Hi Konrad,
you should use the highlightAtomLists parameter rather than
highlightAtoms, then your example will work.
Cheers,
p.
On 25/02/2020 16:02, Konrad Koehler via Rdkit-discuss wrote:
Hi everyone,
I am having trouble using a mol property value to define highlighted
atoms when generating an image.
Starting from the beginning, I have defined a variable
highlight_atom_numbers as a tuple:
>>>type(highlight_atom_numbers)
>>><class 'tuple'>
And set a mol property to this value:
mol.SetProp("highlight_atom_numbers",str(highlight_atom_numbers))
I then tried to create a 2D image of the molecule with the
“highlight_atom_numbers” highlighted:
img=Draw.MolsToGridImage(
act_mols,
molsPerRow=4,
subImgSize=(200,200),
legends=[x.GetProp("_Name") for x in act_mols],
highlightAtoms=[literal_eval(x.GetProp("highlight_atom_numbers")) for
x in act_mols]
)
Which generates the following error message:
TypeError: Boost.Python.function() got multiple values for keyword
argument 'highlightAtoms'
Theliteral_eval function
<https://stackoverflow.com/questions/8494514/converting-string-to-tuple>should
return a single tuple and not multiple values.
Anyone have any ideas for getting this to work? Thanks.
- Konrad
PS: I have tried googling for a solution, for example:
Stack Overflow: TypeError got multiple values for keyword argument
<https://stackoverflow.com/questions/18950054/class-method-generates-typeerror-got-multiple-values-for-keyword-argument>
and tried the suggestions there, but that did not help.
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