event_db

[ShenggengLin]

event_db

[YifanDengWHU]

Hi, Shenggeng!
For the first problem, this is because the same drug-drug pair are recorded twice in the data. For example, (sildenafil, Isosorbide mononitrate) and (Isosorbide mononitrate, sildenafil) for another. But they are the same in fact. So we delete half of them.
For the second problem. Just try to learn the usage of RDKit package. For example, for the drug Isosorbide mononitrate. We can collect its SMILES [H][C@]12OCC@@H[C@@]1([H])OC[C@@h]2O from DrugBank.
So here is the code:

from rdKit import Chem
from rdkit.Chem import AllChem
smile = '[H][C@]12OC[C@@H](O[N+]([O-])=O)[C@@]1([H])OC[C@@H]2O'
mol = Chem.MolFromSmiles(smile)
morgan_hashed = AllChem.GetMorganFingerprintAsBitVect(mol,2,nBits=881)
morgan_hashed.ToBitString()

It will be a bit vector of 881 length.

[ShenggengLin]

Hello, Yifan!

Thank you very much for your reply. I have understand the first question. Thank you very much!

But I still have questions about the second question.

For drug DB01296, his smiles is' N[C@H]1C(O)OC@HC@@H[C@@h]1O '. Through the code you provided, I did get a 881 dimensional vector. But in the event.db , its smiles features are 9|10|14|18|19|20|178|181|283|284|285|286|299|308|332|338|339|340|341|344|345|346|347|351|352|365|366|367|380|393|405|406|528|563|566|567|571|582|592|614|615|617|637|638|639|643|661|662|663|679|680|681|682|683|689|690|691|701|703.
I wonder what these numbers mean?Does it mean that these positions are 1 in the 881 dimensional vector？ But if this is the case, for the drug db01296, its ninth digit is 0, but there are 9 in these numbers. And its 16th digit is 1, but there is no 16 in these numbers.

[YifanDengWHU]

Yes, you are right.
The reason is because the fingerprint methods are different. For the fingerprint in the current dataset, it is obtained by a former student. He used the RDkit in JAVA.
The code in my code used MorganFingerprint. It is the most common method. I have test the result. There is little difference between the current dataset's fingerprint and MorganFingerprint.

[ShenggengLin]

OK, I see. Thank you for your reply!Thank you very much!