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蓝鱼在嘴里
Hello,
I want to understand the fingerprint type of FP2 in Openbabel,where can I find the information?For example,"0616<670>",I know which fragment it represents,but for "0 6 5 6 5 6 1 6 <936>",I do not know.So where can I find the instruction.
If there is someone know,please tell me.Thanks!

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Re: help

Craig James-2


On Thu, Jul 5, 2012 at 3:06 AM, 蓝鱼在嘴里 <[hidden email]> wrote:
Hello,
I want to understand the fingerprint type of FP2 in Openbabel,where can I find the information?For example,"0616<670>",I know which fragment it represents,but for "0 6 5 6 5 6 1 6 <936>",I do not know.So where can I find the instruction.
If there is someone know,please tell me.Thanks!

The bits in a fingerprint don't represent anything specifically.  Certain features in a molecule will cause a particular bit to be set (you can go from features to bits), but you can't go the reverse direction (bits to features).  Any particular bit can theoretically represent thousands of different features.

For a general introduction to fingerprints, see the Daylight Theory Manual:

   http://www.daylight.com/dayhtml/doc/theory/theory.finger.html

Another resource is "Cheminformatics 101: Similarity" from eMolecules:

  http://www.emolecules.com/doc/cheminformatics-101-molecular-similarity.php

FP2 is a slight varient of the general principles discussed in the Daylight Manual:

   http://openbabel.org/wiki/FP2

Craig



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Re: help

Chris Morley-3
On 06/07/2012 16:18, Craig James wrote:

>
>
> On Thu, Jul 5, 2012 at 3:06 AM, 蓝鱼在嘴里 <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hello,
>     I want to understand the fingerprint type of FP2 in Openbabel,where
>     can I find the information?For example,"0616<670>",I know which
>     fragment it represents,but for "0 6 5 6 5 6 1 6 <936>",I do not
>     know.So where can I find the instruction.
>     If there is someone know,please tell me.Thanks!
>
>
> The bits in a fingerprint don't represent anything specifically.
> Certain features in a molecule will cause a particular bit to be set
> (you can go from features to bits), but you can't go the reverse
> direction (bits to features).  Any particular bit can theoretically
> represent thousands of different features.

This hasn't stopped other people asking for more information on what the
bits in FP2 mean. A blog post on what is available is at
http://baoilleach.blogspot.co.uk/2012/01/visualising-fragments-in-path-based.html

The <670> is the bit number and the remaining digits describe the
fragment (possibly one of many) that maps to this bit number. The first
digit is the bond order of the closure bond that makes a ring, and is 0
for linear fragments. The remaining digits indicate the atomic number
and bond order alternatively for the atoms that make up the rest of the
fragment. A bond order of 5 is used for aromatic bonds. <936> above
would be a linear fragment with a SMILES representation of [c][c][c][C]
(Hydrogen is ignored.)

Chris

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