Commits · b80eff3f8fdb13614bc4f1311afde6589ca09bbc · schwede / ProMod3 · GitLab

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Oct 04, 2016
- move all operations, that should lead to a gapless model into one function · b80eff3f
  Studer Gabriel authored 8 years ago
  b80eff3f
Aug 24, 2016
- SCHWED-1316 : catch NaN in energy minimization and abort. · 1007f6c7
  Gerardo Tauriello authored 8 years ago
  
  1007f6c7
Aug 18, 2016
- General cleanup of Python exports. · 3e034d2a
  Gerardo Tauriello authored 8 years ago
  
  3e034d2a
Aug 17, 2016
- Doc update: redesigned modelling module with new loop modelling code. · a8bba72a
  Gerardo Tauriello authored 8 years ago
  
  a8bba72a
Aug 12, 2016
- bugfix · c9a13edf
  Studer Gabriel authored 8 years ago
  
  c9a13edf
Aug 11, 2016
- SCHWED-1268 : Use scoring module in overall pipeline. · 2aa87fd2
  Gerardo Tauriello authored 8 years ago
  2aa87fd2
Aug 10, 2016
- directly connect OverallBackboneScorer with its BackboneScoreEnv to the ModellingHandle · 619cfbda
  Studer Gabriel authored 8 years ago
  
  619cfbda
Aug 09, 2016
- Small fixes and updated doc. · 601aa9fc
  Gerardo Tauriello authored 8 years ago
  
  601aa9fc
Jul 26, 2016
- make distance constraints useful · 884a473e
  Studer Gabriel authored 9 years ago
  
  884a473e
May 24, 2016
- SCHWED-785 : added timers in various parts of the code. · fcf589ec
  Gerardo Tauriello authored 9 years ago
  
  fcf589ec
May 19, 2016
- SCHWED-882 : tested that OpenMM CPU-platform-failure is properly caught with ext. force fields · 8d255672
  Gerardo Tauriello authored 9 years ago
  
  8d255672
May 17, 2016
- SCHWED-882 : tested external ff passing and added parameters to BuildFromRawModel · 16b611d7
  Gerardo Tauriello authored 9 years ago
  
  16b611d7
May 13, 2016
- SCHWED-882 : fixed return value of MinimizeModelEnergy · 3f99da8e
  Gerardo Tauriello authored 9 years ago
  
  3f99da8e
- SCHWED-882 : included externally parametrized ligands in energy minimization · 659edf1b
  Gerardo Tauriello authored 9 years ago
  
  659edf1b
May 12, 2016
- SCHWED-953 : Calpha traces and final models with less than 3 res report error... · e0a4dbaf
  Gerardo Tauriello authored 9 years ago
  e0a4dbaf
- SCHWED-954 : Fixed ring-punch fixing when neighboring residues are punched. · 51e7e0ff
  Gerardo Tauriello authored 9 years ago
  
  51e7e0ff
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
Apr 11, 2016
- SCHWED-843 : allow to call Phenix.MolProbity from PM3 · 4a817def
  Gerardo Tauriello authored 9 years ago
  
  4a817def
Mar 21, 2016
- Implemented fallback for OpenMM to use reference platform if CPU platform failing. · 14bb09b8
  Gerardo Tauriello authored 9 years ago
  
  14bb09b8
- SCHWED-779 : new default settings for minimize energy · e5bc85c0
  Gerardo Tauriello authored 9 years ago
  
  e5bc85c0
Mar 16, 2016
- Bugfix: ring-punch-fix was struggling with unclosed gaps. · 35d8ef84
  Gerardo Tauriello authored 9 years ago
  
  35d8ef84
Mar 10, 2016
- SCHWED-693 : Find and report stereo-chemical problems in final model. · 2e001106
  Gerardo Tauriello authored 9 years ago
  
  2e001106
Mar 08, 2016
- SCHWED-691 : added code to fix ring punches after building sidechains · aca35652
  Gerardo Tauriello authored 9 years ago
  
  aca35652
Mar 07, 2016
- SCHWED-676 : added code to detect ring punchings and report them for final model · 0f6ac979
  Gerardo Tauriello authored 9 years ago
  
  0f6ac979
Mar 02, 2016
- SCHWED-183 : minor logging update · f42c3a1f
  Gerardo Tauriello authored 9 years ago
  
  f42c3a1f
Feb 29, 2016
- SCHWED-368 : Faster OpenMM and allow (opt) usage of multiple CPUs. · bf881601
  Gerardo Tauriello authored 9 years ago
  
  bf881601
Feb 22, 2016
- SCHWED-679 : updated pipeline in BuildFromRawModel · 98fcf663
  Gerardo Tauriello authored 9 years ago
  
  98fcf663
- SCHWED-679 : Optimized loop closing strategy in default pipeline. · c9963b0a
  Gerardo Tauriello authored 9 years ago
  
  c9963b0a
Feb 19, 2016
- Doc and logging update to shorten pipeline code. · 02cce741
  Gerardo Tauriello authored 9 years ago
  
  02cce741
Feb 11, 2016
- Cleaned up python code · 286ec46b
  Gerardo Tauriello authored 9 years ago
  
  286ec46b
Feb 03, 2016
- Modelling update: tests, ClearGaps rewrite, doc · 4e4e8616
  Gerardo Tauriello authored 9 years ago
  
  4e4e8616
Feb 02, 2016
- Simplified BuildFromRawModel and updated doc · 38b630a1
  Gerardo Tauriello authored 9 years ago
  
  38b630a1
Jan 21, 2016
- Last resort functionality to close large deletions · 96c4464a
  Studer Gabriel authored 9 years ago
  
  96c4464a
Jan 12, 2016
- Manually assigning torsionhandles is not necessary anymore · 9c426a8b
  Studer Gabriel authored 9 years ago
  9c426a8b
Jan 04, 2016
- Test, doc and logging fixes · 3ff9bfb3
  Gerardo Tauriello authored 9 years ago
  
  3ff9bfb3
Dec 21, 2015
- minor fixes · bd716e83
  Gerardo Tauriello authored 9 years ago
  
  bd716e83
Dec 15, 2015
- moved pipeline into modelling (and tested, documented) · fe3fcf0f
  Gerardo Tauriello authored 9 years ago
  
  fe3fcf0f
Dec 14, 2015
- added modelling_pipeline steps · 6f424bc7
  Gerardo Tauriello authored 9 years ago
  
  6f424bc7