Hi Michal
I think this is related to a previous mailing list item (
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg03528.html
).
It has probably 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. Maybe
there is something similar for mpld3.
Best,
Sereina
2014-03-21 12:12 GMT+01:00 Michał Nowotka mmm...@gmail.com:
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('COc12cc(C(=O)NN3CCN(c45nccnc54)CC3)oc21')
refmol =
Chem.MolFromSmiles('CCCN(N1CCN(c2c2OC)CC1)Cc1ccc2c2c1')
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('COc12cc(C(=O)NN3CCN(c45nccnc54)CC3)oc21')
refmol =
Chem.MolFromSmiles('CCCN(N1CCN(c2c2OC)CC1)Cc1ccc2c2c1')
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
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