In that case include the cdk-legacy module and use that version of SMSD. Here's the GIST I previously wrote to align to a subgraph:
https://gist.github.com/johnmay/12797a89f4186bc7da881f1f4a706671 On Wed, 14 Aug 2019 at 18:21, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > Hi John, > > Thanks for that info. I did look into SMSD, but found some problems using > it with the latest CDK [1,2]. > > Also, the maven version has not been updated since Jun 2016 so I wonder if > its still active? > > Let me know if you want help with the utility function you mention. Happy > to help, but not sure right now how to approach it. > > CDK rendering is so beautiful! > > Tim > > 1. https://github.com/asad/SMSD/issues/9 > 2. https://github.com/asad/SMSD/issues/10 > > > On 14/08/2019 16:05, John Mayfield wrote: > > 2. Use SMSD or Edmund Duesbury's MCS code. SMSD is a separate library now > as we couldn't smoothly integrate the updates and had tests failing. > > 3. You can fix atoms in place with the *Set<IAtom> afix* option of the > layout. So you copy the coords from MCS you got, fix these in place whilst > you lay out the rest. > > One day I will get around to adding a utility function for this but there > is some example code on the mailing list for No. 3, look for emails from > someone at Dotmatics albeit with a substructure match. > > On Tue, 13 Aug 2019 at 17:01, Tim Dudgeon <tdudgeon...@gmail.com> wrote: > >> I'm wanting to depict molecules that have been aligned to a the MCS of a >> query molecule, and highlight the MCS. >> Are there any examples of this? Seems like some of the relevant CDK code >> is deprecated, but its not clear what should be used. >> >> As an example: >> >> 1. I have a query molecule and a target molecule and they share >> significant MCS, often with the query being a complete subgraph of the >> target. >> >> 2. I identify the MCS >> >> 3. Using that MCS I layout the target molecule (e.g. generate 2D >> coordinates) fixing the parts that are in the MCS to the coordinates >> from the query structure. >> >> 4. I then depict that layed out molecule colouring the MCS. >> >> I know how to do #4 - its steps #2 and #3 that I'm unsure about. >> >> >> >> _______________________________________________ >> 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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