This was a major issue for me too. I was trying to fix a starting config (such as a ring or backbone) and show visually the effect of progressively adding atoms or bonds or groups. Take a glucose molecule, deform it, add another, make sucrose (or fructose). It really doesn’t seem to be set up to make that at all easy.
Regards David M Bennett FACS _____ Polyomino Games – Programming Languages and Players for Games and Puzzles -- http://www.polyomino.com <http://www.polyomino.com/> From: John Mayfield <john.wilkinson...@gmail.com> Sent: Thursday, 18 January 2024 7:24 AM To: Uli Fechner <u...@pending.ai> Cc: cdkuser <cdk-user@lists.sourceforge.net> Subject: Re: [Cdk-user] structure layout alignment To clarify a bit more, CDK already has the APIs to "fix" part of a molecule. So you set the coordinates and then "fix" those atoms you can generate the rest. However you need to know which atoms to fix and what the coordinates should be. On Wed, 17 Jan 2024 at 20:23, John Mayfield <john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com> > wrote: 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 <mailto: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 <mailto:Cdk-user@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/cdk-user
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