https://github.com/cdk/cdk/pull/1032
Possibly some improvements could be made but should be reasonably flexible, I would make this the default on CDK depict. Best, On Wed, 17 Jan 2024 at 23:48, Uli Fechner <u...@pending.ai> wrote: > Thank you John, as always your answer is much appreciated. > > I came across this issue some years ago, so I am aware that this is > anything but simple. I'll certainly be very happy to test any > implementation and provide feedback :) > > Uli Fechner > > Senior Software Developer > > Pending AI > > > > u...@pending.ai > https://pending.ai/ > The National Innovation Centre, Suite 112, 4 Cornwallis St., NSW 2015, > Australia > > > On Thu, Jan 18, 2024 at 9:17 AM dpoly <da...@polyomino.com> wrote: > >> 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> >> 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> 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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