Dear Paolo,
many thanks for this regex-based answer to my question.
Best,
Jean-Marc
Le 26/08/2020 à 23:34, Paolo Tosco a écrit :
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 <mailto: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://eos.univ-reims.fr/LSD/CSNteam.html>
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
<http://www.univ-reims.fr/LSD/JmnSoft/>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
<mailto:Rdkit-discuss@lists.sourceforge.net>
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
<https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
--
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/
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
