Commits · c147e062a075a42b11bd5035a8a5133c3b0d3e9d · tsoc / openmm

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02 Jan, 2016 3 commits
- Fix broken TestTopology test. · c147e062
  John Chodera (MSKCC) authored Jan 01, 2016
  
  c147e062
- Fix uuid issue with TestForceField. · 1c603b1a
  John Chodera (MSKCC) authored Jan 01, 2016
  
  1c603b1a
- Bugfixes in Residue bond accessors and ForceField.createSystem() · 17e2b783
  John Chodera (MSKCC) authored Jan 01, 2016
  
  17e2b783
01 Jan, 2016 9 commits
- Bugfix in TestTopology · 28be5895
  John Chodera (MSKCC) authored Jan 01, 2016
  
  28be5895
- Bugfix in ForceField.registerTemplateGenerator() · 2efac76b
  John Chodera (MSKCC) authored Jan 01, 2016
  
  2efac76b
- Bugfix in _getResidueTemplateMatches · 138d74fb
  John Chodera (MSKCC) authored Jan 01, 2016
  
  138d74fb
- Fix bug in _getResidueTemplateMatches() · 007551a6
  John Chodera (MSKCC) authored Jan 01, 2016
  
  007551a6
- Refactor out nested function in ForceField.createSystem() · f14330ba
  John Chodera (MSKCC) authored Jan 01, 2016
  
  f14330ba
- Add tests for registering forcefield residue template generators. · 594196d4
  John Chodera (MSKCC) authored Jan 01, 2016
  
  594196d4
- Clean up interface for adding bonds to residue templates. · b98273c7
  John Chodera (MSKCC) authored Jan 01, 2016
  
  b98273c7
- Add methods to retrieve all bonds, internal bonds, and external bonds to Topology.Residue · 24d1a213
  John Chodera (MSKCC) authored Jan 01, 2016
  
  24d1a213
- Initial implementation of forcefield handlers · 928caf60
  John Chodera (MSKCC) authored Jan 01, 2016
  
  928caf60
28 Dec, 2015 1 commit
- standardResidues · 130f9e95
  Rafal P. Wiewiora authored Dec 28, 2015
  
  130f9e95
23 Dec, 2015 2 commits
- Pull parameter conversion into the CustomGBForce subclasses themselves. · fc22bf19
  Jason Swails authored Dec 23, 2015
  
  fc22bf19
- Fix parameter checking. · 4a27946c
  Jason Swails authored Dec 23, 2015
  
  4a27946c
21 Dec, 2015 2 commits
- Oops... add code mistakenly left over. · 0804c333
  Jason Swails authored Dec 21, 2015
  
  0804c333
- Convert CustomGBForce implementations of Amber models to subclasses. · 50c7b54c
  Jason Swails authored Dec 21, 2015
  
  50c7b54c
12 Dec, 2015 1 commit
- Add OpenCL to Appveyor and fix nosetests · a802dfc2
  Robert T. McGibbon authored Dec 10, 2015
  
  a802dfc2
10 Dec, 2015 1 commit
- revert changes to only not add bonds between metals and standard residues · 368f4dff
  Rafal P. Wiewiora authored Dec 10, 2015
  
  368f4dff
09 Dec, 2015 3 commits
- fix comment · d44805d7
  Rafal P. Wiewiora authored Dec 09, 2015
  
  d44805d7
- add removeBondsToMetals argument · aff6ab55
  Rafal P. Wiewiora authored Dec 09, 2015
  
  aff6ab55
- is not None · ce042c89
  Rafal P. Wiewiora authored Dec 08, 2015
  
  ce042c89
08 Dec, 2015 2 commits
- fix after final check · f2fc1353
  Rafal P. Wiewiora authored Dec 08, 2015
  
  f2fc1353
- PDBFile change metal bond behavior to that of PDBxFile · 10b9e98a
  Rafal P. Wiewiora authored Dec 08, 2015
  
  10b9e98a
25 Nov, 2015 1 commit
- add CONECT bonds for multimodel pdb files · a56ba941
  Rafal P. Wiewiora authored Nov 25, 2015
  
  a56ba941
20 Nov, 2015 4 commits
- Increased SHAKE iterations when positioning extra particles · 6bb532ac
  peastman authored Nov 20, 2015
  
  6bb532ac
- More clarification. · cb2ad95d
  Jason Swails authored Nov 20, 2015
  
  cb2ad95d
- Fix docstring. · 35adccb0
  Jason Swails authored Nov 20, 2015
  
  35adccb0
- Fix unit handling in switchDistance and add tests. · 9e934f69
  Jason Swails authored Nov 20, 2015
  
  9e934f69
19 Nov, 2015 3 commits
- Deleted GBVIForce · 14e78600
  Peter Eastman authored Nov 19, 2015
  
  14e78600
- Hopefully finished with supporting nucleotides in AMOEBA · 69d7dc4f
  peastman authored Nov 19, 2015
  
  69d7dc4f
- Fixed bugs that affected nucleotides in AMOEBA · 4daa1acb
  Peter Eastman authored Nov 19, 2015
  
  4daa1acb
17 Nov, 2015 1 commit

Fix #1213 addInteractionGroup should accept `set` values as parameters. · 43f07a1a

Philip_Tzou authored Nov 17, 2015

apparently SWIG typemaps maps Python's list but not set with std::set.
Instead, Python's `set` is mapped with `std::unordered_set`.

The original code of `swigInputBuilder.py` is kindly in a mess. Too much
lines in a single method `writeMethods` which causes debug becomes
difficult. Also there are a lot of warnings about
[PEP8](https://www.python.org/dev/peps/pep-0008/).

A refactoring in the future may be a good idea.

43f07a1a

13 Nov, 2015 2 commits
- AMD docstring · 4bbfd3d1
  Robert McGibbon authored Nov 13, 2015
  
  4bbfd3d1
- AMD docstring fix · f5499fbb
  Robert McGibbon authored Nov 12, 2015
  
  f5499fbb
11 Nov, 2015 2 commits
- Code review -- Python docstring fixes · 1db3314e
  Robert McGibbon authored Nov 11, 2015
  
  1db3314e
- Residue templates can specify atoms by name instead of index · 6391f721
  Peter Eastman authored Nov 11, 2015
  
  6391f721
07 Nov, 2015 1 commit
- Added missing support for LocalCoordinatesSite · 3e4f3866
  Peter Eastman authored Nov 06, 2015
  
  3e4f3866
06 Nov, 2015 2 commits
- Bug fix · eb1c5858
  Peter Eastman authored Nov 06, 2015
  
  eb1c5858
- ForceField will not create duplicate constraints · cb0fe1ba
  peastman authored Nov 06, 2015
  
  cb0fe1ba