Hi Ed,
I think this is related to a previous mailing list item (
https://www.mail-archive.com/[email protected]/msg03528.html
).
It has something to do with the bounding boxes (they get scaled during the
map generation process). In the previous case it was enough to set
bbox_inches='tight' when saving the image to solve the problem.
Best,
Sereina
2014-07-16 17:04 GMT+02:00 Edward Pyzer-Knapp <[email protected]>:
> Hi,
>
> I am trying to replicate the tutorial on visualising maps of gasteiger
> charges.
>
> >>> from rdkit.Chem.Draw import SimilarityMaps>>> mol =
> >>> Chem.MolFromSmiles('COc1cccc2cc(C(=O)NCCCCN3CCN(c4cccc5nccnc54)CC3)oc21')>>>
> >>> AllChem.ComputeGasteigerCharges(mol)>>> contribs =
> >>> [float(mol.GetAtomWithIdx(i).GetProp('_GasteigerCharge')) for i in
> >>> range(mol.GetNumAtoms())]>>> fig =
> >>> SimilarityMaps.GetSimilarityMapFromWeights(mol, contribs, colorMap='jet',
> >>> contourLines=10)
>
> However when I visualise the image:
> >>> fig.show()
>
> The window only shows a small portion of the image. Saving the figure has
> the same problem.
>
> Any help much appreciated!
>
> Ed Pyzer-Knapp
>
>
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