How to remove all charges from SMILES?
1
1
Entering edit mode
7.7 years ago
Annalischen ▴ 10

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.

Smiles Programming Cheminformatics • 2.6k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
7.4 years ago

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.

ADD COMMENT

Login before adding your answer.

Traffic: 1820 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6