Commits · b3143ff5b2917cd6729a636a060f0bd28d630f16 · schwede / ProMod3 · GitLab

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Mar 17, 2019
- Add SCWRL3 scoring function for sidechain modelling · b3143ff5
  Studer Gabriel authored 6 years ago
  b3143ff5
- Refactor rotamer construction · b0fd18f9
  Studer Gabriel authored 6 years ago
  b0fd18f9
Mar 09, 2019
- make Particle class agnostic of underlying energy function · 282b2ce2
  Studer Gabriel authored 6 years ago
  282b2ce2
Nov 30, 2018
- Apply Apache Version 2.0 License · f0e8b7c9
  Studer Gabriel authored 6 years ago
  
  f0e8b7c9
Oct 03, 2018
- replace Dunbrack lib by our own backbone dependent rotamer libary · d4805f58
  Studer Gabriel authored 6 years ago
  
  d4805f58
Dec 17, 2017
- Control with a flag, whether the CB atom should be counted as sidechain or backbone atom · afbd3969
  Studer Gabriel authored 7 years ago
  afbd3969
Aug 19, 2017
- Properly handle keep_sidechains flag in case of disulfid bonds · 81485e55
  Studer Gabriel authored 7 years ago
  81485e55
Mar 12, 2017
- move sidechain modelling pipelines into modelling module · d0a6e492
  Studer Gabriel authored 8 years ago
  
  d0a6e492
Jan 27, 2017
- Make optimize_subrotamers handling default. · 23aadc7d
  Gerardo Tauriello authored 8 years ago
  
  23aadc7d
Jan 19, 2017
- use FRM rotamer model in any case for cystein disulfid bond evaluation · 97662e57
  Studer Gabriel authored 8 years ago
  
  97662e57
- implement subrotamer optimizer in C · c1632429
  Studer Gabriel authored 8 years ago
  
  c1632429
Jan 18, 2017
- Allow to optimize subrotamers when FRM rotamer model is used in Reconstruct · 1975720f
  Studer Gabriel authored 8 years ago
  
  1975720f
- Implement a ToFrameResidue function for Rotamers · c41e3f4e
  Studer Gabriel authored 8 years ago
  
  c41e3f4e
Jan 17, 2017
- Optimize subrotamers if Flexible rotamers participate in disulfid bonds · d3dd47a2
  Studer Gabriel authored 8 years ago
  
  d3dd47a2
- resolve disulfid bond network · f9c38e9e
  Studer Gabriel authored 8 years ago
  f9c38e9e
Dec 01, 2016
- Code cleanup: remove consider_hbonds traces and fix comments. · cb15daea
  Gerardo Tauriello authored 8 years ago
  
  cb15daea
Nov 21, 2016
- Added parametrized graph.TreeSolve params for sidechain.Reconstruct · 587014e9
  Gerardo Tauriello authored 8 years ago
  
  587014e9
Nov 02, 2016
- get rid of the last traces of the evil RotamerSettings object · 559107c0
  Studer Gabriel authored 8 years ago
  
  559107c0
Nov 01, 2016
- update documentation of sidechain module · fe5f16fb
  Studer Gabriel authored 8 years ago
  
  fe5f16fb
Oct 30, 2016
- change frame.SetFrameEnergy(rot_group) to rot_group.SetFrameEnergy(frame) · 7e6c2cba
  Studer Gabriel authored 8 years ago
  
  7e6c2cba
Oct 20, 2016
- delegate the internal energy calculation to the rotamer constructors · 6af296e8
  Studer Gabriel authored 8 years ago
  6af296e8
Oct 19, 2016
- use SCWRLRotamerConstructor instead of the previous functions · 47b60874
  Studer Gabriel authored 8 years ago
  
  47b60874
Sep 30, 2016
- SCHWED-1421 : Added documentation for SidechainReconstructor. · cafcf25a
  Gerardo Tauriello authored 8 years ago
  
  cafcf25a
Sep 22, 2016
- several changes in graph solving algorithms · 598c7b6c
  Studer Gabriel authored 8 years ago
  598c7b6c
Sep 20, 2016
- refactoring rotamer graph solving by using generalized minimal width tree from core · 49044f37
  Studer Gabriel authored 8 years ago
  
  49044f37
Sep 07, 2016
- Code cleanup: dependency and layout · 480771dc
  Gerardo Tauriello authored 8 years ago
  
  480771dc
Aug 28, 2016
- Rename Graph in sidechain module to RotamerGraph to avoid confusion · 766f76c5
  Studer Gabriel authored 8 years ago
  
  766f76c5
May 24, 2016
- SCHWED-785 : added timers in various parts of the code. · fcf589ec
  Gerardo Tauriello authored 9 years ago
  
  fcf589ec
May 10, 2016
- SCHWED-877 : add heuristic frame residue constructors for ligands · fc8be251
  Gerardo Tauriello authored 9 years ago
  
  fc8be251
May 09, 2016
- SCHWED-877 : add special treatment for peptide ligands · 0797fe29
  Gerardo Tauriello authored 9 years ago
  
  0797fe29
May 04, 2016
- SCHWED-876 : Refactored reconstruct_sidechain to add consider_ligands flag · 2451a216
  Gerardo Tauriello authored 9 years ago
  
  2451a216
Apr 27, 2016
- SCHWED-872 : take over ligands of templates and (for now) ignore them while modelling · 76f1bfc9
  Gerardo Tauriello authored 9 years ago
  
  76f1bfc9
Mar 22, 2016
- SCHWED-775 : Assign backbone torsions in BackboneList::InsertInto · 856ca262
  Gerardo Tauriello authored 9 years ago
  
  856ca262
Mar 04, 2016
- Connect all atoms in the constructed sidechains · 73a95017
  Studer Gabriel authored 9 years ago
  
  73a95017
Jan 12, 2016
- cleanup of sidechain reconstruction script · ec28c353
  Studer Gabriel authored 9 years ago
  
  ec28c353
Dec 10, 2015
- refactor - move rawmodel to modelling · 940efe8e
  Gerardo Tauriello authored 9 years ago
  
  940efe8e
Dec 09, 2015
- refactor - removed reconstruct_sidechains module · cbdff1ef
  Gerardo Tauriello authored 9 years ago
  
  cbdff1ef
Nov 04, 2015
- two main changes · 418ce5a0
  Studer Gabriel authored 9 years ago
  418ce5a0
Jul 02, 2015
- Added possibility to keep all polar hydrogens after sidechain reconstruction · b476635d
  BIOPZ-Johner Niklaus authored 10 years ago
  
  b476635d
May 12, 2015
- Generalize backbone dependent rotamer library and add reader functionality · 722cfb1b
  Studer Gabriel authored 10 years ago
  722cfb1b