| Name | Description | Type | Package | Framework |
| ADP | A class representing an Adenosine Di Phosphate molecule. | Class | org.jscience.biology.molecules | JScience |
| AMP | A class representing an Adenosine Mono Phosphate molecule. | Class | org.jscience.biology.molecules | JScience |
| ATP | A class representing an Adenosine Tri Phosphate molecule. | Class | org.jscience.biology.molecules | JScience |
| Cholesterol | A class representing the Cholesterol lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| Citronellol | A class representing the Citronellol lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| CO2 | A class representing the carbon dioxide (CO2). | Class | org.jscience.biology.molecules | JScience |
| Deoxyribose | A class representing the Deoxyribose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| Fructose | A class representing the Fructose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| Galactose | A class representing the Galactose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| Glucose | A class representing the Glucose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| H2O | A class representing the water molecule (H2O). | Class | org.jscience.biology.molecules | JScience |
| Hemoglobin | A class representing the human Hemoglobin molecule. | Class | org.jscience.biology.molecules.proteins | JScience |
| Insulin | A class representing the human Insulin (precursor) molecule. | Class | org.jscience.biology.molecules.proteins | JScience |
| Lactose | A class representing the Lactose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| NAD | A class representing an nicotinamide adenine dinucleotide (NAD+)See Also:Serialized Form | Class | org.jscience.biology.molecules | JScience |
| O2 | A class representing the dioxygen (O2). | Class | org.jscience.biology.molecules | JScience |
| PhosphatidylCholine | A class representing the PhosphatidylCholine lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |
| Ribose | A class representing the Ribose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| Sucrose | A class representing the Sucrose carbohydrate molecule. | Class | org.jscience.biology.molecules.carbohydrates | JScience |
| Triacylglycerol | A class representing the Triacylglycerol lipid molecule. | Class | org.jscience.biology.molecules.lipids | JScience |