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Calculating fingerprints of a list of SMILES

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Calculating fingerprints of a list of SMILES

Mehmet Aziz YIRIK

Dear all,

 

I am new with openbabel and need your help. I have a list of SMILES and for each compound, I need to calculate different fingerprint types provided by openbabel. I installed the package but there is no information for how to calculate fingerprints. I read the webpage of openbabel however it mentions about similarity search in a ligand set. I dont need the similarity search right now, just let me know how to calculate  4 types of fingerprints for my SMILES list.

 

Best,

Aziz

 

Windows 10 için Posta ile gönderildi

 


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Re: Calculating fingerprints of a list of SMILES

Andrew Dalke
On Apr 15, 2017, at 22:24, Mehmet Aziz YIRIK <[hidden email]> wrote:
> I need to calculate different fingerprint types provided by openbabel. ... how to calculate  4 types of fingerprints for my SMILES list.

You didn't say if you want to do that from the command-line or from a programming language like C++ or Python. I'll assume that you want to use the command-line, and that you want your output in FPS format.

Use "-ofps" to say you want the output in FPS format.

Use "-xf" to specify the fingerprint type, specifically, "-xfFP2" means to compute FP2 fingerprints (this is the default), "-xfFP3" computes FP3 fingerprints, "-xfFP4" computes FP4 fingerprints, and "-xfMACCS" computes the MACCS fingerprints:


I'll start with a set of structures:

% cat structures.smi
c1ccccc1 benzene
c1ccccc1O phenol
[NH4+] ammonium


I'll convert them to FP2 fingerprints in FPS format:

% obabel structures.smi -ofps -xfFP2
#FPS1
#num_bits=1021
#type=OpenBabel-FP2/1
#software=OpenBabel/2.4.1
#source=structures.smi
#date=2017-04-15T20:35:52
0000000000000000000002000000000000000000000000000000000000000000000000000000000000000008000000000000000000000000000000000000000000000000000000000000000000000000008000000000000040080000000000000000000000000000000000000000000000020000000000000000000000000000 benzene
0000000000000000000002000000000000000000000000000000000000000000000000000000000000000008000000000000020000000000000000000000000008000000000000000000000002000000008000000000000040080000000000000000000000000002000000000000000000020000000000200800000000000000 phenol
0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 ammonium
3 molecules converted


I'll convert them to FP3 fingerprints in FPS format:

% obabel structures.smi -ofps -xfFP3
#FPS1
#num_bits=55
#type=OpenBabel-FP3/1
#software=OpenBabel/2.4.1
#source=structures.smi
#date=2017-04-15T20:35:54
00000000001001 benzene
0000000402b001 phenol
0100000000e000 ammonium
3 molecules converted

I'll convert them to FP4 fingerprints in FPS format:

% obabel structures.smi -ofps -xfFP4
#FPS1
#num_bits=307
#type=OpenBabel-FP4/1
#software=OpenBabel/2.4.1
#source=structures.smi
#date=2017-04-15T20:35:56
000000000000000000000000000000000000000000000000000000000000000000000200000000 benzene
000000000000000000000000000000000000000000010000000000000000000000000200400000 phenol
000040000400000000000000000000000000000000000000000000000000000000000000800200 ammonium
3 molecules converted

I'll convert them to MACCS fingerprints in FPS format:

% obabel structures.smi -ofps -xfMACCS
#FPS1
#num_bits=166
#type=OpenBabel-MACCS/1
#software=OpenBabel/2.4.1
#source=structures.smi
#date=2017-04-15T20:43:42
000000000000000000000000000000000000000016 benzene
00000000000000000000000000000140004480101e phenol
000000000000010000000000000000000000400001 ammonium


                                Andrew
                                [hidden email]



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