From: SourceForge.net <no...@so...> - 2009-11-23 12:16:10
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Patches item #2881374, was opened at 2009-10-18 19:18 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2881374&group_id=20024 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None >Group: Needs Revision Status: Open Resolution: None Priority: 5 Private: No Submitted By: gilleain maclean torrance (gilleain) >Assigned to: gilleain maclean torrance (gilleain) Summary: Re-write of the atom container permutation classes Initial Comment: The attached patches do two things: 1) Add a class called "Permutor" that generates arrays of ints like "[0,2,1]" 2) Re-writes the AtomContainer[Atom|Bond]Permutor classses to use this The reason for doing this is mainly for testing, as the provided permutation generator is more functionally rich. There are N! permutations of N things, so a molecule with 10 atoms has 10! or 3,628,800 permutations while one with 20 atoms has 2,432,902,008,176,640,000 - clearly far too many to test. What can be done with the Permutor class is randomly sample permutations by simply skipping ahead in the list. In addition, the ranking/unranking method that the class uses means it is possible to go to a particular permutation very easily. This is explained to some extent in the comments of the class. The commit hash is : commit 92b9bf22c1c06b33fb03dafe81715f04d37881f8 if that helps. ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2009-11-23 13:16 Message: Hi Gilleain, JavaDoc seems mostly fine, PMD I have not checked yet, but please add unit tests first. I have updated your original two patches to compile against master to compensate for the ILoggingTool patch, and added two patches with template code for you to complete: 0003: please add the year, publisher, ISBN and more if possible 0004: framework for the unit testing ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2009-11-23 12:56 Message: I am applying this patch, and currently doing several fixes... What I noticed so far: * use @cdk.cite and cheminf.bibx for references * unit tests! * missing unit test annotation * improper copyright statement (do not use CDK Project) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2881374&group_id=20024 |