[Rdkit-discuss] similarity maps look strange when displayed

[Michał N. <mm...@gm...>]

Look at the following example:

import gi
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import SimilarityMaps
import matplotlib.pyplot as plt
mol =
Chem.MolFromSmiles('COc1cccc2cc(C(=O)NCCCCN3CCN(c4cccc5nccnc54)CC3)oc21')
refmol = Chem.MolFromSmiles('CCCN(CCCCN1CCN(c2ccccc2OC)CC1)Cc1ccc2ccccc2c1')
fp = SimilarityMaps.GetAPFingerprint(mol, fpType='normal')
fig, maxweight = SimilarityMaps.GetSimilarityMapForFingerprint(refmol, mol,
SimilarityMaps.GetMorganFingerprint)
plt.show()

This displays similarity map. Unfortunately the image is not scaled to fit
available area and it's not centered. This cases problems with mpld3
library, which converts matplotlib to javascript:

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import SimilarityMaps
import mpld3
mol =
Chem.MolFromSmiles('COc1cccc2cc(C(=O)NCCCCN3CCN(c4cccc5nccnc54)CC3)oc21')
refmol = Chem.MolFromSmiles('CCCN(CCCCN1CCN(c2ccccc2OC)CC1)Cc1ccc2ccccc2c1')
fp = SimilarityMaps.GetAPFingerprint(mol, fpType='normal')
fig, maxweight = SimilarityMaps.GetSimilarityMapForFingerprint(refmol, mol,
SimilarityMaps.GetMorganFingerprint)
mpld3.show_d3(fig)

Again, the image is much larger then drawing area and is not aligned.

I've tried several options: changing coordScale or scale parameter but
without success. Any help in displaying the image correctly usiing
plt.show() and/or mpld3.show_d3 would be appreciated.

Regards,
Michal Nowotka