Uses of Interface
de.bioforscher.singa.structure.model.interfaces.AtomContainer

Packages that use AtomContainer

Package	Description
de.bioforscher.singa.structure.algorithms.gyration
de.bioforscher.singa.structure.model.interfaces
de.bioforscher.singa.structure.model.mmtf
de.bioforscher.singa.structure.model.oak
de.bioforscher.singa.structure.parser.pdb.structures

Uses of AtomContainer in de.bioforscher.singa.structure.algorithms.gyration

Methods in de.bioforscher.singa.structure.algorithms.gyration with parameters of type AtomContainer

Modifier and Type	Method and Description
static Gyration	Gyration.of(AtomContainer atomContainer) Calculates the gyration for the atoms in the container.

Uses of AtomContainer in de.bioforscher.singa.structure.model.interfaces

Subinterfaces of AtomContainer in de.bioforscher.singa.structure.model.interfaces

Modifier and Type	Interface and Description
interface	AminoAcid A specific type of LeafSubstructure, representing amino acids.
interface	Chain Chains that represent one continuous macro molecule (most often the biggest macro molecules and its ligands are collected in one model).
interface	LeafSubstructure<FamilyType extends StructuralFamily> A leaf substructure is a collection of atoms with meta data assigned to it.
interface	LeafSubstructureContainer Everything that contains leaf substructures.
interface	Ligand A specific type of LeafSubstructure, representing ligands.
interface	Model Models represent macro molecular structures.
interface	Nucleotide A specific type of LeafSubstructure, representing nucleotides.
interface	Structure Structures represent chemical objects in three dimensional space.

Uses of AtomContainer in de.bioforscher.singa.structure.model.mmtf

Classes in de.bioforscher.singa.structure.model.mmtf that implement AtomContainer

Modifier and Type	Class and Description
class	MmtfAminoAcid The implementation of AminoAcids for mmtf structures.
class	MmtfChain The implementation of Chain for mmtf structures.
class	MmtfLeafSubstructure<FamilyType extends StructuralFamily> The implementation of LeafSubstructure for mmtf structures.
class	MmtfLigand The implementation of Ligands for mmtf structures.
class	MmtfModel The implementation of Model for mmtf structures.
class	MmtfNucleotide The implementation of Nucleotides for mmtf structures.
class	MmtfStructure The implementation of Structures for mmtf structures.

Uses of AtomContainer in de.bioforscher.singa.structure.model.oak

Classes in de.bioforscher.singa.structure.model.oak that implement AtomContainer

Modifier and Type	Class and Description
class	OakAminoAcid
class	OakChain
class	OakLeafSubstructure<FamilyType extends StructuralFamily>
class	OakLigand
class	OakModel
class	OakNucleotide
class	OakStructure
class	StructuralMotif

Methods in de.bioforscher.singa.structure.model.oak with parameters of type AtomContainer

Modifier and Type	Method and Description
static LabeledSymmetricMatrix<Atom>	Structures.calculateAtomDistanceMatrix(AtomContainer atomContainer) Returns the distance matrix of the given Atoms.
static List<Sphere>	Structures.convertToSpheres(AtomContainer atomContainer)

Uses of AtomContainer in de.bioforscher.singa.structure.parser.pdb.structures

Methods in de.bioforscher.singa.structure.parser.pdb.structures with parameters of type AtomContainer

Modifier and Type	Method and Description
static void	StructureWriter.writeToXYZ(AtomContainer atomContainer, Path outputPath)