Commits · 19f3102f7e5352880aea74ac20a78bfdc5f64c65 · tbgl / tools / mrdna · GitLab

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Feb 18, 2020
- SegmentModel.clear_strands() works for merged models · 19f3102f
  cmaffeo2 authored 5 years ago
  
  19f3102f
- Fixed angle potential spring constant; didn't have a significant effect on persistence length · 2dc76a9d
  cmaffeo2 authored 5 years ago
  
  2dc76a9d
- Added deprecated dummy modules for mrdna modules that have moved into arbdmodel · 7d59bb70
  cmaffeo2 authored 5 years ago
  
  7d59bb70
Oct 09, 2019
- Updated import paths to use arbdmodel instead of (model.arbdmodel, coords, model.nonbonded). · 5cb8536a
  cmaffeo2 authored 5 years ago
  
  5cb8536a
- Merge branch 'feat-arbdmodel' · 7bf73f95
  cmaffeo2 authored 5 years ago
  
  7bf73f95
- Sync with commit 94c8820 of arbdmodel package · 52323cd7
  cmaffeo2 authored 5 years ago
  
  https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel
  52323cd7
- Moved oxDNA from arbdmodel.py to segmentmodel.py · 205bb869
  cmaffeo2 authored 5 years ago
  
  205bb869
- Updated arbdmodel to commit 1578c98 from arbdmodel package · 79ff74f3
  cmaffeo2 authored 5 years ago
  
  https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel
  79ff74f3
- Initial copy of commit 5ed0da5 of arbdmodel package · abb67908
  cmaffeo2 authored 5 years ago
  
  https://gitlab.engr.illinois.edu/tbgl/tools/arbdmodel
  abb67908
- Moved files to arbdmodel directory · 9bb84883
  cmaffeo2 authored 5 years ago
  
  9bb84883
Sep 27, 2019
- Fixed grouped transforms in vHelix parser · a8ed3cac
  cmaffeo2 authored 5 years ago
  
  a8ed3cac
- Added sequence to vHelix parser · 465d369a
  cmaffeo2 authored 5 years ago
  
  465d369a
Sep 26, 2019
- Added test to check that model_from_basepair_stack_3prime works with circular... · f2260105
  cmaffeo2 authored 5 years ago
  
  Added test to check that model_from_basepair_stack_3prime works with circular ssDNA; removed warnings and made function work with lists instead of numpy arrays
  f2260105
- Ingore invalid argument to arccos when finding stack in segmentmodel_from_lists · e64fadf3
  cmaffeo2 authored 5 years ago
  
  e64fadf3
- Fixed polygon_mesh reader so that it works with user-generated .ma files, not... · 74d1ddf7
  cmaffeo2 authored 5 years ago
  
  Fixed polygon_mesh reader so that it works with user-generated .ma files, not just autogenerated ones
  74d1ddf7
- find_stacks routine moved to segmentmodel_from_lists using only coordinates... · 7b417c83
  cmaffeo2 authored 5 years ago
  
  find_stacks routine moved to segmentmodel_from_lists using only coordinates and transforms; generate stacks automatically if None kept old find_stacks routine in segmentmodel_from_pdb as find_stacks_mdanalysis
  7b417c83
- model_from_basepair_stack_3prime detects circular DNA strands; needs testing · abc6765e
  cmaffeo2 authored 5 years ago
  
  abc6765e
- Multiple improvements to validation model_from_basepair_stack_3prime · 6f9552db
  cmaffeo2 authored 5 years ago
  
  1) Passthrough of mrdna.segmentmodel arguments 2) Improved input validation 3) Stacks are removed unless stack[bp[stack]] == stack 4) Cleaner code for assigning ends of terminally-connected "segments"
  6f9552db
Sep 25, 2019
- Added maintainer variable to mrdna.version · afa963d2
  cmaffeo2 authored 5 years ago
  
  afa963d2
- Eliminated numpy log(0) error message when writing bond potentials, which is... · 7c4a0d67
  cmaffeo2 authored 5 years ago
  
  Eliminated numpy log(0) error message when writing bond potentials, which is caught anyway by .isnan
  7c4a0d67
- More restrictive condition for creating crossover dihedral potentials · 06d30673
  cmaffeo2 authored 5 years ago
  
  06d30673
- Accept log_file option for model.simulate() to redirect arbd stdout · 3404c828
  cmaffeo2 authored 5 years ago
  
  3404c828
Sep 05, 2019
- Update README.md · bd544678
  cmaffeo2 authored 5 years ago
  
  bd544678
Sep 04, 2019
- Increased default oxDNA minimization to 500 steps · ecfc517b
  cmaffeo2 authored 5 years ago
  
  ecfc517b
Aug 27, 2019
- Added _set_cadnano2_sequence method to SegmentModel · 3392db1a
  cmaffeo2 authored 5 years ago
  
  3392db1a
Aug 20, 2019
- Fixed sequence assignment in segmentmodel_from_lists · 4afd6909
  cmaffeo2 authored 5 years ago
  
  View commits for tag 0.4 0.4
  
  4afd6909
- Made intrahelical dsDNA bonds have geometric term subtracted · 4acb9595
  cmaffeo2 authored 5 years ago
  
  4acb9595
- Added temperature argument to mrdna · bd969cce
  cmaffeo2 authored 5 years ago
  
  bd969cce
- Extended WLCSKBond · 86565771
  cmaffeo2 authored 5 years ago
  
  86565771
- Added improved WLC model parameters for ssDNA, still imperfect · d150e38e
  cmaffeo2 authored 5 years ago
  
  d150e38e
Aug 13, 2019
- Prepared code structure in potential section so that dsDNA and ssDNA are... · b349e427
  cmaffeo2 authored 5 years ago
  
  Prepared code structure in potential section so that dsDNA and ssDNA are treated using separate defs
  b349e427
- Pass oxdna arguments during minimization · 3006dcba
  cmaffeo2 authored 5 years ago
  
  3006dcba
- Made oxDNA configuration writer use arbdmodel.debye_length if salt_concentration not provided · 7732a822
  cmaffeo2 authored 5 years ago
  
  7732a822
- Moved _connect_ends routine from 'DoubleStrandedSegment' to parent 'Segment' · 5455d407
  cmaffeo2 authored 5 years ago
  
  5455d407
- Added ability to add custom extra lines to BD file using extra_bd_file_lines attribute in arbdmodel · f506105a
  cmaffeo2 authored 5 years ago
  
  f506105a
- Added 'fix_linking_number' option to mrdna script; fixed bug in --debug option · 5bd0d211
  cmaffeo2 authored 5 years ago
  
  5bd0d211
- Slightly improved error when circular DNA is encountered · 42f941f9
  cmaffeo2 authored 5 years ago
  
  42f941f9
- Do better job selecting stack in pdb reader · 6c55001d
  cmaffeo2 authored 5 years ago
  
  6c55001d
- Fixed minor issues with segentmodel_from_lists · 466df3d2
  cmaffeo2 authored 5 years ago
  
  466df3d2
- Added support for circular structures in segmentmodel_from_lists · 76463bb3
  cmaffeo2 authored 5 years ago
  
  76463bb3