Re: [Open Babel] 2D fingerprints

[Fabien F. <ffo...@im...>]

There is na small documentation in the file fingerprint.cpp.
Here is the doc pasted:

/** \class fingerprint
\brief 2D Fingerprint class

To compute the fingerprint fpt for a molecule mol
\code
   fingerprint fpt(mol.GetTitle());
   fpt.HashMol(mol);
\endcode

The fingerprint computation requires the execution of the following steps:
- Obtain the fragments
- Remove duplicate fragments and get a hash number for each fragment
- Obtain the fingerprint of the fragments

The fragments are obtained by means of a recursive algorithm. The 
algorithm finds all linear fragments up to a size of seven atoms. Cyclic 
fragments are also identified by checking if there are ring closures in 
the linear fragment. However, the algorithm does not identify branched 
fragments if there are not part of a ring.
for example CC(C)C will have the fragments:
C
CC
CCC
and C1C(C)C1 will have the fragments:
C
CC
CCC
C1CC1
CC1CC1

Duplicate fragments, i.e. fragment generated by the same atoms, are 
removed from the fragment list. The only fragment that are kept are the 
ones which produce the lowest hash numbers.
The hash number for a fragment is an integer number which is generated 
from the atoms and bonds of the fragment. The value of this number 
depends on the position, the atomic number and type (aromatic or not) of 
the atoms of the fragment, the position and the type of the bonds of the 
fragments, the position and the type of the ring closures.

The fingerprint is a bitstring of 1021 bits. It is evident that there 
are many more possible fragments than 1021, and consequently the hash 
number is often higher than 1021. It is easy to obtain a number lower 
than 1021 from the hash number, just by dividing the hash number by 1021 
and by keeping the reminder. this reminder is then used to set a bit to 
one in the fingerprint.
Actually, the size of the bitstring is of 1024 bits but we divide by 
1021 because 1021 is a prime number which produces a better hashing than 
an even number such as 1024. Consequently, the three last bits of the 
fingerprint are always set to zero.

To print the fingerprint in ascii format use the function printFingerprint.

*/

Peter Murray-Rust wrote:
> At 12:18 04/10/2004 +0200, Fabien Fontaine wrote:
> 
>> Hi,
>>
>> I have implemented a new type of output for openbabel. It is -ofpt which
>> stands for 2D fingerprint. For each molecule The output are two ASCII
>> lines. The first line contains the molecule name, e.g.:
>>  >molname1
>> The second line contains the fingerprint, e.g.:
>> 000010001000....00000
>> The size of the fingerprint is 1024 bits, each bit set to one correspond
>>   to the presence of a 2D fragment. The fragments are linear or with
>> ring closures but not branched. The maximum fragment size is 7 atoms.
>>
>> I have also added a little tool called obtanimoto which computes the
>> tanimoto coefficient between a query molecule and a database of 
>> fingerprint.
>>
>> I haven't applied these fingerprint yet so any testing and comparison
>> with already existing fingerprint is welcomed.
> 
> 
> This looks like being very useful for some of the things we want to do. 
> Is there documentation as to how the fingerprints are generated? Are the 
> 1024 fragments handcoded? or are there more and are they folded into a 
> fixed length?
> 
> P.
> 
> 
> Peter Murray-Rust
> Unilever Centre for Molecular Informatics
> Chemistry Department, Cambridge University
> Lensfield Road, CAMBRIDGE, CB2 1EW, UK
> Tel: +44-1223-763069
> 
> 
> 
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-- 
Fabien Fontaine
Engineer in Biotechnology
Computer-Assisted Drug Design Laboratory
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF

Passeig Maritim de la Barceloneta, 37-49	Tel: +34 93 224 08 94
E-08003 Barcelona (Spain)		       	Fax: +34 93 224 08 75
e-mail: ffo...@im...			http://www.imim.es/grib