Uses of Class
de.bioforscher.singa.structure.elements.Element

Packages that use Element

Package	Description
de.bioforscher.singa.structure.algorithms.molecules
de.bioforscher.singa.structure.elements
de.bioforscher.singa.structure.model.interfaces
de.bioforscher.singa.structure.model.mmtf
de.bioforscher.singa.structure.model.molecules
de.bioforscher.singa.structure.model.oak

Uses of Element in de.bioforscher.singa.structure.algorithms.molecules

Method parameters in de.bioforscher.singa.structure.algorithms.molecules with type arguments of type Element

Modifier and Type	Method and Description
static List<LinkedList<MoleculeAtom>>	MoleculePathFinder.findMultiPathInMolecule(MoleculeGraph molecule, LinkedList<Set<Element>> multiPath)
static List<LinkedList<MoleculeAtom>>	MoleculePathFinder.findPathInMolecule(MoleculeGraph molecule, LinkedList<Element> path)

Uses of Element in de.bioforscher.singa.structure.elements

Fields in de.bioforscher.singa.structure.elements declared as Element

Modifier and Type	Field and Description
static Element	ElementProvider.ACTINIUM
static Element	ElementProvider.ALUMINIUM
static Element	ElementProvider.AMERICIUM
static Element	ElementProvider.ANTIMONY
static Element	ElementProvider.ARGON
static Element	ElementProvider.ARSENIC
static Element	ElementProvider.ASTATINE
static Element	ElementProvider.BARIUM
static Element	ElementProvider.BERKELIUM
static Element	ElementProvider.BERYLLIUM
static Element	ElementProvider.BISMUTH
static Element	ElementProvider.BOHRIUM
static Element	ElementProvider.BORON
static Element	ElementProvider.BROMINE
static Element	ElementProvider.CADMIUM
static Element	ElementProvider.CALCIUM
static Element	ElementProvider.CALIFORNIUM
static Element	ElementProvider.CARBON
static Element	ElementProvider.CERIUM
static Element	ElementProvider.CESIUM
static Element	ElementProvider.CHLORINE
static Element	ElementProvider.CHROMIUM
static Element	ElementProvider.COBALT
static Element	ElementProvider.COPPER
static Element	ElementProvider.CURIUM
static Element	ElementProvider.DEUTERIUM
static Element	ElementProvider.DUBNIUM
static Element	ElementProvider.DYSPROSIUM
static Element	ElementProvider.EINSTEINIUM
static Element	ElementProvider.ERBIUM
static Element	ElementProvider.EUROPIUM
static Element	ElementProvider.FERMIUM
static Element	ElementProvider.FLUORINE
static Element	ElementProvider.FRANCIUM
static Element	ElementProvider.GADOLINIUM
static Element	ElementProvider.GALLIUM
static Element	ElementProvider.GERMANIUM
static Element	ElementProvider.GOLD
static Element	ElementProvider.HAFNIUM
static Element	ElementProvider.HASSIUM
static Element	ElementProvider.HELIUM
static Element	ElementProvider.HOLMIUM
static Element	ElementProvider.HYDROGEN
static Element	ElementProvider.INDIUM
static Element	ElementProvider.IODINE
static Element	ElementProvider.IRIDIUM
static Element	ElementProvider.IRON
static Element	ElementProvider.KRYPTON
static Element	ElementProvider.LANTHANUM
static Element	ElementProvider.LAWRENCIUM
static Element	ElementProvider.LEAD
static Element	ElementProvider.LITHIUM
static Element	ElementProvider.LUTETIUM
static Element	ElementProvider.MAGNESIUM
static Element	ElementProvider.MANGANESE
static Element	ElementProvider.MENDELEVIUM
static Element	ElementProvider.MERCURY
static Element	ElementProvider.MOLYBDENUM
static Element	ElementProvider.NEODYMIUM
static Element	ElementProvider.NEON
static Element	ElementProvider.NEPTUNIUM
static Element	ElementProvider.NICKEL
static Element	ElementProvider.NIOBIUM
static Element	ElementProvider.NITROGEN
static Element	ElementProvider.NOBELIUM
static Element	ElementProvider.OSMIUM
static Element	ElementProvider.OXYGEN
static Element	ElementProvider.PALLADIUM
static Element	ElementProvider.PHOSPHORUS
static Element	ElementProvider.PLATINUM
static Element	ElementProvider.PLUTONIUM
static Element	ElementProvider.POLONIUM
static Element	ElementProvider.POTASSIUM
static Element	ElementProvider.PRASEODYMIUM
static Element	ElementProvider.PROMETHIUM
static Element	ElementProvider.PROTACTINIUM
static Element	ElementProvider.RADIUM
static Element	ElementProvider.RADON
static Element	ElementProvider.RHENIUM
static Element	ElementProvider.RHODIUM
static Element	ElementProvider.RUBIDIUM
static Element	ElementProvider.RUTHENIUM
static Element	ElementProvider.RUTHERFORDIUM
static Element	ElementProvider.SAMARIUM
static Element	ElementProvider.SCANDIUM
static Element	ElementProvider.SEABORGIUM
static Element	ElementProvider.SELENIUM
static Element	ElementProvider.SILICON
static Element	ElementProvider.SILVER
static Element	ElementProvider.SODIUM
static Element	ElementProvider.STRONTIUM
static Element	ElementProvider.SULFUR
static Element	ElementProvider.TANTALUM
static Element	ElementProvider.TECHNETIUM
static Element	ElementProvider.TELLURIUM
static Element	ElementProvider.TERBIUM
static Element	ElementProvider.THALLIUM
static Element	ElementProvider.THORIUM
static Element	ElementProvider.THULIUM
static Element	ElementProvider.TIN
static Element	ElementProvider.TITANIUM
static Element	ElementProvider.TRITIUM
static Element	ElementProvider.TUNGSTEN
static Element	ElementProvider.UNKOWN
static Element	ElementProvider.URANIUM
static Element	ElementProvider.VANADIUM
static Element	ElementProvider.XENON
static Element	ElementProvider.YTTERBIUM
static Element	ElementProvider.YTTRIUM
static Element	ElementProvider.ZINC
static Element	ElementProvider.ZIRCONIUM

Methods in de.bioforscher.singa.structure.elements that return Element

Modifier and Type	Method and Description
Element	Element.asAnion(int numberOfElectronsGained) Converts this element into an ion (anion) by increasing its electron count.
Element	Element.asCation(int numberOfElectronsLost) Converts this element into an ion (cation) by decreasing its electron count.
Element	Element.asIon(int charge) Converts this element into an ion (cation) by decreasing its electron count.
Element	Element.asIsotope(int massNumber) Converts this element into an isotope by adjusting its neutron count.

Methods in de.bioforscher.singa.structure.elements that return types with arguments of type Element

Modifier and Type	Method and Description
static Optional<Element>	ElementProvider.getElementBySymbol(String symbol) Retrieves an Optional of an Element by ity symbol.
static Set<Element>	ElementProvider.getElements() Contains all the elements of this library.

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

Methods in de.bioforscher.singa.structure.model.interfaces that return Element

Modifier and Type	Method and Description
Element	Atom.getElement() Returns the Element.

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

Methods in de.bioforscher.singa.structure.model.mmtf that return Element

Modifier and Type	Method and Description
Element	MmtfAtom.getElement()

Uses of Element in de.bioforscher.singa.structure.model.molecules

Methods in de.bioforscher.singa.structure.model.molecules that return Element

Modifier and Type	Method and Description
Element	MoleculeAtom.getElement()

Methods in de.bioforscher.singa.structure.model.molecules with parameters of type Element

Modifier and Type	Method and Description
int	MoleculeGraph.addNextAtom(Element element)
int	MoleculeGraph.addNextAtom(Element element, int charge)
int	MoleculeGraph.addNextAtom(Element element, int charge, int massNumber)
static int	MoleculeGraphs.countAtomsOfElement(MoleculeGraph graph, Element element)
static Predicate<MoleculeAtom>	MoleculeGraphs.isElement(Element element)
void	MoleculeAtom.setElement(Element element)

Method parameters in de.bioforscher.singa.structure.model.molecules with type arguments of type Element

Modifier and Type	Method and Description
static List<LinkedList<MoleculeAtom>>	MoleculeGraphs.findMultiPathOfElements(MoleculeGraph graph, LinkedList<Set<Element>> path)
static List<LinkedList<MoleculeAtom>>	MoleculeGraphs.findPathOfElements(MoleculeGraph graph, LinkedList<Element> path)
static Predicate<MoleculeAtom>	MoleculeGraphs.isOneOfElements(Set<Element> elements)

Constructors in de.bioforscher.singa.structure.model.molecules with parameters of type Element

Constructor and Description
MoleculeAtom(int identifier, Vector2D position, Element element)

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

Methods in de.bioforscher.singa.structure.model.oak that return Element

Modifier and Type	Method and Description
Element	AtomName.getElement()
Element	OakAtom.getElement()

Constructors in de.bioforscher.singa.structure.model.oak with parameters of type Element

Constructor and Description
OakAtom(int identifier, Element element, String atomName, Vector3D position) Creates a new atom with the given pdbIdentifier, element, name and position.