Is this expected standardizer behavior?

Hi,

Is the below the expected behavior?  I input a net-charge-0 structure, neutralize, and then get out a structure with a net charge.

Version 5.5.1

echo 'C[N-]C1=C(C=CC=C1)(C)C' | ./standardize -c "neutralize"

CNC1=C(C=CC=C1)(C)C

Hi Andrew,

Neutralization mainly means H+ addition or removal. Quote from the documentation: "converts charged atoms to non charged, if it doesn't cause valence errors".

In case of "C[N-]C1=C(C=CC=C1)(C)C": [N-] is neutralized by H+ addition, cannot be neutralized automatically.

Zsolt

Great .. thanks for the clarification!