How can I remove charges from the molecule?

User 16a108bed5

10-11-2016 02:30:05

I have such smiles string: [O-][N+](=O)c1ccccc1

That is charges.

How do I remove charges and generate the picture without them?

Here is what I have tried:

/Applications/ChemAxon/JChemSuite/bin/standardize -c "neutralize..clean2d:full"

/Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/SMI/mol30.smi -o Downloads/testMolCon.smi

Doesn't remove the charge: [O-][N+](=O)c1ccccc1 - output

Image generation:

/Applications/ChemAxon/JChemSuite/bin/molconvert png:scale500,H_off,#0007e5ed,setcolors:a1:#07e5ed,b1:#07e5ed /Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/SMI/mol30.smi -o /Users/user/Desktop/FolderForAnalysis/IMAGES_GEN/img/mol30.png

What do I use to have picture/smiles/both without the charges?

Many thanks for the support!

ChemAxon 044c6721bc

10-11-2016 09:30:41

Hi,

I've moved your question to the Structure manipulation forum. The relevant expert will answer your question.

Best,

Janos

ChemAxon e08c317633

14-11-2016 10:36:41

Use Standardizer's transform action.

Example:

standardize -c "[#8-:2]-[#7+:1]=[O:3]>>[O:2]=[N:1]=[O:3]" "[O-][N+](=O)c1ccccc1"

O=N(=O)c1ccccc1

User 16a108bed5

14-11-2016 14:29:34

What if I have 1000 molecules and I don't want to write configuration manually?

ChemAxon e08c317633

14-11-2016 15:52:36

Neutralize action will remove the charges in most cases. There are some exceptions, for example mesomer representations like nitro, but for these you have the transform action.