Generate Fingerprint of Single Molecule

Q

How to generate the fingerprint of a single molecule? I want to see the fingerprint value.

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A

If you want see the fingerprint value of a single molecule, you can just specify the molecule as the only input molecule to the "babel ... -o fpt " command. Open Babel will output its fingerprint in hexadecimal format.

Here are some molecule fingerprint examples displayed in hexadecimal format.

Fingerprint of water molecule - The output shows 0 bits in the fingerprint. Because single atom fragments of C, N, and O are ignored as mentioned in the Open Babel FP2 finger print documentation. In other words, atoms of C, N and O are not important in similarity search.

fyicenter$ obabel -:O -o fpt
>   0 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 00000000 

Fingerprint of hydrogen fluoride molecule - The output shows 1 bit in the fingerprint near the end.

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 of benzene ring - The output shows 6 bits in the fingerprint near the end.

fyicenter$ obabel -:c1ccccc1 -o fpt 
>   6 bits set 
00000000 00000000 00000000 00000200 00000000 00000000 
00000000 00000000 00000000 00000840 00000000 00008000 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 08000000 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00020000 
00000000 00000000 

Fingerprint of tyrosine molecule - The output shows 48 bits in the fingerprint near the end.

fyicenter$ babel tyrosine.sdf -o fpt 
>   48 bits set 
00000000 00000008 20000100 00010600 00000000 00000000 
02000000 00000000 00000800 00080840 08100000 4000b000 
04008002 00000000 00000000 00080008 00000000 02000000 
00400008 00020001 00000100 18000a00 03000040 81400010 
00000800 80000000 00120000 00000000 04000000 00060002 
00000000 00000400 

By the way, the default fingerprint type "FP2" has 1024 bits printed out in 256 hexadecimal digits as shown above.

 

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2020-05-25, 157👍, 0💬