drugbank to smile not producing any output

syhuangsanofi / clinical-trial-outcome-prediction

benchmark dataset and Deep learning method (Hierarchical Interaction Network, HINT) for clinical trial approval probability prediction, published in Cell Patterns 2022.

https://www.sciencedirect.com/science/article/pii/S2666389922000186

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drugbank to smile not producing any output #2

Open syhuangsanofi opened 3 months ago

syhuangsanofi commented 3 months ago

py3.7

In drug2smile.py , drug2smiles_func function doesn't produce any output The code doesn't produce any output:

drug2smiles = defaultdict(set)
drug2smiles2 = dict()
for row in reader:
smiles = row[27]
if smiles.strip()=='':
    continue 
drug1 = row[3].lower()
drug2 = row[11].lower()
drug2smiles[drug1].add(smiles)
drug2smiles[drug2].add(smiles)

syhuangsanofi commented 3 months ago

drugbank_drugs_info.csv db doesn't contain SMILE info. to be solved. to do:

go into the .xml file
check if the smile info is available.
if yes, extract the smile info wrt to the data frame setup in the drug2smile.py