Hi Greg,
I have some code that relies on the GenerateDepictionMatching3DStructure
function, that I have found no longer plays nicely with 2010_12_1.
In 2010_09_1, the following works fine:
>>> from rdkit import Chem
>>> from rdkit.Chem import AllChem, Draw
>>> mol = Chem.MolFromSmiles("CCOCCNC")
>>> AllChem.EmbedMolecule(mol)
>>> AllChem.UFFOptimizeMolecule(mol)
>>> AllChem.GenerateDepictionMatching3DStructure(mol, 0)
>>> Draw.MolToImageFile(mol, "C:\\test.png")
However, with 2010_12_1, I get the following at the point of calling
GenerateDepictionMatching3DStructure:
Traceback (most recent call last):
File "<pyshell#5>", line 1, in <module>
AllChem.GenerateDepictionMatching3DStructure(mol, 0)
File "C:\RDKit_2010_12_1\rdkit\Chem\AllChem.py", line 149, in
GenerateDepictionMatching3DStructure
conf = reference.GetConformer(confId)
AttributeError: 'int' object has no attribute 'GetConformer'
I am guessing that something has changed that means a reference
structure is now a requirement(?) Previously I had been just passing in
0 - which I had assumed meant "don't bother trying to align to anything;
just try and make a tidy 2D representation that looks like the 3D
arrangement".
I must confess I was not 100% sure what the reference option was, but
was fairly happy in my ignorance while I could successfully pass 0 in!
However, now I find that I have to pass a mol type in - I think now
doing:
>>> AllChem.GenerateDepictionMatching3DStructure(mol, mol)
is giving the same results as the previous
"AllChem.GenerateDepictionMatching3DStructure(mol, 0)"... Am I doing
this correctly, and is the changed behaviour deliberate?
Kind regards
James
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