How to Display Fingerprint Fragments using "babel" command? I want to know how many fragments are used when taking the fingerprint of a given molecule.

You can using ""-ofpt -xs" options of the "babel" command to Display Fingerprint Fragment information.

Here are some examples of molecule fingerprint fragments:

Fingerprint fragments of water molecule - The output shows no fragment. Because single atom fragments of C, N, and O are ignored as mentioned in the Open Babel FP2 finger print documentation.

fyicenter$ obabel -:O -o fpt -xs
==============================
*** Open Babel Error  in WriteMolecule
  Bit descriptions are not available for this fingerprint type
>
1 molecule converted

Fingerprint fragments of hydrogen fluoride molecule - The output shows 1 fragment of a single atom of F. The first digit of "0" of the fragment indicates fragment type of "linear". Other digits of the fragment forms an atom-bond path, where atom is represented using its atomic number. "F" has an atomic number of 9. The actual fingerprint is also listed to show how the fragment is mapped the fingerprint bit.

fyicenter$ obabel -:F -o fpt -xs
>
0 9 <9>

fyicenter$ obabel -:F -o fpt
>   1 bits set 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000200 

Fingerprint fragments of Ethane molecule - The output shows 1 fragment of "C-C" bond. The fragment path is "6 1 6", which is the same as SMILES of "C-C".

fyicenter$ obabel -:CC -o fpt -xs
>
0 6 1 6 <670>

fyicenter$ obabel -:CC -o fpt
>   1 bits set 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 40000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 

Fingerprint fragments of Propane molecule - The output shows 2 fragments. The first fragment path is "6 1 6", which is the same as SMILES of "C-C". The second fragment path is "6 1 6 1 6", which is the same as SMILES of "C-C-C". 2 fragments are mapped to 2 different fingerprint bits.

fyicenter$ obabel -:CCC -o fpt -xs 
>
0 6 1 6 <670>
0 6 1 6 1 6 <260>

fyicenter$ obabel -:CC -o fpt
>   2 bits set 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 40000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00000010 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 

Fingerprint fragments of a hydrocarbon chain of 9 carbons - The output shows 6 fragments. The longest path is "6 1 6 1 6 1 6 1 6 1 6 1 6", which is the same as SMILES of "C-C-C-C-C-C-C". 2 more paths of "C-C-C-C-C-C-C-C" and "C-C-C-C-C-C-C-C-C" are not used. Because only linear fragments of length from 1-7 atoms are analyzed as mentioned in the Open Babel FP2 finger print documentation. In other words, all hydrocarbon chain with more than 7 carbons will have the same FP2 fingerprints.

fyicenter$ obabel -:CCCCCCCCC -o fpt -xs
>
0 6 1 6 <670>
0 6 1 6 1 6 <260>
0 6 1 6 1 6 1 6 <384>
0 6 1 6 1 6 1 6 1 6 <984>
0 6 1 6 1 6 1 6 1 6 1 6 <429>
0 6 1 6 1 6 1 6 1 6 1 6 1 6 <49>

fyicenter$ obabel -:CCCCCCCCC -o fpt
>   6 bits set 
00000000 01000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 40000000 
00000000 00000000 00000000 00000000 00000000 00000000 
00002000 00000001 00000000 00000000 00000000 00000010 
00000000 00000000 00000000 00000000 00000000 00000000 
00020000 00000000 

⇒ "babel" - FP2 Exhaustive Fingerprint Fragments

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