Commits · fee4e4ddec61ba9d6077cd7cdd5d8394679ada86 · tsoc / openmm

07 May, 2012 3 commits
- Implemented Modeller.add() and Modeller.delete() · 36fced55
  Peter Eastman authored May 07, 2012
  
  36fced55
- Bonds were being added to the Topology incorrectly · 12ff40ef
  Peter Eastman authored May 07, 2012
  
  12ff40ef
- Defined a sum() function that works with Quantities. Also fixed a doctest. · c2e05fe8
  Peter Eastman authored May 07, 2012
  
  c2e05fe8
04 May, 2012 1 commit
- Residue indices for atoms were set incorrectly · 0844f4fe
  Peter Eastman authored May 04, 2012
  
  0844f4fe
23 Apr, 2012 3 commits
- Reporters check for NaNs or infinities in output · a4bf2ceb
  Peter Eastman authored Apr 23, 2012
  
  a4bf2ceb
- Set units correctly on Numpy arrays · cb0b20f5
  Peter Eastman authored Apr 23, 2012
  
  cb0b20f5
- Fixed bugs setting up nonbonded and GB forces · c9d7d1e9
  Peter Eastman authored Apr 23, 2012
  
  c9d7d1e9
21 Apr, 2012 1 commit
- Report density in g/mL · ee1ec687
  Peter Eastman authored Apr 21, 2012
  
  ee1ec687
13 Apr, 2012 1 commit
- The wrong path was being used for the OpenMM library · be8774b0
  Peter Eastman authored Apr 13, 2012
  
  be8774b0
12 Apr, 2012 1 commit
- Tolerate errors uninstalling previous versions · b3fe05e9
  Peter Eastman authored Apr 12, 2012
  
  b3fe05e9
09 Apr, 2012 1 commit
- Tweaked the alignment of the atom name in PDB files · 19d92e1d
  Peter Eastman authored Apr 09, 2012
  
  19d92e1d
04 Apr, 2012 2 commits
- Implement __copy__() and __deepcopy__() for Forces · 681ab7ff
  Peter Eastman authored Apr 04, 2012
  
  681ab7ff
- Bug fix · dea037c3
  Peter Eastman authored Apr 04, 2012
  
  dea037c3
30 Mar, 2012 2 commits
- Lots of improvements to Python API documentation · aab77399
  Peter Eastman authored Mar 30, 2012
  
  aab77399
- Use Doxygen to generate API docs for Python. This involved lots of changes... · cf4c2287
  Peter Eastman authored Mar 30, 2012
```
Use Doxygen to generate API docs for Python.  This involved lots of changes both to Python API generation and to Doxygen doc generation.
```
  cf4c2287
28 Mar, 2012 3 commits
- Lots of optimizations to creating systems from prmtop files · b8bf8fbd
  Peter Eastman authored Mar 28, 2012
  
  b8bf8fbd
- All options for StateDataReporter default to False · 689fd4d4
  Peter Eastman authored Mar 28, 2012
  
  689fd4d4
- Allow specifying solute and solvent dielectrics for GBSAOBCForce · 33badc47
  Peter Eastman authored Mar 28, 2012
  
  33badc47
27 Mar, 2012 3 commits
- Added license notice to Python files · b3f88f6f
  Peter Eastman authored Mar 27, 2012
  
  b3f88f6f
- Support <Script> tag in force field files · 5fd130f4
  Peter Eastman authored Mar 27, 2012
  
  5fd130f4
- Added Christoph Klein's implementation of AMBER GB models as custom forces · dce2d427
  Peter Eastman authored Mar 27, 2012
  
  dce2d427
26 Mar, 2012 1 commit
- Created StateDataReporter · 724e498b
  Peter Eastman authored Mar 26, 2012
  
  724e498b
23 Mar, 2012 2 commits
- Add bonds to Topology based on CONECT records in PDB file · fc71bac8
  Peter Eastman authored Mar 23, 2012
  
  fc71bac8
- Fixed incorrect atom names · b001c4ed
  Peter Eastman authored Mar 23, 2012
  
  b001c4ed
22 Mar, 2012 1 commit
- Fixed capitalization of library name · 6f92b9be
  Peter Eastman authored Mar 22, 2012
  
  6f92b9be
21 Mar, 2012 1 commit
- Generate Python wrapper for RPMDIntegrator · a57facb4
  Peter Eastman authored Mar 21, 2012
  
  a57facb4
20 Mar, 2012 1 commit
- DCDReporter writes the current periodic box size rather than the original one · 6f6bee35
  Peter Eastman authored Mar 20, 2012
  
  6f6bee35
15 Mar, 2012 2 commits
- Fixed error on some platforms · 064bb5e3
  Peter Eastman authored Mar 15, 2012
  
  064bb5e3
- Python API can specify force groups when requesting a State · ee30f308
  Peter Eastman authored Mar 15, 2012
  
  ee30f308
13 Mar, 2012 4 commits
- Avoid writing numbers that are too large to fit in the allowed set of columns · 3eb4fe2e
  Peter Eastman authored Mar 13, 2012
  
  3eb4fe2e
- Apply periodic boundary conditions when reporting coordinates · e59e15b2
  Peter Eastman authored Mar 13, 2012
  
  e59e15b2
- Fixed bug where tuples would sometimes turn into lists when changing their units · da9a3547
  Peter Eastman authored Mar 13, 2012
  
  da9a3547
- Fixed bug where tuples would sometimes turn into lists when changing their units · 63909299
  Peter Eastman authored Mar 13, 2012
  
  63909299
05 Mar, 2012 1 commit
- Improved exception handling: catch any exception, not just OpenMMException · 82159daf
  Peter Eastman authored Mar 05, 2012
  
  82159daf
27 Feb, 2012 1 commit
- Allow boxSize argument to be a list or tuple instead of a Vec3 · 0dd32915
  Peter Eastman authored Feb 27, 2012
  
  0dd32915
25 Feb, 2012 1 commit
- Fixed Python wrapper for CustomIntegrator::getPerDofVariable() · d2a6f00c
  Peter Eastman authored Feb 25, 2012
  
  d2a6f00c
22 Feb, 2012 1 commit
- Added missing units for cases when temperature_factor is absent · 6bfe2d8b
  Mark Friedrichs authored Feb 22, 2012
  
  6bfe2d8b
17 Feb, 2012 1 commit
- Modeller supports SPC/E water · 1878512f
  Peter Eastman authored Feb 17, 2012
  
  1878512f
16 Feb, 2012 2 commits
- Support 4 and 5 site water when loading prmtop files · 4412050a
  Peter Eastman authored Feb 16, 2012
  
  4412050a
- Fixed bugs in adding solvent · 663a8db0
  Peter Eastman authored Feb 16, 2012
  
  663a8db0