HI Lukas, I haven't done the build yet. I will see if I can manage to do one tomorrow.
These changes have been merged onto the trunk and will definitely be in the release. -greg On Tue, Mar 12, 2019 at 10:42 AM Lukas Pravda <lpra...@ebi.ac.uk> wrote: > Hi Greg, > > > > I was wondering If you managed to create the Mac build you were talking > about some time ago. Also I wonder If this functionality is going to be > part of the next RDKit release? > > > > Best, > > Lukas > > > > *From: *Greg Landrum <greg.land...@gmail.com> > *Date: *Tuesday, 5 February 2019 at 14:45 > *To: *Lukas Pravda <lpra...@ebi.ac.uk> > *Cc: *RDKIT mailing list <rdkit-discuss@lists.sourceforge.net> > *Subject: *Re: [Rdkit-discuss] Bond tags in SVGs > > > > Sure. I don't have my Mac with me, so that'll need to wait until I'm back > in Basel on the weekend. > > > > -greg > > > > > > > > On Tue, Feb 5, 2019 at 2:39 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote: > > If it is not too much trouble to ask, please build it for mac os (10.14.3) > python 3.6.x. > > > > Thanks! > > Lukas > > > > *From: *Greg Landrum <greg.land...@gmail.com> > *Date: *Tuesday, 5 February 2019 at 13:40 > *To: *Lukas Pravda <lpra...@ebi.ac.uk> > *Cc: *RDKIT mailing list <rdkit-discuss@lists.sourceforge.net> > *Subject: *Re: [Rdkit-discuss] Bond tags in SVGs > > > > > > > > On Tue, Feb 5, 2019 at 12:23 PM Lukas Pravda <lpra...@ebi.ac.uk> wrote: > > > > Thanks for this. It looks excellent!! Is there a way how I can test this? > Other than cloning and compiling the repository? So far I have been using > rdkit solely from python and its conda builds, so don’t really know how to > test it. > > > > At the moment you would need to get a copy of the repo and build it. I can > do a build so that it's conda-installable though. Which OS are you using? > > > > If I understand this correctly, the atom and bond class ids are added only > after TagAtoms() is called, or are they added at the ‘DrawMolecule()’ > stage? > > > > Bond classes are added as the bonds are written. Atom classes can only be > added at the TagAtoms() stage - there's not an object in the SVG for many > atoms without TagAtoms() being called. > > > > I can imagine a lot of possible scenarios and use cases with this new > functionality. However, in order to make the function TagAtoms() > sufficiently general, a bit more control over the javascript used in the > events would be needed. As a possible suggestions, I can imagine to pass as > the third parameter a lambda selector, which would in turn feed the JS > function with parameters to display names/charges/whatever. Also it would > be nice to have a mean how to pass dict of key-val properties for both > atoms and bonds so that you can incorporate related data into the svg. > > > > Having said that, in my opinion if svgs end up as a part of > html/javascript application, it is the best to expose this interactivity > directly from the client, rather than ‘pre-generating’ the behaviour on the > server. So I’m not sure If it is worth investing time into mimicking this > functionality in C++/python code, Whoever is in a need of generating > interactive svgs, can directly consume the svg string and modify it > according to their needs. > > > > Yeah, that's more or less what I was thinking. We want to write something > that can be reasonably easily modified after the fact to produce something > useful. > > > > > > To sum up, I think it should enough just to tag positions and identifiers > of atoms/bonds exactly as you do and possibly further extend them with a > mean how to pass some extra data to all of it. Then users can modify svgs > whichever way they want, but others might think differently. > > > > Excellent! > > > > -greg > > > > > > Best, > > Lukas > > *From: *Greg Landrum <greg.land...@gmail.com> > *Date: *Sunday, 3 February 2019 at 17:49 > *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, > > > > 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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