rdMolDraw2D, problems during generation of pictures from SMARTS, differences between Cairo and SVG

[wopozka]

Configuration:
import rdkit
rdkit.version
-->

• RDKit Version: 2020.09.1
• Operating system: MacOSX Darwin
• Python version (if relevant): 3.7
• Are you using conda? Yes
• If you are using conda, which channel did you install the rdkit from? rdkit
• If you are not using conda: how did you install the RDKit?

Description:

I would like to generate pictures for some SMARTS definitions using rdMolDraw2D. I found that for some SMARTS it is not possible to generate pictures using Cairo, as it ends up with kekulization error. The same procedure using SVG as is succesful. Setting parameters like prepareMolsBeforeDrawing = False, or PrepareMolForDrawing(mol, kekulize=False), does not help and ends up with the same error. Example code below

1. Working code for SVG engine

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
import rdkit
print(rdkit.__version__)
mol = Chem.MolFromSmarts('c[N+]#[N]')
d2d = rdMolDraw2D.MolDraw2DSVG(300, 300)
d2d.DrawMolecule(mol)
d2d.FinishDrawing()
SVG(d2d.GetDrawingText())

2. The same for Cairo

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
import rdkit
print(rdkit.__version__)
mol = Chem.MolFromSmarts('c[N+]#[N]')
d2d = rdMolDraw2D.MolDraw2DCairo(300, 300)
d2d.DrawMolecule(mol)
d2d.FinishDrawing()

end up with error:
RDKit ERROR: [17:49:00] non-ring atom 0 marked aromatic

It does not work even if I try to switch preparation of molecule before drawing

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem import rdDepictor
rdDepictor.SetPreferCoordGen(True)
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
import rdkit
print(rdkit.__version__)
mol = Chem.MolFromSmarts('c[N+]#[N]')
d2d = rdMolDraw2D.MolDraw2DCairo(300, 300)
d2d.prepareMolsBeforeDrawing = False
Options = d2d.drawOptions()
Options.prepareMolsBeforeDrawing = False
d2d.SetDrawOptions(Options)
mol1 = rdMolDraw2D.PrepareMolForDrawing(mol, kekulize=False)
mol1.UpdatePropertyCache(False)
d2d.DrawMolecule(mol1)
d2d.FinishDrawing()

RDKit ERROR: [17:52:50] non-ring atom 0 marked aromatic

[DavidACosgrove]

The difference is that the Cairo drawer calls addMoleculeMetadata and the exception is being thrown from there. So it's not a drawing error as such.

[greglandrum]

@wopozka , the comment from @DavidACosgrove is correct.
Until we fix the problem (which is a bug), you can work around it by disabling the code which writes metadata to the PNG Options.includeMetadata = False

[wopozka]

@greglandrum, thanks for the valuable advice. As I can use svg that is not a problem for me. I just noticed strange behaviour during png generation and then switched to svg.