Commits · aacf4cbad219cf0d396809ff9996e93bda2de5b2 · tbgl / tools / mrdna

Feb 21, 2020
- Added easy commands for ignoring long bonds during coarse-simulation · aacf4cba
  cmaffeo2 authored 5 years ago
  
  aacf4cba
- Fixed SegmentModel.count_crossovers() to include terminal_crossover connections · d64e2892
  cmaffeo2 authored 5 years ago
  
  d64e2892
Feb 19, 2020
- Deprecated SingleStrandedDNA.connect_5end · 03dc591c
  cmaffeo2 authored 5 years ago
  
  03dc591c
- Fixed small things broken by merge · e49c8d2e
  cmaffeo2 authored 5 years ago
  
  e49c8d2e
Feb 18, 2020
- Merge remote-tracking branch 'mrdna/master' · 17550c85
  cmaffeo2 authored 5 years ago
  
  17550c85
- 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
- Speed up model construction using lookup table for twist spring constants · 7fa86d81
  cmaffeo2 authored 5 years ago
  
  7fa86d81
- Reordered A/B in minimizeRmsd() to be consistent with supplied arguments; does... · f989063d
  cmaffeo2 authored 5 years ago
  
  Reordered A/B in minimizeRmsd() to be consistent with supplied arguments; does not affect return values
  f989063d
- Improved performance for segmentmodel._getParent() · f6b77677
  cmaffeo2 authored 5 years ago
  
  f6b77677
Feb 12, 2020
- Shift segment occupancies when extending segmentmodel · 83af8008
  cmaffeo2 authored 5 years ago
  
  83af8008
Feb 08, 2020
- Added mrdna message · 9dc9ecec
  cmaffeo2 authored 5 years ago
  
  9dc9ecec
- Added routines for getting bounding box · 0d65a721
  cmaffeo2 authored 5 years ago
  
  0d65a721
Feb 07, 2020

Made spring constant for twist between adjacent crossovers draw from a series of "springs": · 12f4edb6

cmaffeo2 authored 5 years ago

a) some intrinsic flexibility associated with the first crossover
b) the spring for the twist of the helix
c) intrinsic flexibility associated with the second crossover

12f4edb6

Improved potentials around crossovers · 62826908

cmaffeo2 authored 5 years ago

1) Proper accounting for a single bond representing a double crossover
2) Parallel-helix dihedral angle spring constant is now computed from three "springs" placed in series that represent:
a) the flexibility of the bond on one side of the crossover
b) the intrinsic flexibility of the crossover
c) the flexibility of the bond on the other side of the crossover

62826908

Added nonbonded exclusions between beads participating in crossovers within 3 bp of the crossover · fa4b1dae
cmaffeo2 authored 5 years ago

fa4b1dae
Distance between beads is now calculated more accurately · 803f652a
cmaffeo2 authored 5 years ago

803f652a

Jan 24, 2020
- Fixed sign error in geometric term for HarmonicBond · f45ec3be
  cmaffeo2 authored 5 years ago
  
  f45ec3be
- Fixed swapped origin/dimensions · 2300c876
  cmaffeo2 authored 5 years ago
  
  2300c876
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