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"babel" - FP2 Exhaustive Fingerprint Fragments
How to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule?
✍: FYIcenter.com
The easiest way to exhaust all possible Open Babel FP2 Fingerprint Fragments in a molecule
to following this algorithm:
Here are some examples of molecule fingerprint fragments:
Fingerprint fragments of "CCCCCCCCCCN" - The output shows 12 fragments. Note that chemically identical fragments are considered as one fragment. For example, "N-C" and "C-N" are chemically identical, so only "N-C", represented as "7 1 6" is record.
fyicenter$ obabel -:CCCCCCCCCCN -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> 0 7 1 6 <82> 0 7 1 6 1 6 <906> 0 7 1 6 1 6 1 6 <348> 0 7 1 6 1 6 1 6 1 6 <711> 0 7 1 6 1 6 1 6 1 6 1 6 <656> 0 7 1 6 1 6 1 6 1 6 1 6 1 6 <324>
Fingerprint fragments of "CCCCCNCCCCC" - The output shows 18 fragments. It has more fragments, after moving N to the middle of the chain.
fyicenter$ obabel -:CCCCCNCCCCC -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 7 1 6 1 6 1 6 <13> 0 6 1 6 1 7 1 6 1 6 <609> 0 6 1 6 1 7 1 6 1 6 1 6 <393> 0 6 1 6 1 7 1 6 1 6 1 6 1 6 <797> 0 6 1 7 1 6 <693> 0 6 1 7 1 6 1 6 <9> 0 6 1 7 1 6 1 6 1 6 <948> 0 6 1 7 1 6 1 6 1 6 1 6 <156> 0 6 1 7 1 6 1 6 1 6 1 6 1 6 <276> 0 7 1 6 <82> 0 7 1 6 1 6 <906> 0 7 1 6 1 6 1 6 <348> 0 7 1 6 1 6 1 6 1 6 <711> 0 7 1 6 1 6 1 6 1 6 1 6 <656>
Fingerprint fragments of "C1CCCCC1" - The output shows 6 fragments. The first digit of "1" of the last fragment indicates fragment type of "ring".
fyicenter$ obabel -:C1CCCCC1 -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> 1 6 1 6 1 6 1 6 1 6 1 6 <441>
Fingerprint fragments of "C1CCNCC1" - The output shows 16 fragments. It has more fragments, after replace a C with a N on the ring.
fyicenter$ obabel -:C1CCNCC1 -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 7 1 6 1 6 <609> 0 6 1 6 1 7 1 6 1 6 1 6 <393> 0 6 1 7 1 6 <693> 0 6 1 7 1 6 1 6 <9> 0 6 1 7 1 6 1 6 1 6 <948> 0 6 1 7 1 6 1 6 1 6 1 6 <156> 0 7 1 6 <82> 0 7 1 6 1 6 <906> 0 7 1 6 1 6 1 6 <348> 0 7 1 6 1 6 1 6 1 6 <711> 0 7 1 6 1 6 1 6 1 6 1 6 <656> 1 7 1 6 1 6 1 6 1 6 1 6 <668>
Fingerprint fragments of "c1ccccc1" - The output shows 16 fragments. The first digit of "1" of the last fragment indicates fragment type of "aromatic ring".
fyicenter$ obabel -:c1ccccc1 -o fpt -xs > 0 6 5 6 <81> 0 6 5 6 5 6 <905> 0 6 5 6 5 6 5 6 <347> 0 6 5 6 5 6 5 6 5 6 <710> 0 6 5 6 5 6 5 6 5 6 5 6 <655> 5 6 5 6 5 6 5 6 5 6 5 6 <715>
Fingerprint fragments of "C/1=C/C/C=C\C1" - The output shows a new type of ring "2".
fyicenter$ obabel "-:C/1=C/C/C=C\C1" -o fpt -xs > 0 6 1 6 <670> 0 6 1 6 1 6 <260> 0 6 1 6 1 6 1 6 1 6 1 6 <429> 0 6 1 6 1 6 2 6 1 6 1 6 <769> 0 6 1 6 2 6 1 6 <182> 0 6 1 6 2 6 1 6 1 6 <303> 0 6 1 6 2 6 1 6 1 6 1 6 <625> 0 6 1 6 2 6 2 6 1 6 1 6 <965> 0 6 2 6 <778> 0 6 2 6 1 6 <58> 0 6 2 6 1 6 1 6 <724> 0 6 2 6 1 6 1 6 1 6 1 6 <554> 0 6 2 6 1 6 1 6 2 6 <267> 0 6 2 6 1 6 1 6 2 6 1 6 <352> 0 6 2 6 1 6 2 6 1 6 1 6 <894> 0 6 2 6 1 6 2 6 2 6 1 6 <692> 0 6 2 6 2 6 1 6 1 6 2 6 <858> 0 6 2 6 2 6 1 6 2 6 1 6 <548> 2 6 1 6 1 6 1 6 1 6 1 6 <453> 2 6 1 6 1 6 2 6 1 6 1 6 <793> 2 6 2 6 1 6 2 6 1 6 1 6 <918>
⇒ "babel" - FP2 Fingerprint Fragment Ends at Ring
⇐ "babel -ofpt -xs" - Display Fingerprint Fragments
2020-12-02, 488👍, 0💬
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Molecule Summary: ID: FYI-1000155 SMILES: CC Received at FYIcenter.com on: 2020-06-17