| Name | Description | Type | Package | Framework |
| PharmacophoreAngleBond | Represents an angle relationship between three pharmacophore groups. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreAtom | A representation of a pharmacophore group. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreBond | Represents a distance relationship between two pharmacophore groups. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreMatcher | Identifies atoms whose 3D arrangement matches a specified pharmacophore query. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQuery | Represents a colleciton of pharmacophore groups and constraints. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQueryAngleBond | Represents a pharmacophore query angle constraint. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQueryAtom | Represents a query pharmacophore group. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreQueryBond | Represents a pharmacophore query distance constraint. | Class | org.openscience.cdk.pharmacophore | CDK |
| PharmacophoreUtils | Provides some utility methods for pharmacophore handling. | Class | org.openscience.cdk.pharmacophore | CDK |