Hi Uli, There is an open issue on cdk/depict from Noel. I'll try and take a look this week but it's not quite as simple as you might think. For basic you would not want to align ring atoms to chain atoms, but also changes in hybridisation cause issues (e.g. a cumulene vs alkane might be mapped). Likewise you probably only want the largest continuous part aligned, what if there are disconnected parts, etc.
Here is how I've done it in the past in our (NextMove's) SmallWorld tool: https://gist.github.com/johnmay/b51fd51e2870554afa00ee75f668e91a You can see I try and balance how aggressive you want the alignment to me. On Wed, 17 Jan 2024 at 06:47, Uli Fechner <u...@pending.ai> wrote: > Hi, > > I would like to individually layout and then render several structures > that are similar to each other (e.g., share a scaffold). > > Is there a way to ensure that these structures are not rotated, that is, > that they are aligned in terms of their shared structural elements? > > And to take this one step further: ideally, I would like to do this using > CDKDepict using its REST API interface. But that might be a separate > question altogether. > > Any help is appreciated. > > Best > Uli > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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