Commits · 3ccbd7fe7c6a569d04e776e3828d59f8697abb71 · tsoc / openmm · GitLab

03 Jan, 2016 2 commits
- Merge remote-tracking branch 'upstream/master' into forcefield-handlers · 3ccbd7fe
  John Chodera (MSKCC) authored Jan 02, 2016
  
  3ccbd7fe
- Added documentation of residue template generator with admonition that feature... · 01016dea
  John Chodera (MSKCC) authored Jan 02, 2016
```
Added documentation of residue template generator with admonition that feature is experimental and API is subject to change.
```
  01016dea
02 Jan, 2016 23 commits
- Clean up comments in TestForceField.py. · 4620cd7c
  John Chodera (MSKCC) authored Jan 02, 2016
  
  4620cd7c
- Fix alanine-dipeptide-explicit.pdb · 6155bdad
  John Chodera (MSKCC) authored Jan 02, 2016
  
  6155bdad
- Working on fixing issues with TestModeller caused by change of alanine-dipeptide-explicit.pdb · 384b89e8
  John Chodera (MSKCC) authored Jan 02, 2016
  
  384b89e8
- Attempt to fix travis test timeout. · ab4d2e2c
  John Chodera (MSKCC) authored Jan 02, 2016
  
  ab4d2e2c
- Fix alanine dipeptide example by including CRYST record in explicit; add... · 1d75fbfc
  John Chodera (MSKCC) authored Jan 02, 2016
```
Fix alanine dipeptide example by including CRYST record in explicit; add .inpcrd files for explicit and implicit.
```
  1d75fbfc
- Fix bug in _AtomType instantiation in ForceField. · 7ccab818
  John Chodera (MSKCC) authored Jan 02, 2016
  
  7ccab818
- Fix issue with simple ffxml StringIO in TestForceField. · 8190f59a
  John Chodera (MSKCC) authored Jan 02, 2016
  
  8190f59a
- Convert atom types from tuple to private inner class. · 92cde5ca
  John Chodera (MSKCC) authored Jan 02, 2016
  
  92cde5ca
- Refine error message on reading file. · c55636e2
  John Chodera (MSKCC) authored Jan 02, 2016
  
  c55636e2
- Add more informative error message when loading ffxml file fails. · 7b767ce4
  John Chodera (MSKCC) authored Jan 02, 2016
  
  7b767ce4
- Fixed simple ffxml file in TestForceField. · 3244fecf
  John Chodera (MSKCC) authored Jan 02, 2016
  
  3244fecf
- Added more helpful error messages when atom type lookup fails. · 48d99fee
  John Chodera (MSKCC) authored Jan 02, 2016
  
  48d99fee
- Modify TestForceField to use atom types instead of classes. · ab60c418
  John Chodera (MSKCC) authored Jan 01, 2016
  
  ab60c418
- Merge pull request #1314 from jchodera/fix-travis-restricted · 2b854804
  Robert T. McGibbon authored Jan 01, 2016
```
Fix travis following migration to legacy precise infrastructure.
```
  2b854804
- Bugfixes in TestForceField · 519d9deb
  John Chodera (MSKCC) authored Jan 01, 2016
  
  519d9deb
- Fix travis following migration to legacy precise infrastructure. · 9cd20029
  John Chodera (MSKCC) authored Jan 01, 2016
  
  9cd20029
- Bugfix in TestForceField tests of registerTemplateGenerator() · c2dd9975
  John Chodera (MSKCC) authored Jan 01, 2016
  
  c2dd9975
- Another travis fix attempt · 948fd273
  John Chodera (MSKCC) authored Jan 01, 2016
  
  948fd273
- 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
- More travis. · 9dd7fbd4
  John Chodera (MSKCC) authored Jan 01, 2016
  
  9dd7fbd4
- Try fixing travis again. · 9a6ec702
  John Chodera (MSKCC) authored Jan 01, 2016
  
  9a6ec702
- Bugfixes in Residue bond accessors and ForceField.createSystem() · 17e2b783
  John Chodera (MSKCC) authored Jan 01, 2016
  
  17e2b783
01 Jan, 2016 12 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
- Revert travis changes · ed60a4c7
  John Chodera (MSKCC) authored Jan 01, 2016
  
  ed60a4c7
- Another attempt to fix travis. · eb9a4b62
  John Chodera (MSKCC) authored Jan 01, 2016
  
  eb9a4b62
- Attempt to fix fglrx travis issues. · 15d92704
  John Chodera (MSKCC) authored Jan 01, 2016
  
  15d92704
- 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 2 commits
- Merge pull request #1285 from rafwiewiora/pdbfile_metals · 42d93901
  peastman authored Dec 28, 2015
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PDBFile - change behavior of connectivity to metals to that of PDBxFile
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  42d93901
- standardResidues · 130f9e95
  Rafal P. Wiewiora authored Dec 28, 2015
  
  130f9e95
24 Dec, 2015 1 commit
- Merge pull request #1310 from swails/gbfrc · 90886d43
  peastman authored Dec 24, 2015
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Change functions in `customgbforces.py` to subclasses
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  90886d43