divnori/protac-design

UROP Project @ Coley Group

protac-design's Issues

GraphInvent -finetune issue

Hi,
Its a outstanding work regarding protac. I just went through this code, i faced some difficulty when execulting GraphInvent.

So during finetune part. I have to specify these(mention below which is in comment) in constants.py file.
"""
scoring_model_activity = pickle.load(open('/home/gridsan/dnori/GraphINVENT/data/protac_scoring_models/Protac_Scoring_Model_1024_100nM.pkl', 'rb'))
scoring_model_structure = pickle.load(open('/home/gridsan/dnori/GraphINVENT/data/protac_scoring_models/Protac_Scoring_Model_Structure.pkl', 'rb'))
with open('/home/gridsan/dnori/GraphINVENT/data/protac_scoring_models/features_1024_100nM.pkl','rb') as fp:
features_activity = pickle.load(fp)
with open('/home/gridsan/dnori/GraphINVENT/data/protac_scoring_models/features_structure.pkl','rb') as fp:
"""

Question 1. How can i get these files or can i use fetaure.pkl and surrogate.pkl files here ? if yes then for which pkl to use
Question 2. How can i get protac _activity result that i s mention in scoring_funtion.py file?
Question 3. after running finetune , in return i am getting files like agent.smi , BASF.smi , .valid and .likelihood , So what are those ?