Commits · b0ecf372f7ff268ac6f584ce89abc35ba7a485f5 · tsoc / openmm

04 Mar, 2015 2 commits
- Merge pull request #843 from peastman/ids · b0ecf372
  peastman authored Mar 03, 2015
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Added keepIds flag to PDBFile.writeFile()
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  b0ecf372
- Added keepIds flag to PDBFile.writeFile() · 6dc44c0e
  peastman authored Mar 03, 2015
  
  6dc44c0e
03 Mar, 2015 2 commits
- Merge pull request #842 from peastman/residue · 410674c0
  peastman authored Mar 03, 2015
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Fixed exception in addExtraParticles()
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  410674c0
- Fixed exception in addExtraParticles() · 36cdbc8d
  peastman authored Mar 03, 2015
  
  36cdbc8d
27 Feb, 2015 6 commits
- Merge pull request #839 from peastman/decode · 8d276c26
  peastman authored Feb 27, 2015
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PdbStructure handles byte streams correctly in Python 3
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  8d276c26
- Added test for binary PDB streams · 9fee45f9
  peastman authored Feb 27, 2015
  
  9fee45f9
- PdbStructure handles byte streams correctly in Python 3 · 8bcc9b3d
  peastman authored Feb 27, 2015
  
  8bcc9b3d
- Merge pull request #837 from peastman/rpmd · decb586c
  peastman authored Feb 27, 2015
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Created a barostat for use with RPMD
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  decb586c
- Merge pull request #836 from peastman/version · 083aeb3d
  peastman authored Feb 27, 2015
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Updated version number to 6.3
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  083aeb3d
- Updated version number to 6.3 · 4662beda
  peastman authored Feb 27, 2015
  
  4662beda
25 Feb, 2015 4 commits
- Merge pull request #834 from peastman/pvec · f816d961
  peastman authored Feb 25, 2015
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Further improvements to PNaCl vectors
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  f816d961
- Further improvements to PNaCl vectors · 49cc84c4
  peastman authored Feb 25, 2015
  
  49cc84c4
- Merge pull request #831 from peastman/pvec · 57045028
  peastman authored Feb 24, 2015
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Optimizations to PNaCl vectors
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  57045028
- Optimizations to PNaCl vectors · d51ad3c3
  peastman authored Feb 24, 2015
  
  d51ad3c3
24 Feb, 2015 5 commits
- Merge pull request #830 from peastman/pnacl · 8f39837a
  peastman authored Feb 24, 2015
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Fixed problems running in PNaCl
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  8f39837a
- Fixed problems running in PNaCl · aa7bd1cf
  peastman authored Feb 24, 2015
  
  aa7bd1cf
- Merge pull request #829 from peastman/state · e670188b
  peastman authored Feb 23, 2015
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Avoid throwing exceptions internally when serializing States
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  e670188b
- Avoid throwing exceptions internally when serializing States · e18eb785
  peastman authored Feb 23, 2015
  
  e18eb785
- Merge pull request #828 from peastman/cleanup · f11bafd9
  peastman authored Feb 23, 2015
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Cleanup to AMOEBA code
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  f11bafd9
23 Feb, 2015 2 commits
- Cleaned up formatting in AMOEBA code · d95b90b9
  peastman authored Feb 23, 2015
  
  d95b90b9
- Deleted more debugging code · a568bb12
  peastman authored Feb 23, 2015
  
  a568bb12
21 Feb, 2015 6 commits
- Merge pull request #827 from peastman/reference · 162d69a2
  peastman authored Feb 20, 2015
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Lots of cleanup to reference platform
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  162d69a2
- Deleted lots of debugging code · c44c956d
  peastman authored Feb 20, 2015
  
  c44c956d
- Cleaned up formatting of AMOEBA reference code · 41cd79a5
  peastman authored Feb 20, 2015
  
  41cd79a5
- Moved AMOEBA reference code into OpenMM namespace · 25a308e6
  peastman authored Feb 20, 2015
  
  25a308e6
- Deleted obsolete debugging code · f72062af
  peastman authored Feb 20, 2015
  
  f72062af
- Combined subfolders in reference source, and renamed a couple of badly named classes · 3d69185a
  peastman authored Feb 20, 2015
  
  3d69185a
20 Feb, 2015 13 commits
- Elimininated obsolete SimTKOpenMMCommon files · 0671c7b0
  peastman authored Feb 20, 2015
  
  0671c7b0
- Cleaned up lots of formatting to be more consistent with the rest of OpenMM · 7fb10336
  peastman authored Feb 20, 2015
  
  7fb10336
- Deleted obsolete logging class · 1d3ffd7b
  peastman authored Feb 20, 2015
  
  1d3ffd7b
- Moved reference platform classes into OpenMM namespace · 9111cca0
  peastman authored Feb 20, 2015
  
  9111cca0
- Merge pull request #826 from peastman/angles · 2379b982
  peastman authored Feb 20, 2015
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Fixed an incorrect unit conversion when constraining angles with AMOEBA
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  2379b982
- Fixed an incorrect unit conversion when constraining angles with AMOEBA · 89ab01de
  peastman authored Feb 20, 2015
  
  89ab01de
- Merge pull request #825 from peastman/remove · 8148f51d
  peastman authored Feb 20, 2015
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Added removeForce() and removeConstraint() to System
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  8148f51d
- Merge pull request #824 from swails/master · 252e03de
  peastman authored Feb 20, 2015
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Fix `unitcell.py`
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  252e03de
- Added removeForce() and removeConstraint() to System · 65d0449e
  peastman authored Feb 20, 2015
  
  65d0449e
- Fix names. · 7a60e434
  Jason Swails authored Feb 20, 2015
  
  7a60e434
- Merge branch 'master' of https://github.com/pandegroup/openmm · 245a7380
  Jason Swails authored Feb 19, 2015
  
  245a7380
- Add a reducePeriodicBoxVectors function, since many helpers (like the one in · fd1827e0
  Jason Swails authored Feb 19, 2015
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mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.
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  fd1827e0
- Fix bug in unitcell.py (computeLengthsAndAngles), which resulted in a NameError. · 1004e6e5
  Jason Swails authored Feb 19, 2015
```
Also added a test suite for them.
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  1004e6e5