René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Add standard documented way how to reduce structure to a subset of chains","articleBody":"...while setting all the metadata consistently and handling ligands intuitively (i.e. keeping the adjacent/bound ligands in).\r\n\r\nThe closest approximation of this functionality can be done via `new StructureName(\"4hhb.A\").reduce(structure)`, but:\r\n1. It is limited to a single chain in implementation and in the name format (this is the main concern),\r\n2. It is not clear if and how it works with structure files that don't have a pdb id (homology models, AlphaFold models, \"bare\" pdb files with just ATOM/HETATM records),\r\n3. This functionality is quite hidden. Adding a more visible method, for example to `StructureTools`, would go a long way.\r\n\r\nSome context to the point 3.: In version 5.4 there used to be a method `Structure getReducedStructure(Structure s, String chainId)` in [`StructureTools`](https://github.com/biojava/biojava/blob/9dcddeb0072ecc29aca8d8b1d43c3b18a430ac30/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java#L1286) (also limited to a single chain), but it was removed in favor of using `StructureIdentifier/StructureName` framework. However, this use is not documented (except in the tests, see `TestStructureName.java`) and furthermore it doesn't seem very intuitive to look into class called `StructureName` if I want to manipulate a structure's content. \r\n\r\nThe implementation of the method `getReducedStructure()` in version 5.4 shows that the process is quite involved and that it is easy to get it wrong if it is left for the users of the library.\r\n\r\nIf you decide to add this functionality, I'm happy to help with implementation/testing.","author":{"url":"https://github.com/rdk","@type":"Person","name":"rdk"},"datePublished":"2021-12-09T12:26:40.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":2},"url":"https://github.com/1003/biojava/issues/1003"}