Clean up README now that docs are online.

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2015-2017 Chodera lab // Memorial Sloan Kettering Cancer Center
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -5,53 +5,23 @@
 [![ReadTheDocs Badge](https://readthedocs.org/projects/openmmtools/badge/?version=latest)](http://openmmtools.readthedocs.io/en/latest/?badge=latest)
 [![Zenodo DOI Badge](https://zenodo.org/badge/25416166.svg)](https://zenodo.org/badge/latestdoi/25416166)
 
-# Various Python tools for OpenMM
+## OpenMMTools
 
-## Integrators
+A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
 
-This repository contains a number of additional integrators for OpenMM in `openmmtools.integrators`, including
-* `MTSIntegrator` - a multiple timestep integrator
-* `DummyIntegrator` - a "dummy" integrator that does not update positions
-* `GradientDescentMinimizationIntegrator` - a simple gradient descent minimizer (without line search)
-* `VelocityVerletIntegrator` - a velocity Verlet integrator
-* `AndersenVelocityVerletIntegrator` - a velocity Verlet integrator with Andersen thermostat using per-particle collisions
-* `MetropolisMonteCarloIntegrator` - a Metropolis Monte Carlo integrator that uses Gaussian displacement trials
-* `HMCIntegrator` - a hybrid Monte Carlo (HMC) integrator
-* `GHMCIntegrator` - a generalized hybrid Monte Carlo (GHMC) integrator
-* `VVVRIntegrator` - a velocity Verlet with velocity randomization (VVVR) integrator
+``openmmtools`` is a Python library layer that sits on top of `OpenMM <http://openmm.org>`_ to provide access to a variety of useful tools for building full-featured molecular simulation packages.
 
-## Test system suite
+Features include:
 
-The `openmmtools.testsystems` module contains a large suite of test systems---including many with simple exactly-computable properties---that can be used to test molecular simulation algorithms
+ - high-quality Langevin integrators, including `g-BAOAB <http://rspa.royalsocietypublishing.org/content/472/2189/20160138>`_, `VVVR <http://pubs.acs.org/doi/abs/10.1021/jp411770f>`_, and other splittings
+ - integrators that support nonequilibrium switching for free energy calculations or `nonequilibrium candidate Monte Carlo (NCMC) <http://dx.doi.org/10.1073/pnas.1106094108>`_
+ - an extensible Markov chain Monte Carlo framework for mixing Monte Carlo and molecular dynamics-based methods
+ - enhanced sampling methods, including replica-exchange (REMD) and self-adjusted mixture sampling (SAMS)
+ - factories for generating `alchemically-modified <http://alchemistry.org>`_ systems for absolute and relative free energy calculations
+ - a suite of test systems for benchmarking, validation, and debugging
 
-## Markov chain Monte Carlo proposal schemes and move compositions
-An implementation of an `MCMCMove` encodes how to propagate an OpenMM `System` to generate a new sample. Different `MCMCMove`s can be combined for more advanced schemes.
-- `LangevinDynamicsMove`: Langevin dynamics segment as a (pseudo) Monte Carlo move (WARNING: Does not preserve the true target distribution.).
-- `HMCMove`: Assigns velocities from the Maxwell-Boltzmann distribution and propagate through velocity Verlet steps.
-- `GHMCMove`: Generalized hybrid Monte Carlo Markov chain Monte Carlo.
-- `MonteCarloBarostatMove`: Attempts to update the box volume using Metropolis-Hastings Monte Carlo updates.
-- `SequenceMove`: Combine multiple `MCMCMove`s to apply in sequence at each iteration.
-- `WeightedMove`: At each iteration, select one `MCMCMove`s to apply from a set with given probability.
+See the [documentation](http://openmmtools.readthedocs.io) at [ReadTheDocs](http://openmmtools.readthedocs.io).
 
-## States
+#### License
 
-The module `openmmtools.states` contains classes to maintain a consistent state of the simulation.
-- `ThermodynamicState`: Represent and manipulate the thermodynamic state of OpenMM `System`s and `Context`s.
-- `SamplerState`: Represent and cache the state of the simulation that changes when the `System` is integrated.
-- `CompoundThermodynamicState`: Extend the `ThermodynamicState` to handle parameters other than temperature and pressure through the implementations of the `IComposableState` abstract class.
-
-## Cache
-
-The module `openmmtools.cache` implements a shared LRU cache for `Context` objects that tries to minimize the number of `Context` in memory at the same time.
-- `LRUCache`: A simple LRU cache with a dictionary-like interface. It supports a maximum capacity and expiration.
-- `ContextCache`: A LRU cache for OpenMM `Context` objects.
-- `global_context_cache`: A shared `ContextCache` that minimizes the number of `Context` creations when employing `MCMCMove`s.
-
-## OpenMM testing scripts
-
-`scripts/` contains a script that may be useful in testing your OpenMM installation is installed:
-
-* `test-openmm-platforms` will test the various platforms available to OpenMM to ensure that all systems in `openmmtools.testsystems` give consistent potential energies.
-If differences in energies in excess of `ENERGY_TOLERANCE` (default: 0.06 kcal/mol) are detected, these systems will be serialized to XML for further debugging.
-
-This is installed onto the command line when the repository is installed.
+OpenMMTools is distributed under the MIT License.

devtools/conda-recipe/meta.yaml

@@ -38,4 +38,4 @@ test:
 
 about:
   home: https://github.com/choderalab/openmmtools
-  license: GNU Lesser General Public License v2 or later (LGPLv2+)
+  license: MIT License