Package chemaxon.descriptors
Class ECFPFeature
java.lang.Object
chemaxon.descriptors.ECFPFeature
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.
- Since:
- JChem 5.5
- See Also:
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Method Summary
Modifier and TypeMethodDescriptionint
Gets the generated bit position for this ECFP feature.Gets the center atom of the represented substructure.int
Gets the diameter of the represented substructure.int
Gets the generated integer identifier for this ECFP feature.Gets the corresponding substructure as aMolecule
object.
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Method Details
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getCenterAtom
Gets the center atom of the represented substructure.- Returns:
- the center atom
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getDiameter
public int getDiameter()Gets the diameter of the represented substructure.- Returns:
- the diameter
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getSubstructure
Gets the corresponding substructure as aMolecule
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.- Returns:
- the represented substructural feature as a molecule
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getIdentifier
public int getIdentifier()Gets the generated integer identifier for this ECFP feature. This is signed value, it can be either positive or negative.- Returns:
- the identifier
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getBitPosition
public int getBitPosition()Gets the generated bit position for this ECFP feature. It is a non-negative index between0
andlength - 1
, wherelength
denotes the length of the binary representation according to the current ECFP configuration.- Returns:
- the bit position
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