[Rdkit-discuss] Aromatic Rings

[עמית ה. <ami...@gm...>]

Hi,

I tried to find a substructure (MCS) between molecules, and put the results
in grid-image. In the output, there is a missing bond in the aromatic
rings, but when I print just one substructure alone it prints this
correctly...

def defult():
   l = 5
   ligs = []
   common_atoms_matrix = []
   #make a list from the ligands that we insert to the code
   for i in range(1, int(l)+1):
      ligand = "ligand_" + str(i) + ".pdb"
      ligs.append(ligand)
   for i in range(len(ligs)):
      mol_object = Chem.MolFromPDBFile(ligs[i])
      Chem.SanitizeMol(mol_object)
      ligs[i] = mol_object
   return ligs

ligs = defult()
ls = []
for a, i in enumerate(ligs):
   ks = []
   for b, j in enumerate(ligs):
      l = rdFMCS.FindMCS([i, j],
bondCompare=rdFMCS. BondCompare.CompareAny).smartsString
      l = Chem.MolFromSmarts(l)
      #Chem.SanitizeMol(l)
      ls.append(l)
Draw.MolsToGridImage(ls, molsPerRow=5, subImgSize=(250,250))
[image: צילום מסך 2023-05-11 132315]
<https://user-images.githubusercontent.com/133215803/237793539-4211b7ec-4020-41a6-8769-23c21505461d.png>

Here is the code to print just one substructure:

l = rdFMCS.FindMCS([Chem.MolFromPDBFile("ligand_5.pdb"),
Chem.MolFromPDBFile("ligand_4.pdb")],
bondCompare=rdFMCS.BondCompare.CompareAny).smartsString
l = Chem.MolFromSmarts(l)
IPythonConsole.drawOptions.addBondIndices = True
l
[image: צילום מסך 2023-05-11 132559]
<https://user-images.githubusercontent.com/133215803/237793698-e417ce3d-d755-4f65-a549-fdef05056309.png>


Why is it happening? and how can I solve this problem?

Thank you,
Amit

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