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How to remove all charges from SMILES?
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3.4 years ago
Annalischen • 10
UCL

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.

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

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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.

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14 months ago
Maastricht

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.

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