Commits · 2e1b1332213f3717067c79a4e73525d03a6d8483 · tbgl / tools / mrdna

Feb 18, 2020
- Merge branch 'dev' · 2e1b1332
  cmaffeo2 authored 5 years ago
  
  2e1b1332
- Sync with arbdmodel 4784882; syntax changes have not yet been propogated to SegmentModel · d3c116bf
  cmaffeo2 authored 5 years ago
  
  d3c116bf
- Added routines for obtaining a bounding box for a nanostructure · 28067c6b
  cmaffeo2 authored 5 years ago
  
  28067c6b
- 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
Jan 22, 2020

Fixed bug introduced in commit where ArbdModel.__init__ arguments were... · bb71bbfb

cmaffeo2 authored 5 years ago

Fixed bug introduced in commit 47b578f2 where ArbdModel.__init__ arguments were incorrectly provided by SegmentModel.__init__

bb71bbfb

Jan 07, 2020
- Fix from Will Kaufhold to add_nick routine when on_fwd_strand==False · 04cbde91
  Will Kaufhold authored 5 years ago and cmaffeo2 committed 5 years ago
  
  04cbde91
Jan 02, 2020
- Optionally run enrg-md simulations · f9d7ee2b
  cmaffeo2 authored 5 years ago
  
  f9d7ee2b
Dec 12, 2019
- Set origin of arbd box using structure in mrdna script · 47b578f2
  cmaffeo2 authored 5 years ago
  
  47b578f2
Dec 06, 2019
- mrdna script now recognizes list files for model creation · 11161c71
  cmaffeo2 authored 5 years ago
  
  11161c71
Nov 18, 2019
- Updated mrdna script to use dimensions of object for system · c6e082b9
  cmaffeo2 authored 5 years ago
  
  c6e082b9
Oct 31, 2019
- Update README.md · a80f8bf4
  cmaffeo2 authored 5 years ago
  
  a80f8bf4
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