Hi Lukas, I had a chance to do a bit of work on this recently and I'd be interested to hear your feedback.
Bonds are now tagged with their bond IDs (using classes) and the "TagAtoms()" function now adds clickable transparent circles above each atom. These are also tagged with atom IDs using classes. TagAtoms() also lets you add callback functions for events associated with the atom circles. At the moment these are simply called with the atom id, but there's almost certainly a better way to do that. Suggestions are very welcome. Here's a gist showing what's currently on the branch: https://gist.github.com/greglandrum/d23517cb449003252cf09b5bd14d8637 On Tue, Dec 4, 2018 at 6:46 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote: > Hi Greg, > > > > that’s what I have been thinking, unlucky. Essentially, I want to color > the molecule in web-browser with various annotations and make it > interactive. For that part I’m converting it internally to the d3.js > internal representation (https://d3js.org/) and connecting it to its > environment. For most of the parts I’m just fine with the position of atoms > in svg using the tag property. > > > > What I wanted to avoid is to replicate rdkit svg drawing code in > javascript so that I don’t want to consume the dump of rdkit.Mol object. > What I wanted to do instead is to use existing svg images and parse them > into d3.js, so I know which paths belong to which bond. > > > > At this point my only idea is to color bonds individually and based on the > overlay/proximity use kd-tree to reverse-engineer which bonds the paths > belong to, which is a bit overkill in my view. > > > > Lukas > > > > > > *From: *Greg Landrum <greg.land...@gmail.com> > *Date: *Tuesday, 4 December 2018 at 17:24 > *To: *Lukas Pravda <lpra...@ebi.ac.uk> > *Cc: *RDKIT mailing list <rdkit-discuss@lists.sourceforge.net> > *Subject: *Re: [Rdkit-discuss] Bond tags in SVGs > > > > 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 > > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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