Uses of Class
com.hfg.chem.Element

Packages that use Element

Package	Description
com.hfg.bio
com.hfg.bio.glyco
com.hfg.bio.seq
com.hfg.chem

Uses of Element in com.hfg.bio

Methods in com.hfg.bio with parameters of type Element

Modifier and Type	Method and Description
AminoAcid	AminoAcid.addAtoms(Element inElement, int inNum)
CTerminalGroup	CTerminalGroup.addAtoms(Element inElement, int inNum)
NTerminalGroup	NTerminalGroup.addAtoms(Element inElement, int inNum)

Constructor parameters in com.hfg.bio with type arguments of type Element

Constructor and Description
AminoAcid(String inName, Map<Element,Float> inElementalComposition)

Uses of Element in com.hfg.bio.glyco

Methods in com.hfg.bio.glyco with parameters of type Element

Modifier and Type	Method and Description
Monosaccharide	Monosaccharide.addAtoms(Element inElement, float inCount)
Monosaccharide	Monosaccharide.addAtoms(Element inElement, int inCount)

Uses of Element in com.hfg.bio.seq

Methods in com.hfg.bio.seq that return types with arguments of type Element

Modifier and Type	Method and Description
Map<Element,Float>	BioSequenceImpl.getElementalComposition() Returns an unmodifiable copy of the elemental composition Map.
Map<Element,Float>	ProteinXLink.getElementalComposition() Returns an unmodifiable copy of the elemental composition Map.
Map<Element,Float>	Protein.getElementalComposition(ProteinAnalysisMode inMode) Returns an unmodifiable copy of the elemental composition Map adjusted (if necessary) for the specified protein analysis mode.

Constructor parameters in com.hfg.bio.seq with type arguments of type Element

Constructor and Description
ProteinXLinkType(String inName, Map<Element,Float> inElementalComposition, Set<AminoAcid> inDonorSpecificity, Set<AminoAcid> inAcceptorSpecificity)

Uses of Element in com.hfg.chem

Subclasses of Element in com.hfg.chem

Modifier and Type	Class and Description
class	Isotope Isotope.

Fields in com.hfg.chem declared as Element

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

Fields in com.hfg.chem with type parameters of type Element

Modifier and Type	Field and Description
OrderedMap<Element,OrderedMap<Integer,int[]>>	ValenceModel.mValenceValueMap

Methods in com.hfg.chem that return Element

Modifier and Type	Method and Description
Element	Atom.getElement()
Element	Isotope.getElement()
static Element	Element.valueOf(Integer inAtomicNum)
static Element	Element.valueOf(String inString)
static Element	Element.valueOf(String inString, Case inCaseSensetive)
static Element[]	Element.values()

Methods in com.hfg.chem that return types with arguments of type Element

Modifier and Type	Method and Description
Map<Element,Float>	Element.getElementalComposition()
Map<Element,Float>	Matter.getElementalComposition() Returns an unmodifiable copy of the elemental composition Map.
Map<Element,Float>	Molecule.getElementalComposition() Returns the elemental composition as an unmodifiable Map.
Collection<Element>	ElementalComposition.keySet()
Map<Element,Float>	ElementalComposition.toMap()

Methods in com.hfg.chem with parameters of type Element

Modifier and Type	Method and Description
ElementalComposition	ElementalComposition.addAtoms(Element inElement, float inNum)
Molecule	Molecule.addAtoms(Element inElement, float inNum)
ElementalComposition	ElementalComposition.addAtoms(Element inElement, int inNum)
Molecule	Molecule.addAtoms(Element inElement, int inNum)
int	Element.compareTo(Element element)
Float	ElementalComposition.get(Element inElement)
int[]	ValenceModel.getValences(Element inElement, int inCharge) Returns the values for the number of valence electrons for the element with the specified charge.
Float	ElementalComposition.put(Element inElement, float inCount)
Float	ElementalComposition.put(Element inElement, int inCount)
static Isotope	Isotope.valueOf(Element inElement, int inMassNum)
static Map<Integer,Isotope>	Isotope.valuesForElement(Element inElement)

Method parameters in com.hfg.chem with type arguments of type Element

Modifier and Type	Method and Description
ElementalComposition	ElementalComposition.add(Map<Element,Float> inMap)
ElementalComposition	ElementalComposition.add(Map<Element,Float> inMap, int inNum)
Molecule	Molecule.addElementalComposition(Map<Element,Float> inMap)
Molecule	Molecule.addElementalComposition(Map<Element,Float> inMap, int inNum)
ElementalComposition	ElementalComposition.remove(Map<Element,Float> inMap)
ElementalComposition	ElementalComposition.remove(Map<Element,Float> inMap, int inNum)
void	Molecule.setElementalComposition(Map<Element,Float> inMap)

Constructors in com.hfg.chem with parameters of type Element

Constructor and Description
Atom(Element inElement)

Constructor parameters in com.hfg.chem with type arguments of type Element

Constructor and Description
ElementalComposition(Map<Element,Float> inMap)
ElementalComposition(Map<Element,Float> inMap, int inNum)
Molecule(Map<Element,Float> inElementalComposition)
Molecule(String inName, Map<Element,Float> inElementalComposition)