Neutralizing protonated aromatic N

Neutralizing protonated aromatic N does not remove the hydrogen

>echo 'c1[nH+]cccc1' | standardize -c "neutralize"
>c1cc[nH]cc1

Is this another manifestation of this post?

Fragmenter can generate incorrect valencies on aromatic N

(that post is locked so I couldn't comment on it)

Stephen

Yes, this is related to that fragmenter issue. We will fix it in Standardizer in JChem 5.5.1. (In fragmenter it will be fixed in JChem 5.5.)

I unlocked the Fragmenter can generate incorrect valencies on aromatic N topic, it was locked accidentally.

Zsolt

Hi

I'm still seeing this behaviour in 5.5.1.0.

standardize 'Cn1cc[nH+]c1' -c 'neutralize'

Cn1cc[nH]c1

Has this been fixed in 5.6?

Thanks

Stephen

Hi Stephen,

Unfortunately it has not ben fixed yet (this bug is different from the bug in Fragmenter). The fix will be available in 5.8 release.

Sorry for the inconvenience.

Zsolt

I'm seeing the same behaviour on quinoline in 5.9 and 5.11

standardize -c "neutralize" -s "c1cc[nH+]c2ccccc12"

c1ccc2[nH]cccc2c1

 

Stephen

StephenPickett wrote:

I'm seeing the same behaviour on quinoline in 5.9 and 5.11 standardize -c "neutralize" -s "c1cc[nH+]c2ccccc12" c1ccc2[nH]cccc2c1   Stephen

It will be fixed in JChem 5.11.2 (coming in 2 weeks).

Zsolt