Hi Lukas,
There's not currently a way to do this at the moment. The closest you can
get is by calling AddMoleculeMetadata():
In [6]: d = Draw.MolDraw2DSVG(200,200)
In [8]: d.DrawMolecule(nm)
In [10]: d.AddMoleculeMetadata(nm)
In [11]: d.FinishDrawing()
In [12]: svg = d.GetDrawingText()
In [14]: print(svg)
<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
xmlns='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='200px' height='200px' >
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='200' height='200'
x='0' y='0'> </rect>
<path d='M 9.09091,126.243 100,73.7568'
style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoi
n:miter;stroke-opacity:1' />
<path d='M 100,73.7568 190.909,126.243'
style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoi
n:miter;stroke-opacity:1' />
<metadata>
<rdkit:mol xmlns:rdkit = "http://www.rdkit.org/xml"; version="0.9">
<rdkit:atom idx="1" atom-smiles="[CH3]" drawing-x="9.09091"
drawing-y="126.243" x="-1.29904" y="-0.25" z="0" />
<rdkit:atom idx="2" atom-smiles="[CH2]" drawing-x="100" drawing-y="73.7568"
x="0" y="0.5" z="0" />
<rdkit:atom idx="3" atom-smiles="[CH3]" drawing-x="190.909"
drawing-y="126.243" x="1.29904" y="-0.25" z="0" />
<rdkit:bond idx="1" begin-atom-idx="1" end-atom-idx="2" bond-smiles="-" />
<rdkit:bond idx="2" begin-atom-idx="2" end-atom-idx="3" bond-smiles="-" />
</rdkit:mol></metadata>
</svg>
This gets you the information you need to connect bond indices to the
atoms, but I suspect that's not what you're looking for.
In general you are guaranteed that the order of the bonds in the output SVG
is the same as the order in the input molecule, but you can have multiple
paths for a given bond. For example here, where the end atoms have
different colors:
In [25]: print(svg)
<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
xmlns='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='200px' height='200px' >
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='200' height='200'
x='0' y='0'> </rect>
<path d='M 9.09091,100 59.1479,100'
style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:mi
ter;stroke-opacity:1' />
<path d='M 59.1479,100 109.205,100'
style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:mi
ter;stroke-opacity:1' />
<text x='109.205' y='107.5'
style='font-size:15px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text
-anchor:start;fill:#FF0000' ><tspan>OH</tspan></text>
<metadata>
<rdkit:mol xmlns:rdkit = "http://www.rdkit.org/xml"; version="0.9">
<rdkit:atom idx="1" atom-smiles="[CH3]" drawing-x="9.09091" drawing-y="100"
x="-0.75" y="5.55112e-17" z="0" />
<rdkit:atom idx="2" atom-smiles="[OH]" drawing-x="122.71" drawing-y="100"
x="0.75" y="-5.55112e-17" z="0" />
<rdkit:bond idx="1" begin-atom-idx="1" end-atom-idx="2" bond-smiles="-" />
</rdkit:mol></metadata>
</svg>
What are you looking to be able to do? That may make it easier to either
come up with a work around or figure out what a new feature addition might
look like.
-greg
On Mon, Dec 3, 2018 at 6:57 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote:
> Hi all,
>
>
>
> I was wondering if there is a way how you can tag <path> elements (bonds)
> in the svg created by rdkit.
>
>
>
> i.e. transform something like this:
>
> <path d='M 265.658,263.25 342.74,218.746' style='...' />
>
> <path d='M 342.74,218.746 419.822,174.241' style='...' />
>
>
>
> Into:
>
> <path bondId='1' d='M 265.658,263.25 342.74,218.746' style='...' />
>
> <path bondId='2' d='M 342.74,218.746 419.822,174.241' style='...' />
>
>
>
> Or similar. I’ve found possibility of tagging atoms in the SVG using
> Draw.rdMolDraw2D.MolDraw2DSVG.drawOptions() method that exposes property
> includeAtomTags. This then renders following additional elements into the
> SVG:
>
> rdkit:atom idx="4" label="O<sup>-</sup>" x="153.479" y="82.8259" />
>
>
>
> But I have not seen anything like this for bonds (latest release of RDKIT
> and python). Thanks, in advance for any hints. I was wondering about using
> *highlightBondLists* and then based on the svg infer the bond annotation,
> but that seems to be a bit of an overkill.
>
>
>
> Cheers,
>
> Lukas
>
>
>
>
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