Version 0.2.6

This is a minor release to (a) roll in any changes since the last release, and (b) mark a milestone corresponding to the last of the changes made prior to our major revamp of BLUES beginning in 2025. This version corresponds most closely to that used in our BLUES papers prior to 2022.

Version 0.2.5

This contains numerous small changes/fixes since the v0.2.4 release, but most notably includes the introduction of water hopping as described at https://doi.org/10.26434/chemrxiv.12429464.v1.

It also includes fixes to documentation.

v0.2.4

This point release:

• adds a simple test system (charged ethylene) which can run quickly on CPU.
• Adds python 3.7 support

Version 0.2.3

• Adds the standard python .gitignore file
• Adds a .github/ which holds template files for PRs and guidelines for contributing to the code
• Adds Sphinx docs and ReadTheDocs to the repository
• Docstrings are now formatted in numpydoc style
• Code is styled in YAPF style; configured by the setup.cfg file
• Re-wrote the tests to use pytest
• Adds CodeCov to the repository
• Adds Versioneer to the repository
• Improvements to Travis-CI
  • Builds and deploys conda packages for py3.5/3.6 for both osx/linux platforms
  • Deploys the conda environment yml file onto anaconda cloud
  • Conda packages follow convention, example for version 0.2.3 on python3.5
    • blues-0.2.3-py35g{SHORTHASH}_{#UNRELEASED COMMITS} or blues-0.2.3-py35g6aaba2d_5
• Minor API changes, renaming some functions in the BLUESSimulation to adhere to conventional python name schemes
  • Move the engine.py module (which housed just one single class) into the moves.py module
  • Fix in the AlchemicalExternalLangevinIntegrator for issue #115 ref
• Make package compatible for openmm=7.2.2 and openmmtools=0.15.0
• Includes changes from #150
  • Removes some code redundancy in syncing the simulation states
  • Correctly resets the velocities before the start of each MD simulation ref
  • Corrects behavior in syncing the simulation states ref
  • Adds some checks in the freezing selection ref

Version 0.2.2

Bug fixes for OpenEye tests and restarting from the YAML; enhancements to the Logger and package installation.

• PR #144, #145 Ensures installation through setup.py installs dependencies
• PR #143 Fixes a bug when restarting through the YAML file
• PR #140 Adds the ability to stream information from the Logger module to stdout or a file
• PR #135, #139 Fixes unittests to isolate OpenEye related code, skips tests if no OE_LICENSE or OpenEye-toolskits installation is found.

Version 0.2.1

PR #125: Critical bug fix in alchemical correction term

Version 0.2.0

Release for changes from PR #117

• BLUES will now support partial configuration from a YAML file
  • Supported settings: Input/output, system parameters, simulation parameters, freezing/restraining atoms, and configuring reporters
• API Changes
  • Addition of SystemFactory class: Provides methods for freezing or restraining atoms in your system
  • Addition of SimulationFactory: Allows addition of a MonteCarloBarostat to your System, enabling NPT simulations
  • Name changes methods in the Simulation class
• Addition of reporters.py module
  • Addition of ReporterConfig class, provides functionality for generating/configuring a some recommended/customized reporters for BLUES simulations:
    • BLUESHDF5Reporter subclass from mdtraj.HDF5Reporter
      • Custom features include:
        • specifying the indices of frames to be recorded,
        • protocolWork/alchemicalLambda from the NCMC simulation
        • simulation parameters
        • exporting your conda environment
    • BLUESStateDataReporter subclass from openmm.app.StateDataReporter
      • Custom features include:
        • title field to set the string prefix that is printed with each report line.
        • enable writing to a file or file-like object for streaming the data (logging.Logger) to the terminal window,
        • specifying the indices of frames to be recorded
        • currentIter/protocolWork/alchemicalLambda from the NCMC simulation
    • NetCDF4Reporter subclass from parmed.openmm.reporters.NetCDFReporter
      • Custom features includes:
        • Add ability to properly flush the data to disc on call to report()
        • specifying the indices of frames to be recorded
        • protocolWork/alchemicalLambda from the NCMC simulation
    • parmed.openmm.reporters.RestartReporter, enabling restarts from the rst7 file

Version 0.1.3

• General enhancements to simulation logging
  • Moved initialization of the logger module into simulation.py
  • Added reporter for the NCMC simulation
  • Print out simulation information/timing
  • Lambda range to add extra propagation steps now controlled by a single parameter prop_lambda
    • Added docstrings for nprop and prop_lambda

version 0.1.2

-Introduction of a new movetype: SideChainMove

• Requires: oeommtools conda install -c openeye/label/Orion oeommtools -c omnia
• Dropped Python 2.7 support
• Fixes for the logger functionality

Version 0.1.1

• Adding extra propagation steps between lambda 0.2 -> 0.8 in the alchemical integrator
  • User parameter nprop = 5 (Default).
• Zeroing masses of atoms outside the 5.0A distance (Default) of the ligand in the alchemical system.
  • Distance for freezing atoms is now a user parameter with freeze_distance
  • Added option to set selection center freeze_center Default: 'LIG'
  • Added option to include solvent freeze_solvent Default: 'HOH,NA,CL'
• Switch print statements for logging module
• Made input parameters for functions in the Simulation class explicit
  • Set default values but can pass the input parameters from the opt dictionary
• New parameter write_move for the acceptRejectNCMC function
  • Setting write_move = True will write the accepted move to a PDB file.
• Changed runNCMC() to run().
  • Avoids potential confusion with function simulateNCMC()
• Simplified NCMC trajectory reporter
  • Replacedwrite_ncmc parameter with ncmc_traj
  • If a string is specified for (i.e. ncmc_traj = ncmc_output, it will write every NCMC step to a DCD file named ncmc_output.dcd
• Added a function _getSimulationInfo() that will print out the simulation time information