unable to replace halogen [missing index 0 on .rep2D]

[Dslab2025]

for Cl no numbering appeared
I want to replace Cl with others

if i use attachment point 1 That is C1 it returns error during build molecule
how to solve

[bieniekmateusz]

Hi @Dslab2025 , do you have a smiles or a file for this molecule?

I recreated the molecule and the Cl atom appears to have an index in this case. Thanks

mol = Chem.MolFromSmiles("C1=CC(=CC=C1C2=NC=C(S2)CNC3=NC=NC4=C3C=NN4)Cl")
mol = Chem.AddHs(mol)
scaffold = fegrow.RMol(mol)
scaffold.rep2D(idx=True, size=(500, 500))

[Dslab2025]

Thank you
Smiles of said molecule
Clc1ccc(cc1)c1ncc(CNc2ncnc3[nH]ncc23)s1

But how to do such things for other molecules?

[bieniekmateusz]

I see, if the atom happens to be the index 0 then its index is not visualised.

In your smiles, if you use the index 0 for replacement, that will point towards the Cl atom.

Thanks for bringing this to our attention. I'll see if I can also add the visualisation for it.

[debanjansen48]

Thank you so much. Shall I update the program or I execute something else in order to continue my work?

[bieniekmateusz]

There is no need to update anything atm. It's just that the missing index means that the index is 0 on that atom. I'll update this issue when I have a neater fix for this. Best, Mat

[Dslab2025]

Thank you sir.