1. 14 Jan, 2020 1 commit
  2. 13 Jan, 2020 1 commit
  3. 10 Jan, 2020 4 commits
  4. 07 Jan, 2020 1 commit
  5. 12 Dec, 2019 3 commits
  6. 19 Nov, 2019 1 commit
  7. 14 Nov, 2019 4 commits
  8. 13 Nov, 2019 1 commit
    • Studer Gabriel's avatar
      Combine positions with identifiers (flags) · f6665ef3
      Studer Gabriel authored
      Instead of only finding motifs based on positions, those positions have
      a flag in range [0,63] attached (default: 0). You can set whatever flag
      you want for each position but the basic idea is that you for example identify
      certain positions as "hydrogen bond donor", "charged" etc. You have to make
      sure by yourself that you use consistent flags in query and target.
      f6665ef3
  9. 09 Nov, 2019 2 commits
  10. 07 Nov, 2019 1 commit
  11. 06 Nov, 2019 3 commits
  12. 05 Nov, 2019 1 commit
    • Studer Gabriel's avatar
      decrease size of hash map · 6a4ff31c
      Studer Gabriel authored
      So far we used all possible triplets to construct triangles.
      But: p1,p2,p3 and p3,p2,p1 describe the exact same triangle.
      The trick is to shuffle the vertices p1, p2 and p3 in a way
      that following inequality holds for the edges a,b and c:
      a<=b<=c.
      This massively reduces the size of the hash map and saves memory
      while computing but also when saving a precomputed query to disk.
      Furthermore it reduces runtime.
      6a4ff31c
  13. 31 Oct, 2019 3 commits
  14. 30 Oct, 2019 3 commits
  15. 28 Oct, 2019 1 commit
  16. 25 Oct, 2019 1 commit
  17. 24 Oct, 2019 3 commits
    • Studer Gabriel's avatar
      Check for profiles being present in StructureDB in FillLoopsByDatabase · 3b61af1b
      Studer Gabriel authored
      Database features are now only used if mhandle AND the used StructureDB
      have profiles. If the mhandle has profiles attached but the StructureDB not,
      a warning is logged.
      3b61af1b
    • Studer Gabriel's avatar
      docu update · 25021ab5
      Studer Gabriel authored
      25021ab5
    • Studer Gabriel's avatar
      Simplify data access of StructureDB · 4a5e3670
      Studer Gabriel authored
      - Every getter function can now also extract information of a full
        entry at a certain index without the FragmentInfo detour.
      - Providing a sequence in GetBackboneList is not mandatory anymore.
        If not provided, the sequence of the returned backbone list
        defaults to the one that is stored in the underlying StructureDB
        instance
      4a5e3670
  18. 23 Oct, 2019 3 commits
  19. 22 Oct, 2019 1 commit
    • Studer Gabriel's avatar
      simplify value in MotifFinder hash map · e4783263
      Studer Gabriel authored
      If the number of elements in each query are known, I can infer
      query idx and triangle idx from one single integer. A custom type
      where I can set the two indices separately is therefore not necessary.
      e4783263
  20. 21 Oct, 2019 1 commit
    • Studer Gabriel's avatar
      update refinement of initial hits · 31557e0b
      Studer Gabriel authored
      Initial hits are refined using an iterative superposition. The initial
      transformation was determined by the position triplets of the underlying
      triangles. Turns out that the iterative superposition is more stable when
      using the positions from the triangles AND the target positions with their
      corresponding query matches from the hash map. Long story short:
      you want more positions in your initial superposition.
      31557e0b
  21. 19 Oct, 2019 1 commit