de.bioforscher.singa.structure.model.mmtf

Class MmtfLeafSubstructure<FamilyType extends StructuralFamily>

java.lang.Object

de.bioforscher.singa.structure.model.mmtf.MmtfLeafSubstructure<FamilyType>

All Implemented Interfaces:

AtomContainer, LeafSubstructure<FamilyType>, Exchangeable<FamilyType>

Direct Known Subclasses:

MmtfAminoAcid, MmtfLigand, MmtfNucleotide

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

The implementation of LeafSubstructure for mmtf structures. Remembers the internal group index, the leaf identifier and the indices of the first and the last atom belonging to this group.

Author:

cl

Field Summary

Fields

Modifier and Type	Field and Description
protected Set<FamilyType>	exchangeableFamilies The families to which the LeafSubstructure can be exchanged.
protected FamilyType	family The structural family of this entity

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	MmtfLeafSubstructure(MmtfLeafSubstructure<?> mmtfLeafSubstructure) A copy constructor that passes all attributes of the given MmtfLeafSubstructure to a new instance.

Method Summary

Modifier and Type	Method and Description
boolean	containsAtomWithName(String atomName)
boolean	equals(Object o)
List<Atom>	getAllAtoms() Returns all Atoms.
Optional<Atom>	getAtom(Integer internalAtomIndex) Returns an Optional of the Atom with the given identifier.
Optional<Atom>	getAtomByName(String atomName)
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.
String	getThreeLetterCode() Returns the three letter code of the chemical compound represented by this leaf substructure.
int	hashCode()
void	removeAtom(Integer atomIdentifier) Removes an atom from this container.
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, isAnnotatedAsHeteroAtom

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

addExchangeableFamily, getContainingFamilies

Field Detail

family

protected FamilyType extends StructuralFamily family

The structural family of this entity

exchangeableFamilies

protected Set<FamilyType extends StructuralFamily> exchangeableFamilies

The families to which the LeafSubstructure can be exchanged.

Constructor Detail

MmtfLeafSubstructure

protected MmtfLeafSubstructure(MmtfLeafSubstructure<?> mmtfLeafSubstructure)

A copy constructor that passes all attributes of the given MmtfLeafSubstructure to a new instance.

Parameters:

mmtfLeafSubstructure - The MmtfLeafSubstructure 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

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.

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 internalAtomIndex)

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:

internalAtomIndex - 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.

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>

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

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

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