Re: [Rdkit-discuss] Multiline legend in MolsToGridImage

[David Cosgrove]

Hi Gustavo,
If you do create the issue, could you also add that the legend should scale
the font sensibly and also annex its own part of the drawing area. At the
moment it just goes at the bottom and the molecule may obscure it. It would
make sense if these were all done at the same time.
Cheers,
Dave


On Thu, 9 Apr 2020 at 06:00, Greg Landrum  wrote:

> Hi Gustavo,
>
> I don't believe that this is currently possible. I'm pretty sure we would
> need to add explicit code to handle this case.
> This would be a good thing to create a github issue for, if you're
> interested.
>
> -greg
>
>
> On Wed, Apr 8, 2020 at 10:35 PM Gustavo Seabra 
> wrote:
>
>> [image: Screenshot from 2020-04-08 16-28-37.png]
>>
>> Hi,
>>
>> Does anyone know how to write multiline legends when using
>> MolsToGridImage? I've been trying the code [here](
>> https://sourceforge.net/p/rdkit/mailman/message/35561198/), but nothing
>> there seems to work for me, as I only get a blank rectangle in place of the
>> \n or \r symbols... (see picture)
>>
>> Are there any ideas?
>> Thanks,
>> --
>> Gustavo Seabra.
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Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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Re: [Rdkit-discuss] Multiline legend in MolsToGridImage

[Greg Landrum]

Hi Gustavo,

I don't believe that this is currently possible. I'm pretty sure we would
need to add explicit code to handle this case.
This would be a good thing to create a github issue for, if you're
interested.

-greg


On Wed, Apr 8, 2020 at 10:35 PM Gustavo Seabra 
wrote:

> [image: Screenshot from 2020-04-08 16-28-37.png]
>
> Hi,
>
> Does anyone know how to write multiline legends when using
> MolsToGridImage? I've been trying the code [here](
> https://sourceforge.net/p/rdkit/mailman/message/35561198/), but nothing
> there seems to work for me, as I only get a blank rectangle in place of the
> \n or \r symbols... (see picture)
>
> Are there any ideas?
> Thanks,
> --
> Gustavo Seabra.
> ___
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> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] Multiline legend in MolsToGridImage

[Gustavo Seabra]

[image: Screenshot from 2020-04-08 16-28-37.png]

Hi,

Does anyone know how to write multiline legends when using MolsToGridImage?
I've been trying the code [here](
https://sourceforge.net/p/rdkit/mailman/message/35561198/), but nothing
there seems to work for me, as I only get a blank rectangle in place of the
\n or \r symbols... (see picture)

Are there any ideas?
Thanks,
--
Gustavo Seabra.
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Re: [Rdkit-discuss] multiline legend in MolsToGridImage

[Pavel Polishchuk]

Thank you, that helped!
I noticed that I need to substantially increase the height of the image 
to make the second line visible. If I'll want to draw more lined I 
should increase the height further.


Pavel.

On 12/20/2016 03:14 PM, Peter Gedeck wrote:

Hello,

I thought we had removed all of these by now. I'll open an issue and 
fix the code.


Best,

Peter


On Tue, Dec 20, 2016 at 6:01 AM David Hall > wrote:


The replace and split methods were removed from the string module
in python3. You can replace the code as follows:

s = s.replace('\r\n', '\n')
s = s.replace('\n\r', '\n')
s = s.replace('\r', '\n')
lines = s.split('\n')


On Tue, Dec 20, 2016 at 2:45 AM, Pavel Polishchuk
mailto:pavel_polishc...@ukr.net>> wrote:

Hi,

I try to print multiline legends for molecules in a grid and
use the following code from notebook

  from rdkit import Chem
  from rdkit.Chem import Draw
  # from rdkit.Chem.Draw import IPythonConsole

  mols = [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]
  legends = ["1\nCCC", "2\nC"]
  Draw.MolsToGridImage(mols, molsPerRow=5,
subImgSize=(200,200), legends=legends)

  it returns error: AttributeError: module 'string' has no
attribute 'replace'(full stack is below)

  If I uncomment IPythonConsole import then it returns the
picture with labels, but with spaces instead of new line symbols.

  What can I do in this situation? RDKit 2016.03.2

Kind regards,
Pavel.



---
AttributeError Traceback (most recent call 
last)
  in() 1 mols = [Chem.MolFromSmiles(s) for 
s in ["CCC",
"C"]]2 legends = ["1\nCCC", "2\nC"]> 3p =
Draw.MolsToGridImage(mols, molsPerRow=5, subImgSize=(200,200),

legends=legends)/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
in MolsToGridImage(mols, molsPerRow, subImgSize, legends,
highlightAtomLists, useSVG, **kwargs) 387 else:388 return
_MolsToGridImage(mols,molsPerRow=molsPerRow,subImgSize=subImgSize,
--> 389legends=legends, highlightAtomLists=highlightAtomLists,
**kwargs) 390 391 def ReactionToImage(rxn,

subImgSize=(200,200),**kwargs):/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
in _MolsToGridImage(mols, molsPerRow, subImgSize, legends,
highlightAtomLists, **kwargs) 334
highlights=highlightAtomLists[i]335 if mol is not None:-->
336img =
_moltoimg(mol,subImgSize,highlights,legends[i],**kwargs)337
res.paste(img,(col*subImgSize[0],row*subImgSize[1]))338 return

res/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
in _moltoimg(mol, sz, highlights, legend, **kwargs) 302 if not
hasattr(rdMolDraw2D,'MolDraw2DCairo'):303 img =
MolToImage(mol,sz,legend=legend,highlightAtoms=highlights, -->
304**kwargs) 305 else:306 nmol =

rdMolDraw2D.PrepareMolForDrawing(mol,kekulize=kwargs.get('kekulize',True))/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
in MolToImage(mol, size, kekulize, wedgeBonds, fitImage,
options, canvas, **kwargs) 132 #
color=(0,0,1),fill=False,stroke=True)133
font=Font(face='sans',size=12)-->
134canvas.addCanvasText(legend,pos,font)135 136 if

kwargs.get('returnCanvas',False):/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/spingCanvas.py
in addCanvasText(self, text, pos, font, color, **kwargs) 72
labelP = pos[0]-txtWidth/2+offset,pos[1]+txtHeight/273 color =
convertColor(color)--->
74self.canvas.drawString(text,labelP[0],labelP[1],font,color=color)75
return (bw,bh,offset)76

/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/PIL/pidPIL.py
in drawString(self, s, x, y, font, color, angle, **kwargs) 313
if '\n' in s or '\r' in s:314 self.drawMultiLineString(s, x,y,
font, color, angle, --> 315**kwargs) 316 return317 if not
font: font =

self.defaultFont/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/pid.py
in drawMultiLineString(self, s, x, y, font, color, angle,
**kwargs) 393 dy = h * math.cos(angle*math.pi/180.0)394 dx = h
* math.sin(angle*math.pi/180.0)--> 395s = string.replace(s,
'\r\n', '\n')396 s = string.replace(s, '\n\r', '\n')397 s =
string.replace(s, '\r', '\n')AttributeError: module 'string'
has no attribute 'replace'




-

Re: [Rdkit-discuss] multiline legend in MolsToGridImage

[Peter Gedeck]

Hello,

I thought we had removed all of these by now. I'll open an issue and fix
the code.

Best,

Peter


On Tue, Dec 20, 2016 at 6:01 AM David Hall  wrote:

> The replace and split methods were removed from the string module in
> python3. You can replace the code as follows:
>
> s = s.replace('\r\n', '\n')
> s = s.replace('\n\r', '\n')
> s = s.replace('\r', '\n')
> lines = s.split('\n')
>
>
> On Tue, Dec 20, 2016 at 2:45 AM, Pavel Polishchuk <
> pavel_polishc...@ukr.net> wrote:
>
> Hi,
>
>   I try to print multiline legends for molecules in a grid and use the
> following code from notebook
>
>   from rdkit import Chem
>   from rdkit.Chem import Draw
>   # from rdkit.Chem.Draw import IPythonConsole
>
>   mols = [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]
>   legends = ["1\nCCC", "2\nC"]
>   Draw.MolsToGridImage(mols, molsPerRow=5, subImgSize=(200,200),
> legends=legends)
>
>   it returns error: AttributeError: module 'string' has no attribute
> 'replace' (full stack is below)
>
>   If I uncomment IPythonConsole import then it returns the picture with
> labels, but with spaces instead of new line symbols.
>
>   What can I do in this situation? RDKit 2016.03.2
>
> Kind regards,
> Pavel.
>
>
> ---AttributeError
> Traceback (most recent call 
> last) in ()  1 mols = 
> [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]  2 legends = ["1\nCCC", 
> "2\nC"]> 3 p = Draw.MolsToGridImage(mols, molsPerRow=5, 
> subImgSize=(200,200), legends=legends)
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in MolsToGridImage(mols, molsPerRow, subImgSize, legends, 
> highlightAtomLists, useSVG, **kwargs)387   else:388   return 
> _MolsToGridImage(mols,molsPerRow=molsPerRow,subImgSize=subImgSize,--> 389 
> legends=legends, highlightAtomLists=highlightAtomLists, **kwargs) 
>390 391 def ReactionToImage(rxn, subImgSize=(200,200),**kwargs):
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in _MolsToGridImage(mols, molsPerRow, subImgSize, legends, 
> highlightAtomLists, **kwargs)334   highlights=highlightAtomLists[i]   
>  335 if mol is not None:--> 336   img = 
> _moltoimg(mol,subImgSize,highlights,legends[i],**kwargs)337   
> res.paste(img,(col*subImgSize[0],row*subImgSize[1]))338   return res
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in _moltoimg(mol, sz, highlights, legend, **kwargs)302 if not 
> hasattr(rdMolDraw2D,'MolDraw2DCairo'):303 img = 
> MolToImage(mol,sz,legend=legend,highlightAtoms=highlights,--> 304 
>  **kwargs)305 else:306 nmol = 
> rdMolDraw2D.PrepareMolForDrawing(mol,kekulize=kwargs.get('kekulize',True))
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in MolToImage(mol, size, kekulize, wedgeBonds, fitImage, options, canvas, 
> **kwargs)132 # 
> color=(0,0,1),fill=False,stroke=True)133 
> font=Font(face='sans',size=12)--> 134 
> canvas.addCanvasText(legend,pos,font)135 136   if 
> kwargs.get('returnCanvas',False):
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/spingCanvas.py
>  in addCanvasText(self, text, pos, font, color, **kwargs) 72 labelP = 
> pos[0]-txtWidth/2+offset,pos[1]+txtHeight/2 73 color = 
> convertColor(color)---> 74 
> self.canvas.drawString(text,labelP[0],labelP[1],font,color=color) 75 
> return (bw,bh,offset) 76
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/PIL/pidPIL.py
>  in drawString(self, s, x, y, font, color, angle, **kwargs)313 if 
> '\n' in s or '\r' in s:314   self.drawMultiLineString(s, x,y, font, 
> color, angle,--> 315**kwargs)316   
> return317 if not font: font = self.defaultFont
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/pid.py
>  in drawMultiLineString(self, s, x, y, font, color, angle, **kwargs)393   
>   dy = h * math.cos(angle*math.pi/180.0)394 
> dx = h * math.sin(angle*math.pi/180.0)--> 395 s = 
> string.replace(s, '\r\n', '\n')396 s = string.replace(s, 
> '\n\r', '\n')397 s = string.replace(s, '\r', '\n')
> AttributeError: module 'string' has no attribute 'replace'
>
>
>
>
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Re: [Rdkit-discuss] multiline legend in MolsToGridImage

[David Hall]

The replace and split methods were removed from the string module in
python3. You can replace the code as follows:

s = s.replace('\r\n', '\n')
s = s.replace('\n\r', '\n')
s = s.replace('\r', '\n')
lines = s.split('\n')


On Tue, Dec 20, 2016 at 2:45 AM, Pavel Polishchuk 
wrote:

> Hi,
>
>   I try to print multiline legends for molecules in a grid and use the
> following code from notebook
>
>   from rdkit import Chem
>   from rdkit.Chem import Draw
>   # from rdkit.Chem.Draw import IPythonConsole
>
>   mols = [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]
>   legends = ["1\nCCC", "2\nC"]
>   Draw.MolsToGridImage(mols, molsPerRow=5, subImgSize=(200,200),
> legends=legends)
>
>   it returns error: AttributeError: module 'string' has no attribute
> 'replace' (full stack is below)
>
>   If I uncomment IPythonConsole import then it returns the picture with
> labels, but with spaces instead of new line symbols.
>
>   What can I do in this situation? RDKit 2016.03.2
>
> Kind regards,
> Pavel.
>
>
> ---AttributeError
> Traceback (most recent call 
> last) in ()  1 mols = 
> [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]  2 legends = ["1\nCCC", 
> "2\nC"]> 3 p = Draw.MolsToGridImage(mols, molsPerRow=5, 
> subImgSize=(200,200), legends=legends)
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in MolsToGridImage(mols, molsPerRow, subImgSize, legends, 
> highlightAtomLists, useSVG, **kwargs)387   else:388   return 
> _MolsToGridImage(mols,molsPerRow=molsPerRow,subImgSize=subImgSize,--> 389 
> legends=legends, highlightAtomLists=highlightAtomLists, **kwargs) 
>390 391 def ReactionToImage(rxn, subImgSize=(200,200),**kwargs):
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in _MolsToGridImage(mols, molsPerRow, subImgSize, legends, 
> highlightAtomLists, **kwargs)334   highlights=highlightAtomLists[i]   
>  335 if mol is not None:--> 336   img = 
> _moltoimg(mol,subImgSize,highlights,legends[i],**kwargs)337   
> res.paste(img,(col*subImgSize[0],row*subImgSize[1]))338   return res
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in _moltoimg(mol, sz, highlights, legend, **kwargs)302 if not 
> hasattr(rdMolDraw2D,'MolDraw2DCairo'):303 img = 
> MolToImage(mol,sz,legend=legend,highlightAtoms=highlights,--> 304 
>  **kwargs)305 else:306 nmol = 
> rdMolDraw2D.PrepareMolForDrawing(mol,kekulize=kwargs.get('kekulize',True))
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py
>  in MolToImage(mol, size, kekulize, wedgeBonds, fitImage, options, canvas, 
> **kwargs)132 # 
> color=(0,0,1),fill=False,stroke=True)133 
> font=Font(face='sans',size=12)--> 134 
> canvas.addCanvasText(legend,pos,font)135 136   if 
> kwargs.get('returnCanvas',False):
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/spingCanvas.py
>  in addCanvasText(self, text, pos, font, color, **kwargs) 72 labelP = 
> pos[0]-txtWidth/2+offset,pos[1]+txtHeight/2 73 color = 
> convertColor(color)---> 74 
> self.canvas.drawString(text,labelP[0],labelP[1],font,color=color) 75 
> return (bw,bh,offset) 76
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/PIL/pidPIL.py
>  in drawString(self, s, x, y, font, color, angle, **kwargs)313 if 
> '\n' in s or '\r' in s:314   self.drawMultiLineString(s, x,y, font, 
> color, angle,--> 315**kwargs)316   
> return317 if not font: font = self.defaultFont
> /home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/pid.py
>  in drawMultiLineString(self, s, x, y, font, color, angle, **kwargs)393   
>   dy = h * math.cos(angle*math.pi/180.0)394 
> dx = h * math.sin(angle*math.pi/180.0)--> 395 s = 
> string.replace(s, '\r\n', '\n')396 s = string.replace(s, 
> '\n\r', '\n')397 s = string.replace(s, '\r', '\n')
> AttributeError: module 'string' has no attribute 'replace'
>
>
>
> 
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[Rdkit-discuss] multiline legend in MolsToGridImage

[Pavel Polishchuk]

Hi,

I try to print multiline legends for molecules in a grid and use the 
following code from notebook


  from rdkit import Chem
  from rdkit.Chem import Draw
  # from rdkit.Chem.Draw import IPythonConsole

  mols = [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]
  legends = ["1\nCCC", "2\nC"]
  Draw.MolsToGridImage(mols, molsPerRow=5, subImgSize=(200,200), 
legends=legends)


  it returns error: AttributeError: module 'string' has no attribute 
'replace'(full stack is below)


  If I uncomment IPythonConsole import then it returns the picture with 
labels, but with spaces instead of new line symbols.


  What can I do in this situation? RDKit 2016.03.2

Kind regards,
Pavel.


---
AttributeError Traceback (most recent call last)
  in() 1 mols = [Chem.MolFromSmiles(s) for s in ["CCC", "C"]]2 
legends = ["1\nCCC", "2\nC"]> 3p = Draw.MolsToGridImage(mols, 
molsPerRow=5, subImgSize=(200,200), 
legends=legends)/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py 
in MolsToGridImage(mols, molsPerRow, subImgSize, legends, 
highlightAtomLists, useSVG, **kwargs) 387 else:388 return 
_MolsToGridImage(mols,molsPerRow=molsPerRow,subImgSize=subImgSize, --> 
389legends=legends, highlightAtomLists=highlightAtomLists, **kwargs) 390 
391 def ReactionToImage(rxn, 
subImgSize=(200,200),**kwargs):/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py 
in _MolsToGridImage(mols, molsPerRow, subImgSize, legends, 
highlightAtomLists, **kwargs) 334 highlights=highlightAtomLists[i]335 if 
mol is not None:--> 336img = 
_moltoimg(mol,subImgSize,highlights,legends[i],**kwargs)337 
res.paste(img,(col*subImgSize[0],row*subImgSize[1]))338 return 
res/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py 
in _moltoimg(mol, sz, highlights, legend, **kwargs) 302 if not 
hasattr(rdMolDraw2D,'MolDraw2DCairo'):303 img = 
MolToImage(mol,sz,legend=legend,highlightAtoms=highlights, --> 
304**kwargs) 305 else:306 nmol = 
rdMolDraw2D.PrepareMolForDrawing(mol,kekulize=kwargs.get('kekulize',True))/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py 
in MolToImage(mol, size, kekulize, wedgeBonds, fitImage, options, 
canvas, **kwargs) 132 # color=(0,0,1),fill=False,stroke=True)133 
font=Font(face='sans',size=12)--> 
134canvas.addCanvasText(legend,pos,font)135 136 if 
kwargs.get('returnCanvas',False):/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/Chem/Draw/spingCanvas.py 
in addCanvasText(self, text, pos, font, color, **kwargs) 72 labelP = 
pos[0]-txtWidth/2+offset,pos[1]+txtHeight/273 color = 
convertColor(color)---> 
74self.canvas.drawString(text,labelP[0],labelP[1],font,color=color)75 
return (bw,bh,offset)76 
/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/PIL/pidPIL.py 
in drawString(self, s, x, y, font, color, angle, **kwargs) 313 if '\n' 
in s or '\r' in s:314 self.drawMultiLineString(s, x,y, font, color, 
angle, --> 315**kwargs) 316 return317 if not font: font = 
self.defaultFont/home/pavel/anaconda3/envs/my-rdkit-env/lib/python3.5/site-packages/rdkit/sping/pid.py 
in drawMultiLineString(self, s, x, y, font, color, angle, **kwargs) 393 
dy = h * math.cos(angle*math.pi/180.0)394 dx = h * 
math.sin(angle*math.pi/180.0)--> 395s = string.replace(s, '\r\n', 
'\n')396 s = string.replace(s, '\n\r', '\n')397 s = string.replace(s, 
'\r', '\n')AttributeError: module 'string' has no attribute 'replace'



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