from rdkit import Chem
from rdkit.Chem import rdDepictor, rdCoordGen, AllChem

query_smiles = "Cn1cnc(CN2CC(C(N)=O)CCC2=O)c1-c1ncccn1"
template_mol_block = """
  Ketcher 12192413482D 1   1.00000     0.00000     0

  8  8  0  0  0  0  0  0  0  0999 V2000
   10.7840   -3.9992    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.7840   -4.9992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6500   -5.4992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5160   -4.9992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5160   -3.9992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6500   -3.4992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6500   -2.4992    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.9180   -3.4992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0     0  0
  1  2  1  0     0  0
  2  3  1  0     0  0
  3  4  1  0     0  0
  4  5  1  0     0  0
  5  6  1  0     0  0
  6  7  2  0     0  0
  1  8  1  0     0  0
M  END

"""

mol = Chem.MolFromSmiles(query_smiles)
template = Chem.MolFromMolBlock(template_mol_block)
    
# first scale the template, usually defined by a molV3000
# scales to RDKit default size
rdDepictor.NormalizeDepiction(template, canonicalize=0)

# we now do the same for mol
# but need to compute 2D coords first since came from SMILES
AllChem.Compute2DCoords(mol)
rdDepictor.NormalizeDepiction(mol, canonicalize=0)

# now do the alignment
AllChem.GenerateDepictionMatching2DStructure(mol, template, acceptFailure=True)