You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi guys,
I've been using bingo-elastic(python) to get some similarities to certain compounds, but got confused. Here is the situation:
I was trying to get some similarities using the following code:
compoud = indigo.loadMoleculeFromFile("CH1.mol")
sim = TanimotoSimilarityMatch(compoud, 0.5)
similar_records = repository.filter(query_subject=[sim])
for record in similar_records:
print(record.as_indigo_object(indigo).smiles(), indigo.similarity(compoud, record.as_indigo_object(indigo)))
What I meant was trying to get the top similarities and the corresponding similarity values, but I got the following outputs:
C:...\python.exe D:...\test.py
CC(=O)C12OC1CC1C3CC=C4CC(O)CCC4(C)C3CCC21C 0.5970149040222168
O=C1CCCCCCCCCOCCCCCO1 0.38333332538604736
CCCC/C=C\O/C=C/C=C\CCCCCCCC(=O)[O-] 0.3636363744735718
COc1ccc(OC)c(/C=C2\Oc3c(C)c4c(cc3C\2=O)CNH+CO4)c1 0.25641027092933655
O=C1N=C([O-])NC(=O)C1(Cc1ccc2c(OCO2)c1)CN1CC2C[n]3c(=O)cccc3C(C2)C1 0.16249999403953552
COc1ccc(C(=O)COc2ccc3c(O/C(=C\c4cc(Br)ccc4OC)/C3=O)c2C)cc1 0.22727273404598236
COc1cc(/C=C2/Oc3c(CN4CCN(c5cccc[nH+]5)CC4)c([O-])cc(C)c3C/2=O)cc(OC)c1OC 0.21167883276939392
COc1ccc(/C=C2\C(=O)N=C([O-])NC\2=O)cc1OC 0.1818181872367859
CCOC(=O)c1c(C)oc2cc(Br)c(OC(=O)c3ccccc3Cl)cc12 0.15267175436019897
Cc1c(OCC#N)ccc2c1O/C(=C\c1cccc(Br)c1)/C2=O 0.2232142835855484
As far as I understood, I had set the min threhold of the similarity(which=0.5 in this case), but I got so many compounds with similarties less than the threhold, what happened? Did I do something wrong?
How could I get the similar compounds and order them in similarities at the first place? (i.e. Could I use some parameters in TanimotoSimilarityMatch or some other functions to make them in similarity order(desc or asc) at the first place?
Best,
The text was updated successfully, but these errors were encountered:
Hi guys,
I've been using bingo-elastic(python) to get some similarities to certain compounds, but got confused. Here is the situation:
I was trying to get some similarities using the following code:
compoud = indigo.loadMoleculeFromFile("CH1.mol")
sim = TanimotoSimilarityMatch(compoud, 0.5)
similar_records = repository.filter(query_subject=[sim])
for record in similar_records:
print(record.as_indigo_object(indigo).smiles(), indigo.similarity(compoud, record.as_indigo_object(indigo)))
What I meant was trying to get the top similarities and the corresponding similarity values, but I got the following outputs:
C:...\python.exe D:...\test.py
CC(=O)C12OC1CC1C3CC=C4CC(O)CCC4(C)C3CCC21C 0.5970149040222168
O=C1CCCCCCCCCOCCCCCO1 0.38333332538604736
CCCC/C=C\O/C=C/C=C\CCCCCCCC(=O)[O-] 0.3636363744735718
COc1ccc(OC)c(/C=C2\Oc3c(C)c4c(cc3C\2=O)CNH+CO4)c1 0.25641027092933655
O=C1N=C([O-])NC(=O)C1(Cc1ccc2c(OCO2)c1)CN1CC2C[n]3c(=O)cccc3C(C2)C1 0.16249999403953552
COc1ccc(C(=O)COc2ccc3c(O/C(=C\c4cc(Br)ccc4OC)/C3=O)c2C)cc1 0.22727273404598236
COc1cc(/C=C2/Oc3c(CN4CCN(c5cccc[nH+]5)CC4)c([O-])cc(C)c3C/2=O)cc(OC)c1OC 0.21167883276939392
COc1ccc(/C=C2\C(=O)N=C([O-])NC\2=O)cc1OC 0.1818181872367859
CCOC(=O)c1c(C)oc2cc(Br)c(OC(=O)c3ccccc3Cl)cc12 0.15267175436019897
Cc1c(OCC#N)ccc2c1O/C(=C\c1cccc(Br)c1)/C2=O 0.2232142835855484
Best,
The text was updated successfully, but these errors were encountered: