de.bioforscher.singa.structure.model.interfaces

Interface LeafSubstructure<FamilyType extends StructuralFamily>

All Superinterfaces:

AtomContainer, Exchangeable<FamilyType>

All Known Subinterfaces:

AminoAcid, Ligand, Nucleotide

All Known Implementing Classes:

MmtfAminoAcid, MmtfLeafSubstructure, MmtfLigand, MmtfNucleotide, OakAminoAcid, OakLeafSubstructure, OakLigand, OakNucleotide

public interface LeafSubstructure<FamilyType extends StructuralFamily>
extends AtomContainer, Exchangeable<FamilyType>

A leaf substructure is a collection of atoms with meta data assigned to it. A leaf substructure can be part of a macro molecule, such as amino acid residues or nucleotides, or independent small molecules.

Author:

cl

Method Summary

Modifier and Type	Method and Description
boolean	containsAtomWithName(String atomName)
default String	flatToString() Returns the flat String representation of this leaf substructure in the form:
Optional<Atom>	getAtomByName(String atomName)
default String	getChainIdentifier()
<LeafImplementation extends LeafSubstructure> LeafImplementation	getCopy() Returns a copy of this LeafSubstructure.
LeafIdentifier	getIdentifier() Returns the complete leaf identifier.
default char	getInsertionCode()
default Integer	getModelIdentifier()
default String	getPdbIdentifier()
default List<String>	getPdbLines()
default Vector3D	getPosition()
default Integer	getSerial()
String	getThreeLetterCode() Returns the three letter code of the chemical compound represented by this leaf substructure.
boolean	isAnnotatedAsHeteroAtom()

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

getAllAtoms, getAtom, removeAtom

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

addExchangeableFamily, getContainingFamilies, getExchangeableFamilies, getFamily

Method Detail

getIdentifier

LeafIdentifier getIdentifier()

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.

Returns:

The leaf identifier.

See Also:

LeafIdentifier

getPdbIdentifier

default String getPdbIdentifier()

getModelIdentifier

default Integer getModelIdentifier()

getChainIdentifier

default String getChainIdentifier()

getSerial

default Integer getSerial()

getInsertionCode

default char getInsertionCode()

getPosition

default Vector3D getPosition()

getPdbLines

default List<String> getPdbLines()

containsAtomWithName

boolean containsAtomWithName(String atomName)

getAtomByName

Optional<Atom> getAtomByName(String atomName)

isAnnotatedAsHeteroAtom

boolean isAnnotatedAsHeteroAtom()

getThreeLetterCode

String getThreeLetterCode()

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

Returns:

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

getCopy

<LeafImplementation extends LeafSubstructure> LeafImplementation getCopy()

Returns a copy of this LeafSubstructure.

Type Parameters:

LeafImplementation - The type of the LeafSubstructure.

Returns:

A copy of this leaf substructure.

flatToString

default String flatToString()

Returns the flat String representation of this leaf substructure in the form:

     [LeafIdentifier] [ThreeLetterCode]
 

For example:

     1C0A-1-B-631 C
     1C0A-1-A-78 ARG
     1C0A-1-A-1048 HOH
 

Returns:

The flat String representation of this leaf substructure.