Hi Pat,
>From my experience rdkit uses more or less 1.5 units bond length for 2D
>depictions. So it makes sense if you rescale your template so that the bond
>length is 1.5.
This is the code snippet I use for the same thing to upscale template with bond
lengths 1.0 to 1.5
import numpy
factor = 1.5
mol = Chem.MolFromMolFile(src, sanitize=True)
matrix = numpy.zeros((4, 4), numpy.float)
for i in range(3):
matrix[i, i] = factor
matrix[3, 3] = 1
AllChem.TransformMol(mol, matrix)
Chem.MolToMolFile(mol, dst)
Let me know if this is what you were looking for.
Lukas
From: Patrick Walters <wpwalt...@gmail.com>
Date: Thursday, 23 May 2019 at 13:22
To: RDKIT mailing list <rdkit-discuss@lists.sourceforge.net>
Subject: [Rdkit-discuss] GenerateDepictionMatching2DStructure question
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.
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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