Class ECFPFeature

  • @PublicAPI
    public class ECFPFeature
    extends Object
    Class for representing the substructural features of ECFP fingerprints. An ECFP feature captures a circular atom neighborhood in the input molecule by recording a central atom and a diameter.
    JChem 5.5
    See Also:
    • Method Detail

      • getCenterAtom

        public MolAtom getCenterAtom()
        Gets the center atom of the represented substructure.
        the center atom
      • getDiameter

        public int getDiameter()
        Gets the diameter of the represented substructure.
        the diameter
      • getSubstructure

        public Molecule getSubstructure()
        Gets the corresponding substructure as a Molecule object. The returned structure contains a copy of the represented circular atom neighborhood from the original input molecule. The designated center atom and its neighboring atoms and bonds are stored up to the given diameter. The "borders" of the substructure are represented by ANY atoms and ANY bonds.

        Note that the ECFP generation method does not recognize rings in the molecule. However, this function is intended to give back a real substructure of the input molecule, so it handles rings as they appear in the molecule. It means that the returned substructure can contain more structural information than actually captured by the ECFP feature.

        For example, let us consider a carbon atom of a cyclohexane. The corresponding substructural features with diameter 0, 2, 4, 6 are represented as follows (in SMARTS format): *~[#6]~*; *~[#6]C[#6]~*; *~1~[#6]CCC[#6]~1; C1CCCCC1, respectively.

        This function builds a new Molecule object each time it is called. You should store its result instead of multiple calls.

        the represented substructural feature as a molecule
      • getIdentifier

        public int getIdentifier()
        Gets the generated integer identifier for this ECFP feature. This is signed value, it can be either positive or negative.
        the identifier
      • getBitPosition

        public int getBitPosition()
        Gets the generated bit position for this ECFP feature. It is a non-negative index between 0 and length - 1, where length denotes the length of the binary representation according to the current ECFP configuration.
        the bit position