Hi Jean-Marc,
You can strip the valence field from the MolBlock with a regex:
import re
regex = re.compile(r"^(\s*\d+\.\d{4}\s*\d+\.\d{4}\s*\d+\.\d{4} ... \d \d
\d \d \d )(\d)(.*)$")
print("\n".join(regex.sub(r"\g<1>0\g<3>", ...: line) for line in
Chem.MolToMolBlock(Chem. ...: MolFromSmiles("[NH4+]")).split("\n")))
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 1
M END
HTH, cheers
p.
On Wed, Aug 26, 2020 at 5:00 PM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
> Dear all,
>
> the atom block of the Connection Table produced by RDKit
> (Chem.MolToMolBlock() function)
> from the '[NH4+]' SMILES chain is
> 0.0000 0.0000 0.0000 N 0 0 0 0 0 4 0 0 0 0 0
>
> in which the '4' in column 10 indicates that the number of bonds of the
> N atoms (implicit Hs included) is 4.
> This makes sense but may be not necessary because the electric charge
> information is brought by the
> "M CHG 1 1 1" line.
> My ctfile.pdf file (by accelrys, dated 2011, any more recent version
> around?) shows the example of alanine
> in zwitterionic form and the valence column in the atom block only
> contains '0' values.
> Having this '4' for any organic ammonium ion is misinterpreted by the
> ACDLabs software
> I use for NMR chemical shift prediction. Replacing the '4' by a '0'
> solves the problem.
>
> Apart editing by myself the atom block (by hand or by scripting), is
> there a way
> to keep the value of the valence field to 0 for electrically charged
> atoms when writing sdf files?
>
> Best,
>
> Jean-Marc
>
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 66
> http://www.univ-reims.fr/icmr
> http://eos.univ-reims.fr/LSD/CSNteam.html
>
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
>
>
>
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