Commits · f20a449ce30cb26f889343908cc85efcf8605935 · tbgl / tools / mrdna · GitLab

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Dec 03, 2020
- Fix to productpotential · f20a449c
  cmaffeo2 authored 4 years ago
  
  f20a449c
- Exposed seq_dep_file option for oxDNA · 4a48abc6
  cmaffeo2 authored 4 years ago
  
  4a48abc6
- Added external_forces_file option to simulate_oxdna · 55af01d1
  cmaffeo2 authored 4 years ago
  
  55af01d1
- Added option to exclude interhelical bonds from atomic ENM · 32ce45a6
  cmaffeo2 authored 4 years ago
  
  32ce45a6
- Added convenience function to Segments and SegmentModel to select blunt DNA ends · 97f92674
  cmaffeo2 authored 4 years ago
  
  97f92674
- Fixed ENM so it produces bonds across intrahelical connections · 64462997
  cmaffeo2 authored 4 years ago
  
  64462997
- Added one_bea_per_monomer option to generate_bead_model · 8fc5e3da
  cmaffeo2 authored 4 years ago
  
  8fc5e3da
Aug 20, 2020
- Added some convenience routines for pulling infomration from strands · a5651d9d
  cmaffeo2 authored 4 years ago
  
  a5651d9d
- Added support to arbdmodel for product potentials · 0d46571b
  cmaffeo2 authored 4 years ago
  
  0d46571b
- Updated bondAngle to be two angles, one bond · 5d01a8a5
  cmaffeo2 authored 4 years ago
  
  5d01a8a5
- Initial commit of bondAngle (one angle, two bonds) · 9f55d328
  cmaffeo2 authored 4 years ago
  
  9f55d328
Jul 28, 2020
- Fixed model_from_lists for 3'-to-5' structures; fixed issue with... · 7ffdf594
  cmaffeo2 authored 4 years ago
  
  Fixed model_from_lists for 3'-to-5' structures; fixed issue with single-nucleotide 'crossovers'; added debug flag for tracing strands
  7ffdf594
- Fixed oxDNA topology for circular strands; increased default max_backbone_force · 0befffbe
  cmaffeo2 authored 4 years ago
  
  0befffbe
Jun 10, 2020
- Made cadnano reader set azimuthal angle more accurately; some problems could... · c37732c5
  cmaffeo2 authored 4 years ago
  
  Made cadnano reader set azimuthal angle more accurately; some problems could arise with cadnano2 files that are saved in cadnano2.5 due to incorrect assignment of eulerZ in cadnano2.5
  c37732c5
- Made SegmentModel.get_location_at() search all location types, by default · 07e916b3
  cmaffeo2 authored 4 years ago
  
  07e916b3
- Added ability to apply a grid potential to just some particles · e9cbc62d
  cmaffeo2 authored 4 years ago
  
  e9cbc62d
- Removed os.sync() lines prior to running arbd/oxDNA simulations because they... · ca0cda9b
  cmaffeo2 authored 4 years ago
  
  Removed os.sync() lines prior to running arbd/oxDNA simulations because they can hang indefinitely; needs testing
  ca0cda9b
- Added lazy lookup of attributes from parents for ParticleType objects · d00d4bcf
  cmaffeo2 authored 4 years ago
  
  d00d4bcf
Jun 05, 2020
- Segmentmodel_from_lists will now guess stacks based on connectivity if not supplied · 1d5f21b8
  cmaffeo2 authored 4 years ago
  
  1d5f21b8
Apr 22, 2020
- Added routines for writing atomic bp restraints and for changing debye length · 4526e407
  cmaffeo2 authored 4 years ago
  
  4526e407
Mar 18, 2020
- Updated routines for removing DNA to optionally allow removing locations as well · 28d4d277
  cmaffeo2 authored 5 years ago
  
  28d4d277
Mar 09, 2020
- Added option for assigning hj equilibrium angle · a72a792f
  cmaffeo2 authored 5 years ago
  
  a72a792f
Mar 05, 2020
- Made an option for specifying a frame range for readAvgArbdCoords · 561b8d26
  cmaffeo2 authored 5 years ago
  
  View commits for tag 1.0a 1.0a
  
  561b8d26
Mar 03, 2020
- Fixed version script so it changes directories to version.__file__ · 45bbc767
  cmaffeo2 authored 5 years ago
  
  45bbc767
- Slightly updated routine for circular DNA in case beads overlap · 22534586
  cmaffeo2 authored 5 years ago
  
  22534586
Feb 28, 2020
- Fixed edge case with model_from_lists when circular helices have crossovers near their 'ends' · 6f40a20c
  cmaffeo2 authored 5 years ago
  
  6f40a20c
Feb 25, 2020
- Minor bug fix: Segment.rotate() provides numpy array of quaternions instead of list · 5e2b9f05
  cmaffeo2 authored 5 years ago
  
  5e2b9f05
- Improved atomic pdb basepair assignment by making distance metric symmetric... · 5d2010c5
  cmaffeo2 authored 5 years ago
  
  Improved atomic pdb basepair assignment by making distance metric symmetric and by assigning basepairs in order of quality of fit
  5d2010c5
Feb 24, 2020
- Various changes to make it easy to run circular structures · ee1e3264
  cmaffeo2 authored 5 years ago
  
  ee1e3264
Feb 21, 2020
- Option and commands to convert crossovers into intrahelical · 385f358c
  cmaffeo2 authored 5 years ago
  
  385f358c
- Made minimum automatic dimensions 1000 · e4583787
  cmaffeo2 authored 5 years ago
  
  e4583787
- 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