Hi All,
I'm trying to align a set of structures to a template that I have as
molfile. When I call GenerateDepictionMatching2DStructure it appears that
the coordinate for the template are directly copied. This results in a
structure like the one below, where the bond lengths for the template are
different from those in the rest of the molecule.
[image: image.png]
Is there a way around this so that all of the bond lengths will be the same?
My code is below, thanks in advance,
Pat
from rdkit import Chem
from rdkit.Chem import rdDepictor
mb = """
RDKit 2D
9 10 0 0 0 0 0 0 0 0999 V2000
2.1845 0.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4701 -0.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4701 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1845 -1.4500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.8990 -1.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8990 -0.2125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6836 0.0425 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.6836 -1.2924 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
4.1685 -0.6250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
5 6 1 0
7 9 1 0
6 7 2 0
8 9 1 0
1 6 1 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 8 2 0
M END"""
tmplt = Chem.MolFromMolBlock(mb)
smiles = "FC(F)(F)Oc1cccc(-n2nnc3ccc(NC4CCOCC4)nc32)c1"
mol = Chem.MolFromSmiles(smiles)
rdDepictor.GenerateDepictionMatching2DStructure(mol, tmplt)
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