Hi Vin,
If you are running the IPython console on a terminal emulator that supports
graphics, you could display the molecule by printing out the necessary
terminal escape codes followed by the image buffer. The solution is
terminal-specific; here's an example that works using the Kitty terminal:
from base64 import standard_b64encode
import io
def serialize_gr_command(cmd, payload=None):
cmd = ','.join('{}={}'.format(k, v) for k, v in cmd.items())
ans = []
w = ans.append
w(b'\033_G'), w(cmd.encode('ascii'))
if payload:
w(b';')
w(payload)
w(b'\033\\')
return b''.join(ans)
def write_chunked(cmd, data):
data = standard_b64encode(data)
while data:
chunk, data = data[:4096], data[4096:]
m = 1 if data else 0
cmd['m'] = m
sys.stdout.buffer.write(serialize_gr_command(cmd, chunk))
sys.stdout.flush()
cmd.clear()
def cat_mol(mol):
img = Chem.Draw.MolToImage(mol)
buf = io.BytesIO()
img.save(buf, format='png')
write_chunked({'a': 'T', 'f': 100}, buf.getvalue())
And then you can do something like this:
[image: image.png]
I'm sure the above could be adapted to work with iterm2 or other terminals
that support graphics, but that's left as an exercise to the reader.
An alternative I often use when graphics are not available is to render the
structure as ASCII art, but that may be an acquired taste. The above would
look like this:
[image: image.png]
I'll leave the code that does that for some other day.
Best,
Ivan
On Tue, Sep 1, 2020 at 9:57 AM Scalfani, Vincent <vfscalf...@ua.edu> wrote:
> Hello,
>
> Is it possible to display a molecule image directly in an IPython console
> (not a Jupyter Notebook)? Or maybe I need to send the image file directly
> to my image viewer? I would like to be able to quickly view the molecules
> without using a Jupyter Notebook or having to save the PNGs. For example:
>
> In [6]: from rdkit import Chem
> ...: from rdkit.Chem.Draw import IPythonConsole
> ...: from rdkit.Chem import Draw
>
>
> In [7]: m = Chem.MolFromSmiles('c1ncncc1C(=O)[O-]')
>
>
> In [8]: m
>
> Out[8]: <rdkit.Chem.rdchem.Mol at 0x....>
>
> In [9]: Chem.Draw.MolToImage(m)
>
> Out[9]: <PIL.PngImagePlugin.PngImageFile image mode=RGB size=300x300 at
> 0x...>
>
>
> Thanks for your help.
>
> Vin
>
> ---
>
> Vincent F. Scalfani
> The University of Alabama
>
> <vfscalf...@ua.edu>
>
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> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
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