Re: [Rdkit-discuss] Reaction Arrows

[Greg L. <gre...@gm...>]

Hi Libby,

On Tue, Jan 23, 2018 at 11:19 PM, Phipps, Elizabeth C <eph...@tu...>
wrote:

>
> Thank you for the response. Just to clarify, your thought process is that
> once you get the location/index of atoms you could be able to add in arrows
> in specific locations?
>

Yeah. It's not the nicest solution, but it will likely work.


> While trying to implement your code, an error with DrawReaction occurred:
>
> AttributeError: 'MolDraw2DSVG' object has no attribute 'DrawReaction'
>
>
> We cannot find a solution because DrawReaction seems to be an attribute to
> MolDraw2DSVG. Do you have any ideas as to why this error occurs?
>
>
Could it be that you're using an older version of the RDKit? That feature
was added as part of the 2017.09 release:

In [4]: rdkit.__version__
Out[4]: '2017.09.1'

In [5]: rdMolDraw2D.MolDraw2DSVG.DrawReaction
Out[5]: <function MolDraw2D.DrawReaction>

Best,
-greg



> Thanks,
> Libby
>
> On Dec 5, 2017, at 10:49 AM, Greg Landrum <gre...@gm...> wrote:
>
> Hi Libby,
>
> There's not currently anything directly available to do this, but some
> pieces that might help are sort of there.
>
> You could imagine getting drawings of the reactions as SVG and then adding
> the arrows that indicate the mechanism to that.
> In order to do this, you'd likely want to be able to figure out where the
> atoms are in the SVG. This is mostly possible, if in an ugly way.
>
> Here's an example, which I'll explain below:
>
> In [6]: rxn = AllChem.ReactionFromSmarts('C=CCBr.[I-]>>C=CCI.[Br-]',
> useSmiles=True)
>
> In [12]: canv = rdMolDraw2D.MolDraw2DSVG(300,300)
>
> In [13]: canv.drawOptions().includeAtomTags = True
>
> In [14]: canv.DrawReaction(rxn)
>
> In [15]: canv.FinishDrawing()
>
> In [16]: print(canv.GetDrawingText())
> <?xml version='1.0' encoding='iso-8859-1'?>
> <svg:svg version='1.1' baseProfile='full'
>               xmlns:svg='http://www.w3.org/2000/svg'
>                       xmlns:rdkit='http://www.rdkit.org/xml'
>                       xmlns:xlink='http://www.w3.org/1999/xlink'
>                   xml:space='preserve'
> width='300px' height='300px' >
> <svg:rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='300'
> height='300' x='0' y='0'> </svg:rect>
> <rdkit:atom idx="1" x="13.6364" y="151.983" />
> <rdkit:atom idx="2" x="33.6927" y="143.449" />
> <rdkit:atom idx="3" x="51.1119" y="156.551" />
> <rdkit:atom idx="4" label="Br" x="71.1682" y="148.017" />
> <rdkit:atom idx="5" label="I<sup>-</sup>" x="100.23" y="150" />
> <rdkit:atom idx="6" x="194.682" y="151.983" />
> <rdkit:atom idx="7" x="214.739" y="143.449" />
> <rdkit:atom idx="8" x="232.158" y="156.551" />
> <rdkit:atom idx="9" label="I" x="252.214" y="148.017" />
> <rdkit:atom idx="10" label="Br<sup>-</sup>" x="281.276" y="150" />
> <svg:path d='M 14.4898,153.989 34.5461,145.455' style='fill:none;fill-rule:
> evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;
> stroke-linejoin:miter;stroke-opacity:1' />
>
>  ... SNIP ...
>
>
> <svg:path d='M 169.98,148.063 172.886,150' style='fill:none;fill-rule:
> evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;
> stroke-linejoin:miter;stroke-opacity:1' />
> </svg:svg>
>
>
> Notice the rdkit:atom properties there. Those are the positions of the
> corresponding atoms in the output SVG.
> The ugliness comes due to the fact that, currently at least, you get these
> in increasing order with no indication of whether they belong to an
> reactant (and if so, which reactant) or a product (and if so, which
> product). You are safe assuming that the reactants are output in order,
> followed by the products, and that the atoms within each are output in
> order. So atom idx 1 above is atom 0 in the first reactant, atom idx 5 is
> atom 0 in the second reactant, atom idx 7 is atom 1 in the first product,
> etc.
> I'm going to think about ways to make this output a bit easier to handle
> for reactions (suggestions appreciated), but that's what is currently there.
>
> It's also worth thinking about what the API would look like to add the
> arrows directly
>
> Apologies that this isn't straightforward, but this may be enough to get a
> start?
>
> -greg
>
>
>
>
>
> On Tue, Dec 5, 2017 at 4:27 PM, Phipps, Elizabeth C <eph...@tu...>
> wrote:
>
>> Hi,
>>
>> The goal is to help students visualize reactions and to do so we have
>> been working to figure out how to get reaction arrows in the reaction
>> output. We cannot seem to find much information as to whether it is
>> possible to have the output (a visual organic reaction) contain reaction
>> arrows using RDKit with SMILES and SMIRKS even though some examples have
>> arrows.
>> I am wondering if there is any further information as to whether it is
>> possible to show reaction arrows.
>>
>> For example:
>> <Screen Shot 2017-12-04 at 11.37.31 AM.png>
>>
>> Thanks,
>> Libby
>>
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>
>