Commits · 671f16053f14a6cb1e75ed64a3f618385f039b68 · tbgl / tools / mrdna

17 Sep, 2018 2 commits

Fixed multiple issues; 3-prime ends of nucleotides now terminate correctly;... · 671f1605

cmaffeo2 authored Sep 17, 2018

Fixed multiple issues; 3-prime ends of nucleotides now terminate correctly; strands not cleared unless atoms exist; strands regenerated with atomic model; cadnano models initialized with more correct azimuthal angle

671f1605

Added routines for applying grid potentials · b7c3f69d
cmaffeo2 authored Sep 17, 2018

b7c3f69d

15 Sep, 2018 1 commit
- Improved psf/pdb writer · 34556ed5
  cmaffeo2 authored Sep 15, 2018
  
  34556ed5
10 Sep, 2018 2 commits
- Update some camel case to be pythonic · 1d4edc3a
  cmaffeo2 authored Sep 10, 2018
  
  1d4edc3a
- Added 'directory' option to arbdmodel.simulate · 967b04d8
  cmaffeo2 authored Sep 10, 2018
  
  967b04d8
06 Sep, 2018 1 commit
- Moved null.dx into 'potentials' directory · 845b516c
  cmaffeo2 authored Sep 06, 2018
  
  845b516c
05 Sep, 2018 1 commit
- Renamed project to 'mrdna' · d291aa85
  cmaffeo2 authored Sep 05, 2018
  
  d291aa85
28 Aug, 2018 1 commit
- Moved modules to new locations; still need to update import statements and references to resources · 16fc597e
  cmaffeo2 authored Aug 28, 2018
  
  16fc597e
24 Aug, 2018 1 commit
- Fixed issue with PSF writer; fixed issue with orientation when no spline exists · e138ec52
  cmaffeo2 authored Aug 24, 2018
  
  e138ec52
21 Aug, 2018 1 commit
- Fixed psf writer for atomsitic simulations; add NAMD configuration writer; fixed bug with ENM · ac887d18
  cmaffeo2 authored Aug 21, 2018
  
  ac887d18
10 Aug, 2018 1 commit
- Added os.sync call to ensure all files are written before ARBD/NAMD run · 541789d7
  cmaffeo2 authored Aug 10, 2018
  
  541789d7
10 Jul, 2018 1 commit
- Fixed PDB writer to correctly include system dimensions and to write the segname to the pdb · 4412e203
  cmaffeo2 authored Jul 10, 2018
  
  4412e203
03 Jul, 2018 1 commit
- Removed mutable default arguments · 9c5c3cdf
  cmaffeo2 authored Jul 03, 2018
  
  9c5c3cdf
14 Jun, 2018 2 commits
- tmp commit of older work; changed how duplicate bonds are handled · 2175845a
  cmaffeo2 authored May 23, 2018
  
  2175845a
- Likely fixed most backmapping bugs · cf915a07
  cmaffeo2 authored May 16, 2018
  
  cf915a07
13 Jun, 2018 1 commit
- Fixed bugs in psf bond writing · dc623af9
  cmaffeo2 authored Jun 13, 2018
  
  dc623af9
05 Apr, 2018 2 commits
- Fixed how timestep is read · c73289a3
  New Tbgl User authored Apr 05, 2018
  
  c73289a3
- Fixed minor pdb/psf writing issues · c3cb9ecb
  New Tbgl User authored Apr 05, 2018
  
  c3cb9ecb
04 Apr, 2018 1 commit
- Updated arbdmodel writePdb and nucleotide generation · f87c6dfe
  cmaffeo2 authored Apr 03, 2018
  
  f87c6dfe
01 Apr, 2018 1 commit
- Fixed some small bugs · 1eb40b0b
  cmaffeo2 authored Apr 01, 2018
  
  1eb40b0b
30 Mar, 2018 1 commit
- Fixed numerous issues; code seems to work · 2161b99c
  cmaffeo2 authored Mar 27, 2018
  
  2161b99c
27 Mar, 2018 1 commit
- Working towards compatibility with cadnano structures; fixed some issues · daa829dd
  cmaffeo2 authored Mar 26, 2018
  
  daa829dd
23 Mar, 2018 1 commit
- Added all-atom model · fca5b912
  cmaffeo2 authored Mar 23, 2018
  
  fca5b912
22 Mar, 2018 1 commit
- Fixed some small bugs; updated intrahelical iteration to use linked-list... · bd20f326
  cmaffeo2 authored Mar 22, 2018
```
Fixed some small bugs; updated intrahelical iteration to use linked-list scheme; updated bead generation
```
  bd20f326
20 Mar, 2018 3 commits
- Initial implementation of splined positions/orientations in segmentModel · a36bc78c
  cmaffeo2 authored Mar 20, 2018
  
  a36bc78c
- arbdmodel now preserves particle order · 6457307f
  cmaffeo2 authored Mar 20, 2018
  
  6457307f
- arbdmodel now creates potentials directory · 47414bcf
  cmaffeo2 authored Mar 20, 2018
  
  47414bcf
02 Mar, 2018 1 commit
- Added parser for maya files and fixed some issues with segmentmodel · 314efe04
  cmaffeo2 authored Mar 02, 2018
  
  314efe04
01 Mar, 2018 1 commit
- Added models with twist · 287af0d9
  cmaffeo2 authored Feb 28, 2018
  
  287af0d9
28 Feb, 2018 1 commit
- Initial implementation of segmentmodel · d3361ce8
  cmaffeo2 authored Feb 28, 2018
  
  d3361ce8