAtom, getLigand, getNucleotide, getNumberOfLeafSubstructures, removeLeafSubstructure, removeLeafSubstructuresNotRelevantFor

Field Detail

leafSubstructures

public final LinkedHashMap<LeafIdentifier,LeafSubstructure<?>> leafSubstructures

Method Detail

fromLeafIdentifiers

public static StructuralMotif fromLeafIdentifiers(Structure structure,
                                                  List<LeafIdentifier> leafIdentifiers)

Creates a StructuralMotif by extracting the given residues identified by a list of LeafIdentifiers.

Parameters:

structure - The Structure from which the StructuralMotif should be extracted.

leafIdentifiers - The LeafIdentifiers of the residues that should compose the StructuralMotif.

Returns:

A new StructuralMotif.

fromLeafSubstructures

public static StructuralMotif fromLeafSubstructures(List<LeafSubstructure<?>> leafSubstructures)

Forms a StructuralMotif out of the given LeafSubstructures.

Parameters:

leafSubstructures - The LeafSubstructures that should compose the StructuralMotif.

Returns:

A new StructuralMotif.

getAllLeafSubstructures

public List<LeafSubstructure<?>> getAllLeafSubstructures()

Description copied from interface: LeafSubstructureContainer

Returns all LeafSubstructures.

Specified by:

getAllLeafSubstructures in interface LeafSubstructureContainer

Returns:

All LeafSubstructures.

getLeafSubstructure

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

Description copied from interface: LeafSubstructureContainer

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

Specified by:

getLeafSubstructure in interface LeafSubstructureContainer

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

An Optional encapsulating the LeafSubstructure.

getFirstLeafSubstructure

public LeafSubstructure<?> getFirstLeafSubstructure()

Specified by:

getFirstLeafSubstructure in interface LeafSubstructureContainer

removeLeafSubstructure

public boolean removeLeafSubstructure(LeafIdentifier leafIdentifier)

Description copied from interface: LeafSubstructureContainer

Removes a LeafSubstructure from this container.

Specified by:

removeLeafSubstructure in interface LeafSubstructureContainer

Parameters:

leafIdentifier - The identifier of the leaf.

Returns:

True if the LeafSubstructure was removed.

addLeafSubstructure

public void addLeafSubstructure(LeafSubstructure leafSubstructure)

size

public int size()

Returns the size of the structural motif (the number of contained LeafSubstructures).

Returns:

The size of the motif.

getAtom

public Optional<Atom> getAtom(Integer atomIdentifier)

Description copied from interface: AtomContainer

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

Specified by:

getAtom in interface AtomContainer

Parameters:

atomIdentifier - The identifier of the atom.

Returns:

An Optional encapsulating the Atom.

removeAtom

public void removeAtom(Integer atomIdentifier)

Description copied from interface: AtomContainer

Removes an atom from this container.

Specified by:

removeAtom in interface AtomContainer

Parameters:

atomIdentifier - The identifier of the atom to be removed.

addExchangeableFamily

public void addExchangeableFamily(LeafIdentifier leafIdentifier,
                                  MatcherFamily matcherFamily)

For a given LeafIdentifier a possible exchange is added. This exchange is considered when searching with Fit3D. The MatcherFamily allows exchanges for groups of LeafSubstructures with similar physicochemical attributes.

Parameters:

leafIdentifier - The leaf to add the exchange to.

matcherFamily - The MatcherFamily.

addExchangeableFamily

public void addExchangeableFamily(LeafIdentifier leafIdentifier,
                                  NucleotideFamily nucleotideFamily)

For a given LeafIdentifier a possible exchange is added. This exchange is considered when searching with Fit3D.

Parameters:

leafIdentifier - The leaf to add the exchange to.

nucleotideFamily - The Nucleotide that can be exchanged.

addExchangeableFamily

public void addExchangeableFamily(LeafIdentifier leafIdentifier,
                                  AminoAcidFamily aminoAcidFamily)

For a given LeafIdentifier a possible exchange is added. This exchange is considered when searching with Fit3D.

Parameters:

leafIdentifier - The leaf to add the exchange to.

aminoAcidFamily - The AminoAcid that can be exchanged.

addExchangeableFamilyToAll

public void addExchangeableFamilyToAll(AminoAcidFamily aminoAcidFamily)

Assigns an AminoAcidFamily to all members of this motif as exchange.

Parameters:

aminoAcidFamily - The AminoAcidFamily which should be assigned as exchangeable type.

addExchangeableFamilyToAll

public void addExchangeableFamilyToAll(NucleotideFamily nucleotideFamily)

Assigns an NucleotideFamily to all members of this motif as exchange.

Parameters:

nucleotideFamily - The NucleotideFamily which should be assigned as exchangeable type.

addExchangeableFamilyToAll

public void addExchangeableFamilyToAll(MatcherFamily matcherFamily)

Assigns each member of a MatcherFamily to all members of this motif as exchange.

Parameters:

matcherFamily - The MatcherFamily that bundles all members which should be assigned as exchangeable type.

toString

public String toString()

Overrides:

toString in class Object

getCopy

public StructuralMotif getCopy()

Specified by:

getCopy in interface LeafSubstructureContainer