Dear all,
The 2D structure drawing code
from rdkit import Chem
from rdkit.Chem import rdCoordGen
m =
Chem.MolFromSmiles('CN1C[C@H]2[C@]3([C@@H]1C[C@@H](C=C3)OC)C4=CC5=C(C=C4[C@@H](O2)O)OCO5')
template = Chem.MolFromMolFile('template.mol')
params = rdCoordGen.CoordGenParams()
params.SetTemplateMol(template)
rdCoordGen.AddCoords(m, params)
writer = Chem.SDWriter('compound_2D.sdf')
writer.write(m)
writer.close()
with file template.mol containing
template.mol
ChemDraw03232214592D
9 9 0 0 1 0 0 0 0 0999 V2000
-1.4289 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4289 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7146 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0002 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0002 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7146 1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7141 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4289 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7141 -1.2375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
4 7 1 0
7 8 1 0
7 9 1 0
M END
The template looks like
in which the H in OH groups have been added to have a nice drawing
but are not part of the mol file.
The result in compound_2D.sdf is
as if no template were provided.
I succeeded already to obtain what I wanted with the same code
but for other molecules and templates.
I use rdkit version 2021.03.2 .
Can you reproduce that?
Is there a better way to do it?
Best,
Jean-Marc Nuzillard
--
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
ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10
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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