Chemistry (Package) - singa-bio/singa GitHub Wiki

The chemistry package is roughly divided into an descriptive and physical approach to represent chemical entities. The physical section contains classes and methods concerned with the three dimensional representation of small and macro molecules. Descriptive on the other hand provides classes to handle and process information arising from chemical entities.

The elements package provides all elements with some often used attributes. It is also possible to quickly create isotopes and ions from elements.

Quantity<MolarMass> atomicMass = ElementProvider.RUBIDIUM.getAtomicMass();

Apart from the atomic mass, features such as number of protons and electrons can be fetched.

ElementProvider.OXYGEN.asIon(-2);

Ions and isotopes can be created.

ElementProvider.getElementBySymbol("C");

Elements can also dynamically be fetched.

Different parsers are implemented for a variety of use cases. Chemical entities can be parsed from the ChEBI Database and imported from PubChem XML Files. Macro molecular structures can be parsed using the Structure Parser StructureParser.