cannot pass drawOptions to MolsToGridImage when using notebook

[slochower]

Configuration:

• RDKit Version: 2020.03.1
• Operating system: macOS 10.14
• Python version (if relevant): 3.7.5
• Are you using conda? Yes
• If you are using conda, which channel did you install the rdkit from? conda-forge

Description:

Based on #1854 and #2691, I believe it should be possible to pass drawingOptions to MolsToGridImage. I can't find documentation showing how these options can be passed as kwargs.

from rdkit import Chem
from rdkit.Chem.Draw.MolDrawing import DrawingOptions

UpdatedDrawingOptions = DrawingOptions()
UpdatedDrawingOptions.atomLabelFontSize = 16
UpdatedDrawingOptions.defaultColor = (0, 1, 0)

smiles = ["CCCC", "CCCCC"]
molecules = [Chem.MolFromSmiles(i) for i in smiles]
MolsToGridImage(molecules, options=UpdatedDrawingOptions)

---------------------------------------------------------------------------
ArgumentError                             Traceback (most recent call last)
<ipython-input-16-36b6c0d46c18> in <module>
      8 smiles = ["CCCC", "CCCCC"]
      9 molecules = [Chem.MolFromSmiles(i) for i in smiles]
---> 10 MolsToGridImage(molecules, options=UpdatedDrawingOptions)

~/opt/anaconda3/envs/XXX/lib/python3.7/site-packages/rdkit/Chem/Draw/IPythonConsole.py in ShowMols(mols, maxMols, **kwargs)
    191       if prop in kwargs:
    192         kwargs[prop] = kwargs[prop][:maxMols]
--> 193   res = fn(mols, drawOptions=drawOptions, **kwargs)
    194   if kwargs['useSVG']:
    195     return SVG(res)

~/opt/anaconda3/envs/XXX/lib/python3.7/site-packages/rdkit/Chem/Draw/__init__.py in MolsToGridImage(mols, molsPerRow, subImgSize, legends, highlightAtomLists, highlightBondLists, useSVG, **kwargs)
    577     return _MolsToGridImage(mols, molsPerRow=molsPerRow, subImgSize=subImgSize, legends=legends,
    578                             highlightAtomLists=highlightAtomLists,
--> 579                             highlightBondLists=highlightBondLists, **kwargs)
    580 
    581 

~/opt/anaconda3/envs/XXX/lib/python3.7/site-packages/rdkit/Chem/Draw/__init__.py in _MolsToGridImage(mols, molsPerRow, subImgSize, legends, highlightAtomLists, highlightBondLists, drawOptions, **kwargs)
    523           del kwargs[k]
    524     d2d.DrawMolecules(list(mols), legends=legends, highlightAtoms=highlightAtomLists,
--> 525                       highlightBonds=highlightBondLists, **kwargs)
    526     d2d.FinishDrawing()
    527     res = _drawerToImage(d2d)

ArgumentError: Python argument types in
    MolDraw2D.DrawMolecules(MolDraw2DCairo, list)
did not match C++ signature:
    DrawMolecules(RDKit::MolDraw2D {lvalue} self, boost::python::api::object mols, boost::python::api::object highlightAtoms=None, boost::python::api::object highlightBonds=None, boost::python::api::object highlightAtomColors=None, boost::python::api::object highlightBondColors=None, boost::python::api::object highlightAtomRadii=None, boost::python::api::object confIds=None, boost::python::api::object legends=None)

[AustinApple]

Hello, I also have the same problem now. Do you figure this out?

[slochower]

Unfortunately not. I don't know a solution.

[wagerc97]

have you found a solution?

[DavidACosgrove]

From an answer to someone else today. Sorry about the formatting. dopts = rdMolDraw2D.MolDrawOptions() dopts.prepareMolsForDrawing = True results = Draw.MolsToGridImage( self.hits[:k + 1], molsPerRow=2, subImgSize=(600, 600), legends=[x.GetProp("_Name") for x in self.hits[:k]], drawOptions=dopts)

On Thu, 6 May 2021 at 20:56, fakepasta ***@***.***> wrote: have you found a solution? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3101 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACGF2FQ65Q2BWWIZCVFKZHLTMLX6VANCNFSM4MMWHAGA> .

-- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk

[dww100]

If I try

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D

smiles = ["CCCC", "CCCCC"]
molecules = [Chem.MolFromSmiles(i) for i in smiles]
dopts = rdMolDraw2D.MolDrawOptions()
Draw.MolsToGridImage(molecules, drawOptions=dopts)

I get the error

TypeError: rdkit.Chem.Draw.MolsToGridImage() got multiple values for keyword argument 'drawOptions'

What am I doing wrong?

[ptosco]

@dww100 That looks like a bug. If you apply the following patch to your rdkit/Chem/Draw/IPythonConsole.py file, it should then work:

diff --git a/rdkit/Chem/Draw/IPythonConsole.py b/rdkit/Chem/Draw/IPythonConsole.py
index ac78c2d..5ae5fc9 100644
--- a/rdkit/Chem/Draw/IPythonConsole.py
+++ b/rdkit/Chem/Draw/IPythonConsole.py
@@ -194,7 +194,9 @@ def ShowMols(mols, maxMols=50, **kwargs):
     for prop in ('legends', 'highlightAtoms', 'highlightBonds'):
       if prop in kwargs:
         kwargs[prop] = kwargs[prop][:maxMols]
-  res = fn(mols, drawOptions=drawOptions, **kwargs)
+  if not "drawOptions" in kwargs:
+    kwargs["drawOptions"] = drawOptions
+  res = fn(mols, **kwargs)
   if kwargs['useSVG']:
     return SVG(res)
   else:

[dww100]

Thanks @ptosco that works perfectly