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How can I remove charges from the molecule?
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Anastasia

Joined: 27 Feb 2015
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Link to postPosted: Thu Nov 10, 2016 3:30 amPost subject: How can I remove charges from the molecule? Reply with quote

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!
Janos
ChemAxon personnel
Joined: 02 May 2011
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Link to postPosted: Thu Nov 10, 2016 10:30 amPost subject: Reply with quote

Hi,

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

Best,

Janos
Zsolt
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Joined: 11 Jan 2006
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Link to postPosted: Mon Nov 14, 2016 11:36 amPost subject: Reply with quote

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
Anastasia

Joined: 27 Feb 2015
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Link to postPosted: Mon Nov 14, 2016 3:29 pmPost subject: Reply with quote

What if I have 1000 molecules and I don't want to write configuration manually?
Zsolt
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Link to postPosted: Mon Nov 14, 2016 4:52 pmPost subject: Reply with quote

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.  
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Structure manipulation: Canonicalization / standardization
How can I remove charges from the molecule?
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