de.bioforscher.singa.structure.model.oak

Class OakLeafSubstructure<FamilyType extends StructuralFamily>

java.lang.Object

de.bioforscher.singa.structure.model.oak.OakLeafSubstructure<FamilyType>

All Implemented Interfaces:

AtomContainer, LeafSubstructure<FamilyType>, Exchangeable<FamilyType>

Direct Known Subclasses:

OakAminoAcid, OakLigand, OakNucleotide

public abstract class OakLeafSubstructure<FamilyType extends StructuralFamily>
extends Object
implements LeafSubstructure<FamilyType>

Author:

cl

Constructor Summary

Constructors

Constructor and Description
OakLeafSubstructure(LeafIdentifier leafIdentifier, FamilyType family)
OakLeafSubstructure(LeafIdentifier identifer, FamilyType aminoAcidFamily, String threeLetterCode)
OakLeafSubstructure(OakLeafSubstructure<FamilyType> leafSubstructure) This is a copy constructor.

Method Summary

Modifier and Type	Method and Description
void	addAtom(OakAtom atom)
int	addBondBetween(OakAtom source, OakAtom target)
int	addBondBetween(OakAtom source, OakAtom target, BondType bondType)
int	addBondBetween(OakBond edge, OakAtom source, OakAtom target) Adds a bond connecting the the given atoms.
void	addExchangeableFamily(FamilyType exchangeableType) Adds an exchangeable StructuralFamily.
boolean	containsAtomWithName(String atomName)
boolean	equals(Object o)
List<Atom>	getAllAtoms() Returns all Atoms.
Optional<Atom>	getAtom(Integer atomIdentifier) Returns an Optional of the Atom with the given identifier.
Optional<Atom>	getAtomByName(String atomName)
Collection<OakBond>	getBonds()
Set<FamilyType>	getExchangeableFamilies() Returns the StructuralFamilys to which this entity is exchangeable.
FamilyType	getFamily() Returns the StructuralFamily of this entity.
LeafIdentifier	getIdentifier() Returns the complete leaf identifier.
int	getNextEdgeIdentifier()
String	getThreeLetterCode() Returns the three letter code of the chemical compound represented by this leaf substructure.
int	hashCode()
boolean	isAnnotatedAsHeteroAtom()
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
void	setAnnotatedAsHetAtom(boolean annotatedAsHetAtom)
String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

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

flatToString, getChainIdentifier, getCopy, getInsertionCode, getModelIdentifier, getPdbIdentifier, getPdbLines, getPosition, getSerial

Methods inherited from interface de.bioforscher.singa.structure.model.oak.Exchangeable

getContainingFamilies

Constructor Detail

OakLeafSubstructure

public OakLeafSubstructure(LeafIdentifier leafIdentifier,
                           FamilyType family)

OakLeafSubstructure

public OakLeafSubstructure(LeafIdentifier identifer,
                           FamilyType aminoAcidFamily,
                           String threeLetterCode)

OakLeafSubstructure

public OakLeafSubstructure(OakLeafSubstructure<FamilyType> leafSubstructure)

This is a copy constructor. Creates a new leaf with the same attributes as the given leaf. This also recursively creates copies of all the underlying substructures and atoms. The neighbours of this substructure are NOT copied. Due to the nature of this operation it would be bad to keep a part of the relations to the lifecycle of the substructure to copy. If you want to keep the neighbouring substructures, copy the superordinate substructure that contains this substructure and it will also traverse and copy the neighbouring substructures.

Parameters:

leafSubstructure - The leaf to copy.

Method Detail

getIdentifier

public LeafIdentifier getIdentifier()

Description copied from interface: LeafSubstructure

Returns the complete leaf identifier. The leaf identifier consists of the PDB identifer, the model identifier, the chain identifier, the serial of the leaf substructure and optionally an insertion code.

Specified by:

getIdentifier in interface LeafSubstructure<FamilyType extends StructuralFamily>

Returns:

The leaf identifier.

See Also:

LeafIdentifier

containsAtomWithName

public boolean containsAtomWithName(String atomName)

Specified by:

containsAtomWithName in interface LeafSubstructure<FamilyType extends StructuralFamily>

getAtomByName

public Optional<Atom> getAtomByName(String atomName)

Specified by:

getAtomByName in interface LeafSubstructure<FamilyType extends StructuralFamily>

isAnnotatedAsHeteroAtom

public boolean isAnnotatedAsHeteroAtom()

Specified by:

isAnnotatedAsHeteroAtom in interface LeafSubstructure<FamilyType extends StructuralFamily>

setAnnotatedAsHetAtom

public void setAnnotatedAsHetAtom(boolean annotatedAsHetAtom)

getThreeLetterCode

public String getThreeLetterCode()

Description copied from interface: LeafSubstructure

Returns the three letter code of the chemical compound represented by this leaf substructure.

Specified by:

getThreeLetterCode in interface LeafSubstructure<FamilyType extends StructuralFamily>

Returns:

The three letter code of the chemical compound represented by this leaf substructure.

getFamily

public FamilyType getFamily()

Description copied from interface: Exchangeable

Returns the StructuralFamily of this entity.

Specified by:

getFamily in interface Exchangeable<FamilyType extends StructuralFamily>

Returns:

the StructuralFamily

getAllAtoms

public List<Atom> getAllAtoms()

Description copied from interface: AtomContainer

Returns all Atoms.

Specified by:

getAllAtoms in interface AtomContainer

Returns:

All Atoms.

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.

addAtom

public void addAtom(OakAtom 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.

getBonds

public Collection<OakBond> getBonds()

addBondBetween

public int addBondBetween(OakBond edge,
                          OakAtom source,
                          OakAtom target)

Adds a bond connecting the the given atoms. The order of the given atoms does not matter, but is retained. The bond type can be specified beforehand and the pdbIdentifier of the edge is used as the identifer in the leaf.

Parameters:

edge - The edge to be added.

source - The source atom.

target - The target atom.

Returns:

The identifer of the added edge.

addBondBetween

public int addBondBetween(OakAtom source,
                          OakAtom target)

addBondBetween

public int addBondBetween(OakAtom source,
                          OakAtom target,
                          BondType bondType)

getExchangeableFamilies

public Set<FamilyType> getExchangeableFamilies()

Description copied from interface: Exchangeable

Returns the StructuralFamilys to which this entity is exchangeable. By default an entity is always exchangeable to the same StructuralFamily.

Specified by:

getExchangeableFamilies in interface Exchangeable<FamilyType extends StructuralFamily>

Returns:

a set of exchangeable types

addExchangeableFamily

public void addExchangeableFamily(FamilyType exchangeableType)

Description copied from interface: Exchangeable

Adds an exchangeable StructuralFamily.

Specified by:

addExchangeableFamily in interface Exchangeable<FamilyType extends StructuralFamily>

Parameters:

exchangeableType - the StructuralFamily to be added

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object

getNextEdgeIdentifier

public int getNextEdgeIdentifier()