Commits · c3fc9b496fa054541b4cfb6aa693ab1ae0a3fcec · tbgl / tools / arbdmodel · GitLab

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Jul 17, 2023
- Fix setup script · c3fc9b49
  cmaffeo2 authored 1 year ago
  
  c3fc9b49
- Update setup.cfg · 63761a8b
  cmaffeo2 authored 1 year ago
  
  63761a8b
- Update polymer models; add grids · c4e3578e
  cmaffeo2 authored 1 year ago
  
  c4e3578e
Jul 13, 2023
- Many syntax updates · b24de6f9
  cmaffeo2 authored 1 year ago
  
  b24de6f9
Jul 11, 2023
- Renamed abstract_polymer to polymer · f10ad059
  cmaffeo2 authored 1 year ago
  
  f10ad059
- Remove old polymer.py · 3de7bae1
  cmaffeo2 authored 1 year ago
  
  3de7bae1
- Create RigidBody class · 3973fd72
  cmaffeo2 authored 1 year ago
  
  3973fd72
- Split arbdmodel into model and engine; changes numerous keywords · 56460994
  cmaffeo2 authored 5 years ago
  
  56460994
Mar 28, 2023
- Merge branch 'from-mrdna' · eb3d539c
  cmaffeo2 authored 1 year ago
  
  eb3d539c
- Committing things... · 1a6e08bc
  cmaffeo2 authored 1 year ago
  
  1a6e08bc
Feb 14, 2022
- Brought in changes from mrdna package, up to commit a7f370b · d9f7edd6
  cmaffeo2 authored 3 years ago
  
  d9f7edd6
Feb 18, 2020
- Added origin parameter to ArbdModel; made ArbdModel.atomic_simulate() call NAMD · 47848822
  cmaffeo2 authored 5 years ago
  
  47848822
Oct 10, 2019
- Started renaming some keywords · 66d0b785
  cmaffeo2 authored 5 years ago
  
  66d0b785
Oct 09, 2019
- Merge branch 'from-mrdna' · 94c8820d
  cmaffeo2 authored 5 years ago
  
  94c8820d
- Brought in changes from mrdna package to arbdmodel.py from commits 8dafa9f..205bb86 · 02b65fe7
  cmaffeo2 authored 5 years ago
  
  02b65fe7
Jul 23, 2019
- Added basic support for rigid body groups made out of particles · 1578c981
  cmaffeo2 authored 5 years ago
  
  1578c981
- Fixed error in ssDNA model where the terminal dihedral angle was not applied. · 17f8c66a
  cmaffeo2 authored 5 years ago
  
  Added PointerParticle.duplicate()
  17f8c66a
- Improved error checking for arbd in model.simulate() with dry_run=True · 54c51b6e
  cmaffeo2 authored 5 years ago
  
  54c51b6e
Jul 11, 2019
- Improved Parent member functions for adding/removing/inserting children · 8e2fe4f0
  cmaffeo2 authored 5 years ago
  
  8e2fe4f0
- Added dry_run option to model.simulate · 3ab6264b
  cmaffeo2 authored 5 years ago
  
  3ab6264b
Jul 08, 2019
- Added freely jointed chain model · 964584aa
  cmaffeo2 authored 5 years ago
  
  964584aa
- Fixed incorrect name of Leucine from LUE to LEU · 4482eaab
  cmaffeo2 authored 5 years ago
  
  4482eaab
- Added Kim-Hummer model from R. Best's paper 10.1371/journal.pcbi.1005941 · 9635a94e
  cmaffeo2 authored 5 years ago
  
  9635a94e
May 14, 2019
- Added exclusion for intranucleotide P-B bond · b6253e16
  cmaffeo2 authored 5 years ago
  
  b6253e16
Apr 18, 2019
- Set more conservative default pairlistDistance/deompPeriod · 23f963ed
  cmaffeo2 authored 5 years ago
  
  23f963ed
Apr 05, 2019
- Implemented Onck model from Ghavami2014 · 2e3326aa
  cmaffeo2 authored 5 years ago
  
  2e3326aa
- Added support for restart_file · 99b3e224
  cmaffeo2 authored 5 years ago
  
  99b3e224
- Updated HarmonicPotential in interactions.py to more easily allow overriding · fe9db433
  cmaffeo2 authored 6 years ago
  
  fe9db433
- Updated treatment of mass in PDB/PSF writer when this information is missing · 9bfc123b
  cmaffeo2 authored 6 years ago
  
  9bfc123b
Mar 22, 2019
- Made type longer for psf · 13ab973c
  cmaffeo2 authored 6 years ago
  
  13ab973c
- Fixed implementation of HPS model, improved psf/pdb writing · 0b4d1a5b
  cmaffeo2 authored 6 years ago
  
  0b4d1a5b
- Added implementation of Robert Best's HPS model · eeb4bf76
  cmaffeo2 authored 6 years ago
  
  eeb4bf76
- Added ssDNA model · 13c7c2f3
  cmaffeo2 authored 6 years ago
  
  13c7c2f3
- Began refactoring segmentmodel.py · 6161100d
  cmaffeo2 authored 6 years ago
  
  6161100d
- Renamed segmentmodel.py to abstract_polymer.py · 932328f8
  cmaffeo2 authored 6 years ago
  
  932328f8
- Added coords.py from mrdna · 948ff295
  cmaffeo2 authored 6 years ago
  
  948ff295
Jan 24, 2019
- Update README.md · c0af9d42
  cmaffeo2 authored 6 years ago
  
  c0af9d42
- Initial commit · 5ed0da54
  cmaffeo2 authored 6 years ago
  
  View commits for tag 0.1 0.1
  
  5ed0da54