On Apr 15, 2017, at 22:24, Mehmet Aziz YIRIK <mehmetazizyi...@outlook.com>
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
da...@dalkescientific.com
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