== New Features == PyTest framework: - Fully migrated from `unittest` to `pytest`, motivated by inscrutable test failures on Travis when the old framework was used - All tests are now located in `<root>/src/tests` MacOS support: - Mac OS is supported for Python 3.5 or greater. - A small but important fix was added in `nifty.py` to handle streams from processes on Mac OS Torsion profile target: - This target allows 1D relaxed torsion profiles to be included in the objective function, with the option to carry out MM relaxations (with torsion atoms frozen). - Implemented and tested using SMIRNOFF engine but expected to work for OpenMM. - Support in other engines will require implementing energy minimizations with frozen atoms. Optimized geometry target: - This target allows (QM-MM) deviations in energy-minimized bonds and angles to be included in the objective function. - Implemented and tested using SMIRNOFF engine but expected to work for OpenMM and other engines that support energy minimization. Surface tension target: - This target calculates surface tension and enables the deviation of calculated vs. experimental surface tension to be included in the objective function. - Implemented and tested using OpenMM engine. - Implementation is described in publication located at <https://doi.org/10.1021/acs.jpcb.9b05455> PropertyEstimator / Evaluator target: - This target includes an interface to the OpenFF Evaluator framework (previously called PropertyEstimator) to include evaluated properties in the objective function. - Uses Evaluator API to compute parametric gradients. - SMIRNOFF is the only supported engine. - PropertyEstimator can be found here: <https://github.com/openforcefield/propertyestimator> Fitting vibrational frequencies using OpenMM: - `Vibration_OpenMM`: OpenMM can now compute vibrational frequencies and normal modes == Minor changes == - Enable optimization of charges in `.mol2` files when working with SMIRNOFF-formatted force field - Cookiecutter, codecov and versioneer integrations - Sanitizing `.offxml` force field parsing for SMIRKS strings - `constrain_h` option in FB input file for specifying H-bond constraints in OpenMM targets - Improved `tools/install_cctools.sh` script for Work Queue installs - Simplify `AtomContact` function in `molecule.py` - Improvements in performance using SMIRNOFF force fields - Improved remote target file handling - Improved stability of Hessian diagonalization - Keep up to date with SMIRNOFF `.offxml` formatting - Improved handling of Work Queue workers - Fix a bug in radius of gyration calculation in `molecule.py` == Credits == - Yudong Qiu (Optimized geometry target, surface tension target, OpenMM normal modes, SMIRNOFF performance, and various improvements) - Jeffrey Wagner (MacOS support, Pytest framework) - Simon Boothroyd (OpenFF Evaluator / propertyestimator interface) - Hyesu Jang (Pytest framework) - Michael Schauperl (H-bond constraint) - Open Force Field Initiative (financial support)