Hi Greg,
Please see the attachment for the basic code I use to plot spectra and
molecules. It'd be great if I can somehow improve the quality of the
molecule!
@Dima: I'm not using any SVG functionality because matplotlib can't
handle that. So I don't think doing the SVG transform is directly
possible in matplotlib.
Alternatively I could export both the spectrum plot and the molecule to
SVG files and then combine them afterwards. But in that case it's not
possible to manipulate both elements in a single matplotlib figure.
Best,
Wout
On 07/08/2019 21:44, Greg Landrum wrote:
That's an interesting question. I think there probably are some ways of
tweaking this and improving things, but I don't have a convenient way to
test. If you can share the python (+data) you used to construct that PDF
I will see if I can come up with a solution.
-greg
On Thu, Aug 8, 2019 at 2:23 AM Wout Bittremieux <wbittremi...@ucsd.edu
<mailto:wbittremi...@ucsd.edu>> wrote:
Dear RDKit team,
I'm trying to draw a molecule on a spectrum plot from Matplotlib using
MolToImage. This is some abbreviated code:
```
import matplotlib.pyplot as plt
from rdkit import Chem
from rdkit.Chem import Draw
fig, ax = plt.subplots()
ax.plot(...)
im = Draw.MolToImage(Chem.MolFromSmiles(smiles))
ax.imshow(im, aspect='auto', extent=(x, x+width, y, y + height))
plt.savefig('fig.pdf')
plt.close()
```
Unfortunately the quality of the molecule drawing is rather poor (see
attachment; nonsensical spectrum and molecule). This seems to be true
for non-SVG drawing in general, and unfortunately it's not really
possible to combine SVG output with Matplotlib functionality.
Is there any way I can improve the quality of the MolToImage output?
I've tried to change some of the DrawingOptions, but the result always
remains very pixelated and low quality.
Thank you,
Wout
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import matplotlib.pyplot as plt
import numpy as np
from rdkit import Chem
from rdkit.Chem import Draw
np.random.seed(2)
num_peaks = 50
mz = np.random.uniform(100, 1400, num_peaks)
intensity = np.random.lognormal(0, 2, num_peaks)
intensity[intensity < 0] = 0
fig, ax = plt.subplots(figsize=(9, 6))
# Plot peaks.
for mz, intensity in zip(mz, intensity):
ax.plot([mz, mz], [0, intensity], c='black', zorder=10)
# Plot molecule.
im = Draw.MolToImage(Chem.MolFromSmiles('CO\C(CC(C)C(Cl)(Cl)Cl)=C\C(=O)N(C)C(CC1=CC=CC=C1)C1=NC=CS1'))
ax.imshow(im, aspect='auto', extent=(500, 800, 14, 29))
ax.set_xlim(100, 1400)
ax.set_ylim(0, 30)
plt.savefig('plot.pdf')
plt.close()
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