chemaxon.descriptors

Class ECFPFeature

java.lang.Object

chemaxon.descriptors.ECFPFeature

@PublicAPI
public class ECFPFeature
extends java.lang.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.

Since:

JChem 5.5

Author:

Peter Kovacs (pkovacs84)

See Also:

ECFPFeatureLookup

Method Summary

Modifier and Type	Method and Description
int	getBitPosition() Gets the generated bit position for this ECFP feature.
MolAtom	getCenterAtom() Gets the center atom of the represented substructure.
int	getDiameter() Gets the diameter of the represented substructure.
int	getIdentifier() Gets the generated integer identifier for this ECFP feature.
Molecule	getSubstructure() Gets the corresponding substructure as a Molecule object.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getCenterAtom

public MolAtom getCenterAtom()

Gets the center atom of the represented substructure.

Returns:

the center atom

getDiameter

public int getDiameter()

Gets the diameter of the represented substructure.

Returns:

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.

Returns:

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.

Returns:

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.

Returns:

the bit position