On 14/03/2020 23:24, Chris Swain via OpenBabel-discuss wrote:
One of the tools is to calculate spectrophores
Described in details here.
https://open-babel.readthedocs.io/en/latest/Fingerprints/spectrophore.html
I’ve tried this and this gives the following output
ID_000002 1.49538 2.12033 1.7562 3.27156 4.92821 3.76685 3.61875
3.729173.76939 6.28893 6.30063 3.72489 2.83871 2.85013 10.5265 10.5304
15.5199 13.969411.3836 20.0744 16.3271 16.501 20.8502 15.5603 28.4983
31.3098 29.2032 24.146220.224 20.7701 6.87111 23.1492 21.7416 26.0935
9.92935 25.4605 0.9371 0.873542.92003 2.92001 0.822645 0.846267
0.396603 3.15673 1.981910.922839 0.768973 3.02225
ID_000003 6.84965 6.85544 6.72281 6.48777 12.8201 7.05141 6.9188
10.509210.2884 13.2464 13.4809 10.6597 10.729 8.80592 12.2808 12.2669
19.0122 10.959 10.9159 18.9153 18.8156 17.8466 19.1632 15.8986 77.1334
88.843 73.3087 63.837371.6235 62.2845 31.3721 64.6271 66.3996 70.8296
43.6268 77.404 1.96881 1.815534.38761 4.86641 2.14023 2.06807 1.30172
4.25882 4.07622 2.78876 2.91516 4.7208
ID_000004 2.09153 2.57848 3.0399 5.28119 7.0974 6.31162 4.99044
5.058176.08685 7.89896 9.2356 6.84507 1.6726 3.06771 11.507 11.5015
4.95658 5.794594.36526 14.4005 10.6234 6.90563 6.90318 11.5636 45.1809
70.8286 70.3362 87.037378.0632 85.3583 54.6045 87.5461 82.7769 101.74
94.1001 97.7448 1.58159 1.825885.28398 5.281 2.00404 2.0139 1.04747
5.43697 4.41786 2.00631 1.78719 4.85954
How does one use/search using these fingerprints?
Maybe you can ask the authors to be sure:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083603/pdf/1758-2946-3-S1-P7.pdf
As a first guess, maybe treat them as a vector of floats and use
Tanimoto.
Tani(X,Y) = sum(min(x_i, y_i)) / sum(max(x_i, y_i))
Cheers
Chris
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