Commits · cf4c2287c833bd2dd102d40f94e9067fe5542c2a · tsoc / openmm

"platforms/hip/src/HipParameterSet.cpp" did not exist on "eb64fa2f15b33dbad5b4de818d3e93bec8e6298e"

30 Mar, 2012 1 commit

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
15 Feb, 2012 1 commit
- Bug fixes to adding constraints when loading AMBER files: compute constrained... · bc157f03
  Peter Eastman authored Feb 15, 2012
```
Bug fixes to adding constraints when loading AMBER files: compute constrained angles correctly, respect the rigidWater flag
```
  bc157f03
13 Feb, 2012 1 commit
- Improved rounding behavior when computing the number of ions to add · d817b46b
  Peter Eastman authored Feb 13, 2012
  
  d817b46b
11 Feb, 2012 2 commits
- Finished implementing addHydrogens() · c3ca5fc0
  Peter Eastman authored Feb 11, 2012
  
  c3ca5fc0
- Handle alternate locations in PDB files correctly · c7d32e9c
  Peter Eastman authored Feb 11, 2012
  
  c7d32e9c
10 Feb, 2012 2 commits
- Deleted file with wrong capitalization · d51a7a5c
  Peter Eastman authored Feb 10, 2012
  
  d51a7a5c
- Implementing addHydrogens() · dfdf8328
  Peter Eastman authored Feb 10, 2012
  
  dfdf8328
08 Feb, 2012 1 commit
- Implemented addSolvent() · 15c272fd
  Peter Eastman authored Feb 08, 2012
  
  15c272fd
02 Feb, 2012 3 commits
- Replaced TIP4P with TIP4P-Ew · b593e034
  Peter Eastman authored Feb 02, 2012
  
  b593e034
- PdbFile and AmberInpcrdFile can return values as Numpy arrays · e2d8c16e
  Peter Eastman authored Feb 02, 2012
  
  e2d8c16e
- Created Modeller class. Two modeling methods are currently supported:... · deb55264
  Peter Eastman authored Feb 02, 2012
```
Created Modeller class.  Two modeling methods are currently supported: deleteWater() and convertWater()
```
  deb55264
01 Feb, 2012 1 commit
- Use PDB 3.0 nomenclature for the Topology created by AmberPrmtopFile · df60bf0d
  Peter Eastman authored Feb 01, 2012
  
  df60bf0d
30 Jan, 2012 1 commit
- Fixed error in wrapping of arguments that are maps · 12daada5
  Peter Eastman authored Jan 30, 2012
  
  12daada5
26 Jan, 2012 1 commit
- ForceField support TIP4P and TIP5P · 2dd09317
  Peter Eastman authored Jan 26, 2012
  
  2dd09317
23 Jan, 2012 1 commit
- Define both __div__ and __truediv__ to work on all Python versions · bfc1b529
  Peter Eastman authored Jan 23, 2012
  
  bfc1b529