CircularFingerprinter (cdk 2.5 API)

java.lang.Object
- org.openscience.cdk.fingerprint.AbstractFingerprinter
- - org.openscience.cdk.fingerprint.CircularFingerprinter

All Implemented Interfaces:

IFingerprinter
```
public class CircularFingerprinter
extends AbstractFingerprinter
implements IFingerprinter
```
Circular fingerprints: for generating fingerprints that are functionally equivalent to ECFP-2/4/6 and FCFP-2/4/6 fingerprints, which are partially described by Rogers et al. (Rogers and Hahn. J. Chem. Inf. Mod.. 2010. 50).
While the literature describes the method in detail, it does not disclose either the hashing technique for converting lists of integers into 32-bit codes, nor does it describe the scheme used to classify the atom types for creating the FCFP-class of descriptors. For this reason, the fingerprints that are created are not binary compatible with the reference implementation. They do, however, achieve effectively equal performance for modelling purposes.

The resulting fingerprint bits are presented as a list of unique bits, each with a 32-bit hashcode; typically there are no more than a hundred or so unique bit hashcodes per molecule. These identifiers can be folded into a smaller array of bits, such that they can be represented as a single long binary number, which is often more convenient.

The integer hashing is done using the CRC32 algorithm, using the Java CRC32 class, which is the same formula/parameters as used by PNG files, and described in:
http://www.w3.org/TR/PNG/#D-CRCAppendix
Implicit vs. explicit hydrogens are handled, i.e. it doesn't matter whether the incoming molecule is hydrogen suppressed or not.

Implementation note: many of the algorithms involved in the generation of fingerprints (e.g. aromaticity, atom typing) have been coded up explicitly for use by this class, rather than making use of comparable functionality elsewhere in the CDK. This is to ensure that the CDK implementation of the algorithm is strictly equal to other implementations: dependencies on CDK functionality that could be modified or improved in the future would break binary compatibility with formerly identical implementations on other platforms.

For the FCFP class of fingerprints, atom typing is done using a scheme similar to that described by Green et al (Green1994 (not found in db)).

The fingerprints and their uses have been described in Clark et al. (Clark, A. et. al.. J. Cheminformatics. 2014. 6).
Important! this fingerprint can not be used for substructure screening.

Author:

am.clark

Source code:
master

Belongs to CDK module:
standard

Keywords:

fingerprint, similarity

Created on:

2014-01-01

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class CircularFingerprinter.FP

Nested Classes
Modifier and Type	Class and Description
`static class`	`CircularFingerprinter.FP`

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`CLASS_ECFP0`
`static int`	`CLASS_ECFP2`
`static int`	`CLASS_ECFP4`
`static int`	`CLASS_ECFP6`
`static int`	`CLASS_FCFP0`
`static int`	`CLASS_FCFP2`
`static int`	`CLASS_FCFP4`
`static int`	`CLASS_FCFP6`

Constructor Summary

Constructors
Constructor and Description
`CircularFingerprinter()` Default constructor: uses the ECFP6 type.
`CircularFingerprinter(int classType)` Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
`CircularFingerprinter(int classType, int len)` Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`calculate(IAtomContainer mol)` Calculates the fingerprints for the given `IAtomContainer`, and stores them for subsequent retrieval.
`IBitFingerprint`	`getBitFingerprint(IAtomContainer mol)` Calculates the circular fingerprint for the given `IAtomContainer`, and folds the result into a single bitset (see getSize()).
`ICountFingerprint`	`getCountFingerprint(IAtomContainer mol)` Calculates the circular fingerprint for the given `IAtomContainer`, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e.
`CircularFingerprinter.FP`	`getFP(int N)` Returns the requested fingerprint.
`int`	`getFPCount()` Returns the number of fingerprints generated.
`protected List<Map.Entry<String,String>>`	`getParameters()` Base classes should override this method to report the parameters they are configured with.
`Map<String,Integer>`	`getRawFingerprint(IAtomContainer mol)` Invalid: it is not appropriate to convert the integer hash codes into strings.
`int`	`getSize()` Returns the extent of the folded fingerprints.
`void`	`setPerceiveStereo(boolean val)` Sets whether stereochemistry should be re-perceived from 2D/3D coordinates.

Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter
getFingerprint, getVersionDescription

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter
getFingerprint, getVersionDescription

- Field Detail
  - CLASS_ECFP0
```
public static final int CLASS_ECFP0
```
    See Also:
    
    Constant Field Values
  - CLASS_ECFP2
```
public static final int CLASS_ECFP2
```
    See Also:
    
    Constant Field Values
  - CLASS_ECFP4
```
public static final int CLASS_ECFP4
```
    See Also:
    
    Constant Field Values
  - CLASS_ECFP6
```
public static final int CLASS_ECFP6
```
    See Also:
    
    Constant Field Values
  - CLASS_FCFP0
```
public static final int CLASS_FCFP0
```
    See Also:
    
    Constant Field Values
  - CLASS_FCFP2
```
public static final int CLASS_FCFP2
```
    See Also:
    
    Constant Field Values
  - CLASS_FCFP4
```
public static final int CLASS_FCFP4
```
    See Also:
    
    Constant Field Values
  - CLASS_FCFP6
```
public static final int CLASS_FCFP6
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - CircularFingerprinter
```
public CircularFingerprinter()
```
    Default constructor: uses the ECFP6 type.
  - CircularFingerprinter
```
public CircularFingerprinter(int classType)
```
    Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
    
    Parameters:
    
    classType - one of CLASS_ECFP{n} or CLASS_FCFP{n}
  - CircularFingerprinter
```
public CircularFingerprinter(int classType,
                             int len)
```
    Specific constructor: initializes with descriptor class type, one of ECFP_{p} or FCFP_{p}, where ECFP is for the extended-connectivity fingerprints, FCFP is for the functional class version, and {p} is the path diameter, and may be 0, 2, 4 or 6.
    
    Parameters:
    
    classType - one of CLASS_ECFP{n} or CLASS_FCFP{n}
    
    len - size of folded (binary) fingerprint
- Method Detail
  - setPerceiveStereo
```
public void setPerceiveStereo(boolean val)
```
    Sets whether stereochemistry should be re-perceived from 2D/3D coordinates. By default stereochemistry encoded as IStereoElements are used.
    
    Parameters:
    
    val - perceived from 2D
  - getParameters
```
protected List<Map.Entry<String,String>> getParameters()
```
    Description copied from class: AbstractFingerprinter
    
    Base classes should override this method to report the parameters they are configured with.
    
    Overrides:
    
    getParameters in class AbstractFingerprinter
    
    Returns:
    
    The key=value pairs of configured parameters
  - calculate
```
public void calculate(IAtomContainer mol)
               throws CDKException
```
    Calculates the fingerprints for the given IAtomContainer, and stores them for subsequent retrieval.
    
    Parameters:
    
    mol - chemical structure; all nodes should be known legitimate elements
    
    Throws:
    
    CDKException
  - getFPCount
```
public int getFPCount()
```
    Returns the number of fingerprints generated.
    
    Returns:
    
    total number of unique fingerprint hashes generated
  - getFP
```
public CircularFingerprinter.FP getFP(int N)
```
    Returns the requested fingerprint.
    
    Parameters:
    
    N - index of fingerprint (0-based)
    
    Returns:
    
    instance of a fingerprint hash
  - getBitFingerprint
```
public IBitFingerprint getBitFingerprint(IAtomContainer mol)
                                  throws CDKException
```
    Calculates the circular fingerprint for the given IAtomContainer, and folds the result into a single bitset (see getSize()).
    
    Specified by:
    
    getBitFingerprint in interface IFingerprinter
    
    Parameters:
    
    mol - IAtomContainer for which the fingerprint should be calculated.
    
    Returns:
    
    the fingerprint
    
    Throws:
    
    CDKException - may be thrown if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error
  - getCountFingerprint
```
public ICountFingerprint getCountFingerprint(IAtomContainer mol)
                                      throws CDKException
```
    Calculates the circular fingerprint for the given IAtomContainer, and returns a datastructure that enumerates all of the fingerprints, and their counts (i.e. does not fold them into a bitmask).
    
    Specified by:
    
    getCountFingerprint in interface IFingerprinter
    
    Parameters:
    
    mol - IAtomContainer for which the fingerprint should be calculated.
    
    Returns:
    
    the count fingerprint
    
    Throws:
    
    CDKException - if there is an error during aromaticity detection or (for key based fingerprints) if there is a SMARTS parsing error.
  - getRawFingerprint
```
public Map<String,Integer> getRawFingerprint(IAtomContainer mol)
                                      throws CDKException
```
    Invalid: it is not appropriate to convert the integer hash codes into strings.
    
    Specified by:
    
    getRawFingerprint in interface IFingerprinter
    
    Parameters:
    
    mol - IAtomContainer for which the fingerprint should be calculated.
    
    Returns:
    
    the raw fingerprint
    
    Throws:
    
    CDKException
  - getSize
```
public int getSize()
```
    Returns the extent of the folded fingerprints.
    
    Specified by:
    
    getSize in interface IFingerprinter
    
    Returns:
    
    the size of the fingerprint

Class CircularFingerprinter

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.fingerprint.AbstractFingerprinter

Methods inherited from class java.lang.Object

Methods inherited from interface org.openscience.cdk.fingerprint.IFingerprinter

Field Detail

CLASS_ECFP0

CLASS_ECFP2

CLASS_ECFP4

CLASS_ECFP6

CLASS_FCFP0

CLASS_FCFP2

CLASS_FCFP4

CLASS_FCFP6

Constructor Detail

CircularFingerprinter

CircularFingerprinter

CircularFingerprinter

Method Detail

setPerceiveStereo

getParameters

calculate

getFPCount

getFP

getBitFingerprint

getCountFingerprint

getRawFingerprint

getSize