Defining atom indices impossible(?)

Describe the bug Hi there. Is there any way to map atoms implemented currently? When using atom indices as is legal in SMILES and is accepted in Rdkit, I receive the following error:

autode.exceptions.InvalidSmilesString: C[Br:1] had invalid characters:[‘:’]

This would be useful for enforcing/enabling the computation of isomorphic reactions like [Br-:1].C[Br:2]>C[Br:1].[Br-:2]

To Reproduce molecule = ade.Molecule(smiles='C[Br:1]')

Expected behavior Generation of molecules with fixed atom indices.

Environment

• Operating System: CentOS-7
• Python version: 3.9.10
• autodE version: 1.2.1

[ffmulks]

Lovely! Just in time for the student starting in my lab who will work on the project. 😄

[ffmulks]

Until I encountered my current somewhat odd research question where kinetics of such reactions became interesting to me, I was also neither aware of the possibility nor need for this. Oh I see, in the openSMILES definition the meaning of this seems to be arbitrary. RDKit implements it as enforced atom index.

Thanks for the reply and the pointers @t-young31! At the moment I am not quite familiar enough yet with the structure of autodE but I think I will be using it quite a lot and when I understood sufficiently how to implement this without breaking everything, I may try and give it a shot.