Well the code/logic was already in there just not the convenience methods for a common case :-).
On Fri, 19 Jan 2024 at 13:38, Christoph Steinbeck < christoph.steinb...@gmail.com> wrote: > Brilliant :) > On the wish list for so long. > Thanks so much! > > Kind regards, > > Chris > > > > On 19. Jan 2024, at 13:13, John Mayfield <john.wilkinson...@gmail.com> > wrote: > > > > 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 FACSPolyomino Games – Programming Languages and Players > for Games and Puzzles -- 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 > > _______________________________________________ > > Cdk-user mailing list > > Cdk-user@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/cdk-user > >
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