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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