Re: [Rdkit-discuss] Display Molecules within IPython Console
Hi Greg,
Draw.ShowMol(m) works perfectly and even works in a loop to view multiple
molecules (one at a time). thanks!
Hi Ivan, thanks for the terminal graphics code example. I think the ASCII art
structures are fun and useful. I've used that in Open Babel before to quickly
view molecules. Such an ASCII structure view method in RDKit would be great and
I would be interested in trying it.
Vin
From: Ivan Tubert-Brohman
Sent: Tuesday, September 1, 2020 9:29 AM
To: Scalfani, Vincent
Cc: rdkit-discuss@lists.sourceforge.net
Subject: [EXTERNAL] Re: [Rdkit-discuss] Display Molecules within IPython Console
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.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.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
mailto: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]:
In [9]: Chem.Draw.MolToImage(m)
Out[9]:
Thanks for your help.
Vin
---
Vincent F. Scalfani
The University of Alabama
<mailto:vfscalf...@ua.edu>
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Re: [Rdkit-discuss] Display Molecules within IPython Console
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 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]:
>
> In [9]: Chem.Draw.MolToImage(m)
>
> Out[9]: 0x...>
>
>
> Thanks for your help.
>
> Vin
>
> ---
>
> Vincent F. Scalfani
> The University of Alabama
>
>
>
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Re: [Rdkit-discuss] Display Molecules within IPython Console
Hi Vin,
I added something a long time ago which still seems to work: Draw.ShowMol:
In [3]: from rdkit.Chem import Draw
In [4]: Draw.ShowMol(m)
That, for me at least, opens a window with an image of the molecule. It's
using tkinter, so it should work on all three supported operating systems.
Unfortunately, at least on my machine, I have to close the window before
the ipython prompt becomes active again.
-greg
On Tue, Sep 1, 2020 at 3:59 PM Scalfani, Vincent 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]:
>
> In [9]: Chem.Draw.MolToImage(m)
>
> Out[9]: 0x...>
>
>
> Thanks for your help.
>
> Vin
>
> ---
>
> Vincent F. Scalfani
> The University of Alabama
>
>
>
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