MACCS Fingerprints in pybel

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

MACCS Fingerprints in pybel

david.lagorce
Hello all,

According to Noel O'Boyle useful "guiding lights", here is a special procedure to use MACCS fingerprint method in python pybel links.
Indeed, MACCS is only available in OpenBabel 2.2.3 command line method...

-------
import pybel
pybel.fps.append("MACCS")
pybel._fingerprinters = pybel._getplugins(pybel.ob.OBFingerprint.FindFingerprint, pybel.fps)
mol = pybel.readstring("smi", "CCCC(=O)Cl")
print mol.calcfp("MACCS").bits
# [103, 107, 114, 115, 132, 134, 147, 154, 155, 160, 164]
-------

Alternatively, Noel advice to use the pybel.py included in cinfony, which has this feature already.

regards,



Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: MACCS Fingerprints in pybel

Maritza
Hi all,

I used this code to get maccs fingerprints a month ago, and everything worked fine. However, I am trying again but I keep getting an error every time I try to get the fingerprints.
The list of available descriptors that I get with pybel.fps is: ['fp2', 'fp3', 'fp4', '\xc8\xe3\x81\x87\x7f']
I don't know what is this last term. If I try to get the fingerprint for the smile in your example: 'CCCC(=O)Cl' using the last descriptor  '\xc8\xe3\x81\x87\x7f',  I get this vector: [103, 107, 114, 115, 118, 132, 134, 147, 154, 155, 160, 164], which a bit different from you have have.
So, is this '\xc8\xe3\x81\x87\x7f' the same as maccs?.

The problem with using this last term, is that some time I get an error, it seems that it change the key every time I run it.
Has someone has the same issue? I will really appreciate any comment about this situation.
Thanks a lot!
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

browse around these guys

robertfcrocker
Love to read it,Waiting For More new Update and I Already Read your Recent Post its Great Thanks.
browse around these guys
Loading...