Brilliant :) On the wish list for so long. Thanks so much! Kind regards,
Chris > On 19. Jan 2024, at 13:13, John Mayfield <[email protected]> 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 <[email protected]> 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 > > > [email protected] > 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 <[email protected]> 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 <[email protected]> > Sent: Thursday, 18 January 2024 7:24 AM > To: Uli Fechner <[email protected]> > Cc: cdkuser <[email protected]> > 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 <[email protected]> > 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 <[email protected]> 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
