Thank you very much for your help.
Most of smiles can be processed by Tautomer Canonicalization code. However,
some smiles can not be processed, such as:
Cc1ccc(NC(=O)N=c2[nH]c(C)cn2C)nc1
[cid:image001.jpg@01D690E0.3403B2E0]
C(=O)N=c1nc(C)c2ncn(C)c2[nH]1
[cid:image002.jpg@01D690E0.3403B2E0]
Hi Imran,
I don’t think that’s possible at the moment. In principle you could derive
a class from the base MolDraw2D class and add the matplotlib drawing
commands for drawing lines etc. It wouldn’t be a trivial piece of work,
however.
Regards,
Dave
On Tue, 22 Sep 2020 at 16:27, Imran Shah
Hi Folks,
Does anyone know of an rdkit draw function to render a chemical on a
matplotlib axis in a box (x,y, width, height)? I'm interested in creating a
vector image (i.e. publication quality) that has multiple chemicals (shown
below). I created this raster image using matplotlib and
Hi Norwid,
The inner loop over mols here:
for i in smiles_list:
for mol in mols:
for atom in mol.GetAtoms():
atom.SetAtomMapNum(atom.GetIdx())
mols.append(Chem.MolFromSmiles(i))
is not in the right place. First, because you'll go over the same
Thank you, Max!
It worked nicely and looks like each array is a line in a nxn matrix.
Thanks again
--
Henrique C. S. Junior
From: Max Pinheiro Jr
Sent: Sunday, September 20, 2020 10:41
To: Henrique Castro
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re:
Starting with lists consisting of a compound identifier, an explicit space,
and a SMILES string, I would like to generate illustrations about these
structures including RDKit's atom indices. What is puzzling to me is that
consistently the last entry / compound list is converted into a structure
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