Proteome Informatics Group > Java Proteomic Library

Chemicals Properties


Any chemical monomer may have many physico-chemical properties.

In the package, specific property managers can get the desire property from the monomer.

For instance an amino-acid have pkas and hydropathy properties. JPLAAPKaManager gives you pka for any amino-acid or NH2/COOH ionizable part groups.


Ionizable entities undergo reactions of H+ dissociation equilibria reaction implying weak acid-base couples that is composed of a proton donor and its corresponding proton acceptor making up a conjugate acid-base. Equilibrium constants for ionization reactions are usually called ionization or dissociation constants, often designated Ka or pKa for -log10 Ka.


	// AH <-> A- + H+
	JPLIonizableEntityImpl acidTypeEntity =
	  JPLIonizableEntityImpl.newInstance(2.12, NeutralMoleculeType.ACID);
	// BH+ <-> B + H+
	JPLIonizableEntityImpl baseTypeEntity =
	  JPLIonizableEntityImpl.newInstance(8, NeutralMoleculeType.BASE);

Here is an example of a molecule with many ionizable groups:

	// In dilute aqueous solution, phosphate exists in four forms.
	// H3PO4 <-> H+ + H2PO4-     [pKa1=2.12]
	// H2PO4- <-> H+ + HPO4(2-)  [pka2=7.21]
	// HPO4(2-) <-> H+ + PO4(3-) [pka3=12.67]
	JPLIonizableGroup group =
	      new JPLIonizableGroup.Builder(2.12, NeutralMoleculeType.ACID)