Commits · 328134781069b0a73999f77e308569ea7466a0f0 · tsoc / openmm

01 Nov, 2016 1 commit
- Add Bohrs to units · 32813478
  Robert T. McGibbon authored Nov 01, 2016
  
  32813478
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
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
05 Nov, 2015 3 commits
- Whoops · 48d5437f
  Robert McGibbon authored Nov 05, 2015
  
  48d5437f
- Fix some return values · 8b4a921e
  Robert McGibbon authored Nov 05, 2015
  
  8b4a921e
- Fix some of the return values · f07ac7bd
  Robert McGibbon authored Nov 05, 2015
  
  f07ac7bd
04 Nov, 2015 3 commits
- Fix more python docstrings, especially __init__ functions · bed427e7
  Robert McGibbon authored Nov 03, 2015
  
  bed427e7
- Fix forcefield.py · d3150755
  Robert McGibbon authored Nov 03, 2015
  
  d3150755
- Fix modeller docstring · 6cf90704
  Robert McGibbon authored Nov 03, 2015
  
  6cf90704
03 Nov, 2015 4 commits
- addExtraParticles() can use bonds to select positions · bc41b7a0
  Peter Eastman authored Nov 03, 2015
  
  bc41b7a0
- Update docstrings in amd.py and mtsintegrator.py · 856aab50
  Robert McGibbon authored Nov 02, 2015
  
  856aab50
- Improve docstrings · 98d053d4
  Robert McGibbon authored Oct 30, 2015
```
Swigged python docstrings now include documented return values and type
information or their arguments. They are generated in numpydoc format.
Furthermore, all of the Python app layer docstrings have been changed
to numpydoc format. The filterPythonFiles.py script which helps to
generate the Doxygen Python API docs has been updated to reflect these
changes.
```
  98d053d4
- Added neutralize option to addSolvent() · 85b0ef02
  Peter Eastman authored Nov 02, 2015
  
  85b0ef02
28 Oct, 2015 1 commit
- Support residue template parameters for CustomManyParticleForce · 1f7985e7
  peastman authored Oct 28, 2015
  
  1f7985e7
26 Oct, 2015 4 commits
- Fix typo in getNumAtoms() and getNumResidues() implementation · d74e4789
  John Chodera (MSKCC) authored Oct 26, 2015
  
  d74e4789
- Grumble grumble · 59899650
  John Chodera (MSKCC) authored Oct 26, 2015
  
  59899650
- Simplify Topology.getNumChains() · b5330c31
  John Chodera (MSKCC) authored Oct 26, 2015
  
  b5330c31
- Add getNumAtoms(), getNumResidues(), and getNumChains() to simtk.openmm.app.Topology · 73cfcd68
  John Chodera (MSKCC) authored Oct 26, 2015
  
  73cfcd68
09 Oct, 2015 2 commits
- Per-atom parameters can be taken from residue templates · 65a581bf
  peastman authored Oct 09, 2015
  
  65a581bf
- Add code supporting input with and without units for CharmmPsfFile. · 6b2aa2cc
  Jason Swails authored Oct 09, 2015
```
Add relevant tests (that used to fail). This also fixes a subtle bug where
switching functions were not applied when NBFIXes were specified.
```
  6b2aa2cc
08 Oct, 2015 2 commits
- add switchdistance= to AmberPrmtopFile · a1113e7b
  M J Harvey authored Oct 08, 2015
  
  a1113e7b
- add switchDistance to AmberPrmtopFile constructor · 0b75181b
  M J Harvey authored Oct 08, 2015
  
  0b75181b
07 Oct, 2015 1 commit
- add kwargs to constructor · d6710744
  M J Harvey authored Oct 07, 2015
  
  d6710744
06 Oct, 2015 3 commits
- removed permissive arg on constructor to keep python 2 happy · b2900404
  M J Harvey authored Oct 07, 2015
  
  b2900404
- fix use of permissive · 3dee925d
  M J Harvey authored Oct 07, 2015
  
  3dee925d
- Add permissive flag to permit undefined atomtypes when reading charmm parameter files · 8a6c98c2
  M J Harvey authored Oct 06, 2015
  
  8a6c98c2
27 Aug, 2015 1 commit
- Python 2/3 compatibility in single code base, plus python 3 testing on travis. · b7088b74
  peastman authored Aug 10, 2015
  
  b7088b74