Re: [Rdkit-devel] drawing amino acids

[Igor Filippov]

Greg,

I figured out what the problem is:

getStringSize() calculates the pixel height/width of a given atom label.
For labels such as NH3+ the argument this function is getting is
NH3+

which makes for a very long sting, which throws off the scale calculation.
I am not sure why it works correctly with the drawers other than SVG but
for wxWidgets I need to clean from the label  , , , and

before computing the string width.

Hope this helps to someone who might have the same problem.

Best regards,
Igor




On Fri, Sep 8, 2017 at 8:29 AM, Igor Filippov 
wrote:

> Great - thanks, I'll try it!
>
> Igor
>
> On Fri, Sep 8, 2017 at 8:27 AM, Greg Landrum 
> wrote:
>
>>
>> On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov 
>> wrote:
>>
>>>

 Could it be that you didn't generate coordinates for the molecule?

 The result is the same for me whether I load the molecule from an SD
>>> file with coordinates, or generate 2D or 3D coordinates on the fly.
>>> Does it display correctly for you?
>>>
>>
>> Yeah, This snippet:
>>
>> In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)[NH3+]')
>>
>> In [22]: nm = Draw.PrepareMolForDrawing(m)
>>
>> In [23]: d = Draw.MolDraw2DCairo(200,200)
>>
>> In [24]: d.DrawMolecule(nm)
>>
>> In [25]: d.FinishDrawing()
>>
>> In [26]: open('blah.png','wb+').write(d.GetDrawingText())
>> Out[26]: 2730
>>
>>
>> Produces the png file that's attached.
>>
>>
>>> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
 about.

>>> I am doing it from c++, is there an equivalent there?
>>>
>>
>> Sure, here's some testing code that uses it:
>> https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cd
>> bff9b363d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
>>
>> There are a bunch of other examples in that file too.
>>
>> -greg
>>
>>
>
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Re: [Rdkit-devel] drawing amino acids

[Igor Filippov]

Great - thanks, I'll try it!

Igor

On Fri, Sep 8, 2017 at 8:27 AM, Greg Landrum  wrote:

>
> On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov 
> wrote:
>
>>
>>>
>>> Could it be that you didn't generate coordinates for the molecule?
>>>
>>> The result is the same for me whether I load the molecule from an SD
>> file with coordinates, or generate 2D or 3D coordinates on the fly.
>> Does it display correctly for you?
>>
>
> Yeah, This snippet:
>
> In [21]: m = Chem.MolFromSmiles('NC(=O)C(N)[NH3+]')
>
> In [22]: nm = Draw.PrepareMolForDrawing(m)
>
> In [23]: d = Draw.MolDraw2DCairo(200,200)
>
> In [24]: d.DrawMolecule(nm)
>
> In [25]: d.FinishDrawing()
>
> In [26]: open('blah.png','wb+').write(d.GetDrawingText())
> Out[26]: 2730
>
>
> Produces the png file that's attached.
>
>
>> BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know
>>> about.
>>>
>> I am doing it from c++, is there an equivalent there?
>>
>
> Sure, here's some testing code that uses it:
> https://github.com/rdkit/rdkit/blob/9af90524a41825b67ffb19cdbff9b3
> 63d5a7ca7e/Code/GraphMol/MolDraw2D/test1.cpp#L987
>
> There are a bunch of other examples in that file too.
>
> -greg
>
>
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Re: [Rdkit-devel] drawing amino acids

[Greg Landrum]

Hi Igor,

Could it be that you didn't generate coordinates for the molecule?

BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know about.

-greg


On Thu, Sep 7, 2017 at 2:16 PM, Igor Filippov 
wrote:

> Dear Colleagues,
>
> I seem to remember there already was a discussion about this,
> but I cannot find the relevant email thread, nor recall what was the
> conclusion.
>
> When I try to draw the following molecule I am getting an image of a few
> pixels in size, quite
> unusable.
>
> NC(=O)C(N)[NH3+]
>
> Has anyone else seen this problem?
>
> Best regards,
> Igor
>
>
> 
> --
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