Commits · 8dafa9f909fe83bfbe1fb6ba3ee281a2aa5c2ff2 · tbgl / tools / mrdna

15 Nov, 2018 2 commits
- Added support for harmonic restraints to arbdmodel.py · 8dafa9f9
  cmaffeo2 authored Nov 15, 2018
  
  8dafa9f9
- Fit nb interactions directly against Rau and Parsegian data in 20 Mm Mg, 200 mM Na · de7ef52d
  cmaffeo2 authored Nov 14, 2018
  
  de7ef52d
04 Nov, 2018 1 commit
- Added dihedral angle to DNA backbone for model with twist to obtain correct persistence length · ce97ef38
  cmaffeo2 authored Oct 27, 2018
  
  ce97ef38
17 Oct, 2018 3 commits
- Began to add support for replicas · e13731db
  cmaffeo2 authored Oct 17, 2018
  
  e13731db
- Fixed double-counting of contour length for angle potential · c7ef30bf
  cmaffeo2 authored Oct 17, 2018
  
  c7ef30bf
- Started implementing concentration-dependent nonbonded potentials · ee5c83db
  cmaffeo2 authored Oct 17, 2018
  
  ee5c83db
01 Oct, 2018 1 commit
- Automated versioning · 0ea91b45
  cmaffeo2 authored Oct 01, 2018
  
  0ea91b45
29 Sep, 2018 1 commit
- Fixed corner case for ssDNA in cadnano reader · e86685fe
  cmaffeo2 authored Sep 29, 2018
  
  e86685fe
28 Sep, 2018 1 commit
- Added _user_requested_quit to debug mode for mrdna script · 0e3c7a68
  cmaffeo2 authored Sep 28, 2018
  
  0e3c7a68
27 Sep, 2018 4 commits
- Added --debug option to mrdna script · f942e555
  cmaffeo2 authored Sep 27, 2018
  
  f942e555
- Fixed two issues with ssDNA cadnano reader. · 06033882
  cmaffeo2 authored Sep 27, 2018
```
First, ssDNA segments are now broken at crossovers
Second, ssDNA segments aren't allowed to stack intrahelically
```
  06033882
- Try--except different cadnano versions syntax · 5a5d0b24
  cmaffeo2 authored Sep 27, 2018
  
  5a5d0b24
- Added 'list' (.dat) file reader, fixed setting sequence in segmentmodel_from_lists_ · ae7cd244
  cmaffeo2 authored Sep 27, 2018
  
  ae7cd244
25 Sep, 2018 5 commits
- Fixed handling of --draw-* arguments for mrdna script · 3d3db5dd
  cmaffeo2 authored Sep 25, 2018
  
  3d3db5dd
- Fixed script handling of multiple suffixes · 947532fa
  cmaffeo2 authored Sep 25, 2018
  
  947532fa
- Fixed logic error for terminal sscrossover that placed the strand on the wrong side · 71f1af2c
  cmaffeo2 authored Sep 25, 2018
  
  71f1af2c
- Better placement of ends for cadnano_segments, especially for 1nt/1bp segments · 80d59148
  cmaffeo2 authored Sep 25, 2018
  
  80d59148
- More robust clear_all; removes other.particle · 17a5cd2f
  cmaffeo2 authored Sep 25, 2018
  
  17a5cd2f
23 Sep, 2018 3 commits
- Added tube representation · 9f582572
  cmaffeo2 authored Sep 23, 2018
  
  9f582572
- Fixed print statement in draw_cylinder · a38e19fc
  cmaffeo2 authored Sep 23, 2018
  
  a38e19fc
- Fixed some small issues with cadnano reader for ssDNA · 6a314a50
  cmaffeo2 authored Sep 23, 2018
  
  6a314a50
22 Sep, 2018 3 commits
- Fixed issue with quaternion orientations in segmentmodel_from_lists · 07ed55e0
  cmaffeo2 authored Sep 22, 2018
  
  07ed55e0
- Removed python debugger statement · cc4a7dd4
  cmaffeo2 authored Sep 22, 2018
  
  cc4a7dd4
- Reinstated fixed atoms for atomic simulations · a82c07bc
  cmaffeo2 authored Sep 22, 2018
  
  a82c07bc
21 Sep, 2018 5 commits
- Fixed how dimensions of all-atom structures are set · 9766a1ee
  cmaffeo2 authored Sep 21, 2018
  
  9766a1ee
- Improved readability of code for connection beads · 843a09f8
  cmaffeo2 authored Sep 21, 2018
  
  843a09f8
- Protect intrahelical beads from merging with crossovers · 0a7989b3
  cmaffeo2 authored Sep 21, 2018
  
  0a7989b3
- Added missing angle potential file · aedbdd90
  cmaffeo2 authored Sep 21, 2018
  
  aedbdd90
- remove_dna now removes sequence · ab3f6df3
  cmaffeo2 authored Sep 21, 2018
  
  ab3f6df3
20 Sep, 2018 5 commits
- Updated method for spring constant · 3cfec3ce
  cmaffeo2 authored Sep 20, 2018
  
  3cfec3ce
- Removed cache in resources · dbcd2764
  cmaffeo2 authored Sep 20, 2018
  
  dbcd2764
- Updated nonbonded cache code to take up less space · 740f7904
  cmaffeo2 authored Sep 20, 2018
  
  740f7904
- Updated nonbonded code so that it caches fits to "jj-nar-dna-pmf-100Mg.dat" · 9c4c1637
  cmaffeo2 authored Sep 20, 2018
  
  9c4c1637
- Improved fit for non-bonded potential to all-atom data · ea7ba628
  cmaffeo2 authored Sep 20, 2018
  
  ea7ba628
19 Sep, 2018 4 commits
- clear_atomic now clears sequences from segments when they are the wrong length · 4027b3ae
  cmaffeo2 authored Sep 19, 2018
  
  4027b3ae
- Changed how particles are named so that it no longer reflects the number of... · 78cb44eb
  cmaffeo2 authored Sep 19, 2018
```
Changed how particles are named so that it no longer reflects the number of nucleotides represented, but is more robust to clashes
```
  78cb44eb
- Added configuration file, reporting function and version to mrdna package · 4c1a3d1c
  cmaffeo2 authored Sep 19, 2018
  
  4c1a3d1c
- Added routines for inserting and removing DNA; made it so atomic simulation... · 87a37618
  cmaffeo2 authored Sep 18, 2018
```
Added routines for inserting and removing DNA; made it so atomic simulation doesn't resize model dimensions
```
  87a37618
18 Sep, 2018 2 commits
- Improved strand routing algorithm when a 5prime or 3prime location has a connection · 556b37e1
  cmaffeo2 authored Sep 18, 2018
  
  556b37e1
- edit draw cylinders function · 0087a6d2
  dwinogra authored Sep 18, 2018
  
  0087a6d2