Generate Fingerprint of Single Molecule

Q

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

✍: FYIcenter.com

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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"babel" - FP2 Exhaustive Fingerprint Fragments
How to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule? The easiest way to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule to following this algorithm: Loop through all atoms (except H) in the molecule. Set each atom as the root of a bond-atom tree. An... 2020-12-02, 759👍, 0💬

"babel -ofpt -xs" - Display Fingerprint Fragments
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 fingerprin... 2020-12-02, 735👍, 0💬

Generate Fingerprint of Single Molecule
How to generate the fingerprint of a single molecule? I want to see the fingerprint value. 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 hexadecima... 2020-12-02, 723👍, 0💬

Fingerprint Types Supported in Open Babel
What Fingerprint Types are Supported in Open Babel? You can get a list of fingerprint types supported in Open Babel by running the "babel -L fingerprints" command: fyicenter$ babel -L fingerprints FP2 Indexes linear fragments up to 7 atoms. FP3 SMARTS patterns specified in the file patterns.txt FP4 ... 2020-12-15, 697👍, 0💬

"babel -H fpt" - Fingerprint Help Information
How to get help information on Open Babel Fingerprints? You can use the "babel -H fpt" command to get help information on Open Babel Fingerprints: fyicenter$ babel -H fpt fpt Fingerprint format Generate or display molecular fingerprints. This format constructs and displays fingerprints and (for mult... 2020-11-22, 692👍, 0💬

Other Open Babel Commands
Where to find FAQ (Frequently Asked Questions) on Open Babel Commands other than the format converter? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Open Babel Commands other than the format converter. List of Open Babel Commands "obchiral" -... 2020-11-22, 673👍, 0💬

Substructure Search with Fingerprints
Can I do Substructure Search with fingerprints using Open Babel? Yes, you can do Substructure Search with fingerprints using Open Babel. All you have to do is to take substructure as the query molecule and run a similarity search using the fingerprint output option "-o fpt ". When Open Babel calcula... 2020-12-02, 626👍, 0💬

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