Uses of Class
com.hfg.chem.Molecule

Packages that use Molecule

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

Uses of Molecule in com.hfg.bio

Subclasses of Molecule in com.hfg.bio

Modifier and Type	Class and Description
class	AminoAcid Amino Acid.
class	CTerminalGroup C-terminal protein group.
class	DigestFragment Product of a proteolytic digest.
class	NTerminalGroup N-terminal protein group.
class	Nucleotide Nucleotide.

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

Modifier and Type	Method and Description
KaSet	KaSet.addpKa(Molecule inMolecule, IonizableGroup inIonizableGroup) Adds a pKa value for the specified molecule to the set.
List<IonizableGroup>	KaSet.getIonizableGroups(Molecule inResidue)

Uses of Molecule in com.hfg.bio.glyco

Subclasses of Molecule in com.hfg.bio.glyco

Modifier and Type	Class and Description
class	Glycan Common mammalian polysaccharide structures.
class	Monosaccharide Monosaccharide values.

Uses of Molecule in com.hfg.bio.seq

Subclasses of Molecule in com.hfg.bio.seq

Modifier and Type	Class and Description
class	BioSequenceImpl Biological Protein, DNA, or RNA sequence.
class	BioSequencePlusImpl Exetended biological protein, DNA, or RNA sequence with support for features, citations, db xrefs, etc.
class	NucleicAcid Biological DNA or RNA sequence.
class	Protein Biological protein sequence.
class	ProteinXLink Biological protein sequence crosslink.
class	ProteinXLinkType Biological protein sequence cross-link types.

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

Modifier and Type	Method and Description
protected Map<Molecule,Integer>	BioSequenceImpl.getResidueComposition()
protected Map<Molecule,Integer>	Protein.getResidueComposition()
protected Map<Molecule,Integer>	BioSequenceImpl.getTerminiComposition()
protected Map<Molecule,Integer>	Protein.getTerminiComposition()
protected Map<? extends Molecule,Integer>	BioSequenceImpl.getXLinkComposition()

Uses of Molecule in com.hfg.bio.seq.genomic

Subclasses of Molecule in com.hfg.bio.seq.genomic

Modifier and Type	Class and Description
class	Intron An intron in a gene.

Uses of Molecule in com.hfg.chem

Fields in com.hfg.chem declared as Molecule

Modifier and Type	Field and Description
static Molecule	Molecule.H2O
static Molecule	Molecule.NaCl
static Molecule	Molecule.NH3

Methods in com.hfg.chem that return Molecule

Modifier and Type	Method and Description
Molecule	Molecule.add(Matter inValue)
Molecule	Molecule.add(Matter inValue, int inCount)
Molecule	Molecule.addAtom(Atom inAtom)
Molecule	Molecule.addAtoms(Element inElement, float inNum)
Molecule	Molecule.addAtoms(Element inElement, int inNum)
Molecule	Molecule.addAtoms(List<Atom> inAtoms)
Molecule	Molecule.addElementalComposition(ElementalComposition inElementalComposition, int inNum)
Molecule	Molecule.addElementalComposition(Map<Element,Float> inMap)
Molecule	Molecule.addElementalComposition(Map<Element,Float> inMap, int inNum)
Molecule	Molecule.addKa(IonizableGroup inValue)
Molecule	Molecule.addKa(IonizableGroup inValue, int inCount)
Molecule	Molecule.clone() Returns an unlocked copy of the Molecule.
Molecule	Molecule.lock()
Molecule	Molecule.remove(Matter inValue)
Molecule	Molecule.remove(Matter inValue, int inCount)
Molecule	Molecule.setAverageMass(Double inValue) If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
Molecule	Molecule.setChemicalFormula(String inValue)
Molecule	Molecule.setMonoisotopicMass(Double inValue) If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
Molecule	Molecule.setName(String inValue)
Molecule	Molecule.setOrganicAverageMass(Double inValue) If the elemental composition is known, use setElementalComposition() and the masses will be derived automatically; this method is for use in those (hopefully) rare times when the mass is known but not the elemental composition.
Molecule	Molecule.setPhysicalProperty(PhysicalProperty inProperty, Double inValue)

Uses of Molecule in com.hfg.chem.format

Classes in com.hfg.chem.format with type parameters of type Molecule

Modifier and Type	Class and Description
class	BufferedMoleculeReader<T extends Molecule> Buffered molecule reader.
class	MDL_SDF<T extends Molecule> Basic implementation of the MDL SDF format.
interface	MoleculeFactory<T extends Molecule> Factory Interface for creating Molecule objects.
interface	ReadableChemFormat<T extends Molecule> Interface for readable chemistry formats.
class	ReadableChemFormatBase<T extends Molecule> Base class for readable chemistry formats.

Methods in com.hfg.chem.format that return Molecule

Modifier and Type	Method and Description
Molecule	MoleculeFactoryImpl.createMoleculeObj()
Molecule	SMILES_Parser.parse(String inValue)