Yes, I've just forked your repo, I should submit pull request tomorrow.
What about the first one (BTW: should be 'min' insted of 'max')?
On Thu, Jul 25, 2013 at 12:16 PM, Greg Landrum <[email protected]>wrote:
> Hi Michal,
>
> The second two of those, particularly the last one, are viable
> alternatives that are worth considering. The process would go faster if
> someone were to submit a pull request with a sample implementation (hint,
> hint).
>
> -greg
>
>
>
> On Thu, Jul 25, 2013 at 6:51 AM, Michał Nowotka <[email protected]> wrote:
>
>> I've looked into the code and have some questions:
>>
>> 1. Why not to change MolDrawing constructor to something like:
>>
>> def __init__(self,canvas=None):
>> self.canvas = canvas
>> if canvas:
>> self.canvasSize=canvas.size
>> if self.canvasSize:
>> self.dotsPerAngstrom = int(max(self.canvasSize) / 10)
>> self.atomPs = {}
>> self.boundingBoxes = {}
>>
>> 2. Why not to add MolDrawing as optional argument for methods like
>> MolToImage so then I can set my own values of 'dotsPerAngstrom',
>> 'useFraction', 'colorBonds' etc.
>>
>> 3. Even better - why not to extract drawing parameters like
>> 'dotsPerAngstrom', 'useFraction', 'colorBonds' etc. from MolDrawing to some
>> dict-like class (lets name it 'DrawingOptions') and add this class as an
>> optional parameter to MolDrawing constructor and all methods that construct
>> MolDrawing (MolToImage etc.)
>>
>> Without those changes customization of compound drawing is very limited.
>>
>>
>>
>> On Thu, Jul 25, 2013 at 11:10 AM, Michał Nowotka <[email protected]>wrote:
>>
>>> My mistake again. There is nothing like 'dotsPerAngstrom' in
>>> RDKit_2012_09_1. At least Draw, module doesn't have it. Also, Draw module
>>> doesn't contain 'MolDrawing' module...
>>>
>>>
>>> On Thu, Jul 25, 2013 at 11:06 AM, Michał Nowotka <[email protected]>wrote:
>>>
>>>> OK, i've found 'dotsPerAngstrom' in Draw.
>>>> Unfortunately setting it to any higher value (tried 60, 160, 660, 1000)
>>>> doesn't change anything...
>>>>
>>>>
>>>> On Thu, Jul 25, 2013 at 11:03 AM, Michał Nowotka <[email protected]>wrote:
>>>>
>>>>> I'm getting:
>>>>>
>>>>> Draw.MolDrawing.dotsPerAngstrom=60
>>>>> AttributeError: 'module' object has no attribute 'MolDrawing'
>>>>>
>>>>> I'm using RDKit_2012_09_1
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Jul 25, 2013 at 10:56 AM, Greg Landrum <[email protected]
>>>>> > wrote:
>>>>>
>>>>>>
>>>>>> On Thu, Jul 25, 2013 at 5:36 AM, Michał Nowotka <[email protected]>wrote:
>>>>>>
>>>>>>> When I do this:
>>>>>>>
>>>>>>> image = Draw.MolToImage(mol, size=(200, 200))
>>>>>>>
>>>>>>> I'm getting image with compound taking most of available canvas
>>>>>>> space. But this:
>>>>>>>
>>>>>>> image = Draw.MolToImage(mol, size=(500, 500))
>>>>>>>
>>>>>>> gives me an image with the compound of exact same size - it's just
>>>>>>> the canvas which is bigger. I guess this is because molfile already
>>>>>>> contains fixed 2D coordinates. Is there any possibility to regenerate it
>>>>>>> taking into account current image size?
>>>>>>>
>>>>>>
>>>>>> It's not the molfile.
>>>>>>
>>>>>> The class rdkit.Chem.Draw.MolDrawing.MolDrawing has a data member
>>>>>> called dotsPerAngstrom that is used as the "desired" number of pixels per
>>>>>> Angstrom in the drawing. This number is automatically reduced when a big
>>>>>> molecule is drawn onto a small canvas, but it is never increased in the
>>>>>> drawing code (by design).
>>>>>>
>>>>>> You can, however, change it on your own;
>>>>>> In [2]: from rdkit.Chem import Draw
>>>>>>
>>>>>> In [3]: Draw.MolDrawing.dotsPerAngstrom=60
>>>>>>
>>>>>> In [4]:
>>>>>> Draw.MolToImageFile(Chem.MolFromSmiles('c1ccccn1'),'blah.png',size=(500,500))
>>>>>>
>>>>>> Note: the dotsPerAngstrom value will still be reduced automatically
>>>>>> when rendering a large molecule.
>>>>>>
>>>>>> Hope this helps,
>>>>>> -greg
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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