Scaffold network generator

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Scaffold Network Generator

Repo

Github

Usage

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git clone [email protected]:jach4/scaffold_network_generator.git sng
cd sng
python scaffolds_output.py --np=50 --file_input=data/datasets/input.smi --scaffolds_output=data/datasets/scaffolds.smi --file_output=data/datasets/scaffolds.bin

Read the entire scaffold message from a file

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from data import *
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole

dic = DicSmScaffoldLs()
with open('data/datasets/scaffolds.bin','rb') as f:
    dic.ParseFromString(f.read())
    
print(len(dic.smiles_scaffold))
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402344

Get the 1990th scaffold

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print(scaffold_smiles_idx(1990))
Chem.MolFromSmiles(scaffold_smiles_idx(1990))
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c1n[nH]nc1-c1nnc(-c2cnns2)o1
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dic.smiles_scaffold[scaffold_smiles_idx(1990)]
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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 {
  }
}

The 111,921th molecule containing the 6th scaffold

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Chem.MolFromSmiles(smiles_from_line(111921))
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Get the scaffold network of The 111,921th molecule

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scaffold_list = get_mol_graph(smiles_from_line(111921)).ls_mol_from_sng_u()
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Draw.MolsToGridImage(scaffold_list)
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