How to remove all charges from SMILES?

Question

[Annalischen]

SMILES as .smi or .smiles molecule file format.

As there are many molecules I would prefer command line or to write a script.

I also would like to know which option is better?

I have already tried neutralize in ChemAxom standardize. But it doesn't work.

[GenoMax]

What is smiles for those of us who have not heard of this before?

[Diwan]

SMILES is a way to represent chemical molecules using simple typographical/printable characters. It is widely used in chemistry. For example, benzene ring will be written as c1ccccc1. More details here at Daylight page.

Answer 1

[Egon Willighagen]

SMIRKS have been proposed and you can have a look at this CDK-based code. Keep in mind that some compounds cannot be neutralized without introducing salt counter-ions, such as is the case with R[N(CH3)3]+ groups.