git clone [email protected]:jach4/scaffold_network_generator.git sng
cd sng
python scaffolds_output.py --out_fmt=protobuf --np=50 --nq=100000 --file_input=data/datasets/input.smi --scaffolds_output=data/datasets/idx_sm.bin --file_output=data/datasets/idx_ls.bin
python scaffolds_output.py --out_fmt=postgres --np=80 --nq=100000 --file_input=data/datasets/input.smi --sql_dic=./data1.json --db_name=sc1from data import *
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
dic_scaffold = DicIdxLs()
with open('data/datasets/idx_ls.bin', 'rb') as f:
dic_scaffold.ParseFromString(f.read())
dic_idx_sm = DicIdxSm()
with open('data/datasets/idx_sm.bin', 'rb') as f:
dic_idx_sm.ParseFromString(f.read())
print(len(dic_scaffold.smiles_scaffold))402344
print(dic_idx_sm.sm_sc[1990])
Chem.MolFromSmiles(dic_idx_sm.sm_sc[1990])c1n[nH]nc1-c1nnc(-c2cnns2)o1
dic_scaffold.smiles_scaffold[1990]dic_mol_atoms {
idx_mol: 111921
ls_atom {
idx_atom: 1
idx_atom: 2
idx_atom: 3
idx_atom: 10
idx_atom: 11
idx_atom: 12
idx_atom: 13
idx_atom: 14
idx_atom: 15
idx_atom: 16
idx_atom: 17
idx_atom: 18
idx_atom: 19
idx_atom: 20
idx_atom: 22
}
ls_nh {
idx_atom: 3
}
ls_np {
}
}
Chem.MolFromSmiles(smiles_from_line(111921))
scaffold_list = get_mol_graph(smiles_from_line(111921)).ls_mol_from_sng_u()Draw.MolsToGridImage(scaffold_list)
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