Merge branch 'master' into link-ff-repos

Author: j-wags

.github/workflows/dangerbot.yml

@@ -0,0 +1,25 @@
+name: off-dangerbot
+
+on:
+  pull_request:
+      types: assigned
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Ruby 2.6
+      uses: actions/setup-ruby@v1
+      with:
+        ruby-version: 2.6.x
+    - name: Assign reviewer if prompted
+      # API token for off-dangerbot
+      env:
+          DANGER_GITHUB_API_TOKEN: ${{ secrets.DANGER_GITHUB_API_TOKEN }}
+      run: |
+        gem install danger --version '~> 5.0'
+        danger --version 
+        danger

.travis.yml

@@ -73,7 +73,9 @@ install:
 
 # Install RDKit
 - if [[ "$RDKIT" == true ]]; then conda install --yes -c conda-forge rdkit; fi
-- if [[ "$RDKIT" == true ]]; then conda install --yes -c omnia ambermini; fi
+# This is no longer needed, since the newest version of ParmEd is only available from the 
+# omnia:ambertools repo, which is now included in the test_env.yaml file
+#- if [[ "$RDKIT" == true ]]; then conda install --yes -c omnia ambermini; fi
 
 # Install OpenEye
 - if [[ "$OPENEYE" == true ]]; then conda install -c openeye openeye-toolkits; fi
@@ -99,8 +101,10 @@ script:
     --nbval-lax --cov=openforcefield --cov-config=setup.cfg;
   fi
 
+# Raise a fuss if cron jobs break
 notifications:
-  email: false
+  email:
+    if: type = cron
 
 after_success:
 - codecov

Dangerfile

@@ -0,0 +1,2 @@
+# Run the shared Dangerfile with these settings
+danger.import_dangerfile(github: "openforcefield/dangerbot") 

README.md

@@ -1,6 +1,6 @@
 | **Status** | [![Travis build](https://img.shields.io/travis/openforcefield/openforcefield/master.svg?logo=linux&logoColor=white)](https://travis-ci.org/openforcefield/openforcefield) [![Codecov coverage](https://img.shields.io/codecov/c/github/openforcefield/openforcefield.svg?logo=Codecov&logoColor=white)](https://codecov.io/gh/openforcefield/openforcefield) [![LGTM analysis](https://img.shields.io/lgtm/grade/python/g/openforcefield/openforcefield.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/openforcefield/openforcefield/context:python) |
 | :------ | :------- |
-| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openforcefield.svg)](https://github.com/openforcefield/openforcefield/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openforcefield/0.5.1.svg)](https://github.com/openforcefield/openforcefield/releases/tag/0.5.1)  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597754.svg)](https://doi.org/10.5281/zenodo.597754) |
+| **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openforcefield.svg)](https://github.com/openforcefield/openforcefield/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openforcefield/0.6.0.svg)](https://github.com/openforcefield/openforcefield/releases/tag/0.6.0)  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597754.svg)](https://doi.org/10.5281/zenodo.597754) |
 | **Communication** | [![docs latest](https://img.shields.io/badge/docs-latest-5077AB.svg?logo=read%20the%20docs)](https://open-forcefield-toolkit.readthedocs.io/en/latest/) [![dev chat on slack](https://img.shields.io/badge/dev_chat-on_slack-808493.svg?logo=slack)](https://join.slack.com/t/openforcefieldgroup/shared_invite/enQtNjA4MTMxMDg0MDAxLWY3Y2Q5NDY4MmU1OTIzMDhiYzFjOWFkZGFjN2Y4N2Q4OTRkOWNjODVhMDMxMzkwMDcxNDA5MjYyNjJjYjE2NTM) |
 | **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openforcefield.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/latest/installation.html) [![python](https://img.shields.io/badge/python-3.6%2C%203.7-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/latest/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org) |
 | **Installation** | [![Releases](https://img.shields.io/badge/obtain-latest-green.svg)](https://github.com/openforcefield/openforcefield/releases) [![Conda](https://img.shields.io/conda/v/omnia/openforcefield.svg)](https://anaconda.org/omnia/openforcefield) [![Last updated](https://anaconda.org/omnia/openforcefield/badges/latest_release_relative_date.svg)](https://anaconda.org/omnia/openforcefield) [![Anaconda Cloud downloads](https://anaconda.org/omnia/openforcefield/badges/downloads.svg)](https://anaconda.org/omnia/openforcefield) |

The-SMIRNOFF-force-field-format.md

@@ -219,7 +219,7 @@ For example, to ensure water molecules are assigned partial charges for [TIP3P](
 
 | LibraryCharges section tag version | Tag attributes and default values    | Required parameter attributes   | Optional parameter attributes |
 |------------------------------------|--------------------------------------|---------------------------------|-------------------------------|
-| 0.3                                |                                      | `smirks`, `charges` (indexed)   | `name`, `id`, `parent_id`     |
+| 0.3                                |                                      | `smirks`, `charge` (indexed)    | `name`, `id`, `parent_id`     |
 
 
 

devtools/conda-envs/test_env.yaml

@@ -13,10 +13,10 @@ dependencies:
   - pytest-cov
   - nbval
   - codecov
-  - coverage
+  - coverage < 5.0
   - numpy
   - networkx
-  - parmed
+  - ambertools
   - packaging
   - openmmtools
   - openforcefields

docs/releasehistory.rst

@@ -8,8 +8,26 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
-Current Development
--------------------
+0.6.0 - Library Charges
+-----------------------
+
+This release adds support for a new SMIRKS-based charge assignment method,
+`Library Charges <https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#librarycharges-library-charges-for-polymeric-residues-and-special-solvent-models>`_.
+The addition of more charge assignment methods opens the door for new types of
+experimentation, but also introduces several complex behaviors and failure modes.
+Accordingly, we have made changes
+to the charge assignment infrastructure to check for cases when partial charges do
+not sum to the formal charge of the molecule, or when no charge assignment method is able
+to generate charges for a molecule. More detailed explanation of the new errors that may be raised and
+keywords for overriding them are in the "Behavior Changed" section below.
+
+
+With this release, we update ``test_forcefields/tip3p.offxml`` to be a working example of assigning LibraryCharges.
+However, we do not provide any force field files to assign protein residue ``LibraryCharges``.
+If you are interested in translating an existing protein FF to SMIRNOFF format or developing a new one, please
+feel free to contact us on the `Issue tracker <https://github.com/openforcefield/openforcefield/issues>`_ or open a
+`Pull Request <https://github.com/openforcefield/openforcefield/pulls>`_.
+
 
 New features
 """"""""""""
@@ -19,17 +37,33 @@ New features
   `LibraryCharges tag in the SMIRNOFF specification <https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html#librarycharges-library-charges-for-polymeric-residues-and-special-solvent-models>`_
   using
   :py:class:`LibraryChargeHandler <openforcefield.typing.engines.smirnoff.parameters.LibraryChargeHandler>`.
-  For a molecule to have charges assigned using LibraryCharges, all of its atoms must be covered by
-  at least one LibraryCharge. If an atom is covered by multiple LibraryCharges, then the last
-  one read will be applied (per the hierarchy rules in the SMIRNOFF format).
+  For a molecule to have charges assigned using Library Charges, all of its atoms must be covered by
+  at least one ``LibraryCharge``. If an atom is covered by multiple ``LibraryCharge`` s, then the last
+  ``LibraryCharge`` matched will be applied (per the hierarchy rules in the SMIRNOFF format).
 
   This functionality is thus able to apply per-residue charges similar to those in traditional
   protein force fields. At this time, there is no concept of "residues" or "fragments" during
   parametrization, so it is not possible to assign charges to `some` atoms in a molecule using
-  LibraryCharges, but calculate charges for other atoms in the same molecule using a different
+  ``LibraryCharge`` s, but calculate charges for other atoms in the same molecule using a different
   method. To assign charges to a protein, LibraryCharges SMARTS must be provided for
-  the standard residues, as well as for any capping groups and post-translational modifications
-  that are present.
+  the residues and protonation states in the molecule, as well as for any capping groups
+  and post-translational modifications that are present.
+
+  It is valid for ``LibraryCharge`` SMARTS to `partially` overlap one another. For example, a molecule
+  consisting of atoms ``A-B-C`` connected by single bonds could be matched by a SMIRNOFF
+  ``LibraryCharges`` section containing two ``LibraryCharge`` SMARTS: ``A-B`` and ``B-C``. If
+  listed in that order, the molecule would be assigned the ``A`` charge from the ``A-B`` ``LibraryCharge``
+  element and the ``B`` and ``C`` charges from the ``B-C`` element. In testing, these types of
+  partial overlaps were found to frequently be sources of undesired behavior, so it is recommended
+  that users define whole-molecule ``LibraryCharge`` SMARTS whenever possible.
+
+- `PR #455 <https://github.com/openforcefield/openforcefield/pull/455>`_: Addresses
+  `Issue #393 <https://github.com/openforcefield/openforcefield/issues/393>`_ by adding
+  :py:meth:`ParameterHandler.attribute_is_cosmetic <openforcefield.typing.engines.smirnoff.parameters.ParameterHandler.attribute_is_cosmetic>`
+  and
+  :py:meth:`ParameterType.attribute_is_cosmetic <openforcefield.typing.engines.smirnoff.parameters.ParameterType.attribute_is_cosmetic>`,
+  which return True if the provided attribute name is defined for the queried object
+  but does not correspond to an allowed value in the SMIRNOFF spec.
 
 Behavior changed
 """"""""""""""""
@@ -44,10 +78,10 @@ Behavior changed
   ``Molecule.partial_charges`` array to be all zeroes, and including the molecule in the
   ``charge_from_molecules`` keyword argument to ``create_openmm_system``.
 - `PR #433 <https://github.com/openforcefield/openforcefield/pull/433>`_: Due to risks
-  introduced by permitting charge assignment using partially-overlapping ``LibraryCharge``s,
+  introduced by permitting charge assignment using partially-overlapping ``LibraryCharge`` s,
   the toolkit will now raise a
   ``openforcefield.typing.engines.smirnoff.parameters.NonIntegralMoleculeChargeException``
-  if the sum of partial charges on a molecule are found to be more than 0.001 elementary charge units
+  if the sum of partial charges on a molecule are found to be more than 0.01 elementary charge units
   different than the molecule's formal charge. This exception can be overridden by providing
   the ``allow_nonintegral_charges=True`` keyword argument to ``ForceField.create_openmm_system``.
 

examples/README.md

@@ -7,6 +7,7 @@ The following examples are available in [the openforcefield toolkit repository](
 * [SMIRNOFF_simulation](https://github.com/openforcefield/openforcefield/tree/master/examples/SMIRNOFF_simulation) - simulation of a molecule in the gas phase with the SMIRNOFF forcefield format
 * [forcefield_modification](https://github.com/openforcefield/openforcefield/tree/master/examples/forcefield_modification) - modify forcefield parameters and evaluate how system energy changes
 * [using_smirnoff_in_amber_or_gromacs](https://github.com/openforcefield/openforcefield/tree/master/examples/using_smirnoff_in_amber_or_gromacs) - convert a System generated with the Open Forcefield Toolkit, which can be simulated natively with OpenMM, into AMBER prmtop/inpcrd and GROMACS top/gro input files through the ParmEd library.
+* [swap_amber_parameters](https://github.com/openforcefield/openforcefield/tree/master/examples/swap_amber_parameters) - take a prepared AMBER protein-ligand system (prmtop and crd) along with a structure file of the ligand, and replace ligand parameters with OpenFF parameters.
 * [inspect_assigned_parameters](https://github.com/openforcefield/openforcefield/tree/master/examples/inspect_assigned_parameters) - check which parameters are used in which molecules and generate parameter usage statistics.
 * [using_smirnoff_with_amber_protein_forcefield](https://github.com/openforcefield/openforcefield/tree/master/examples/using_smirnoff_with_amber_protein_forcefield) - use SMIRNOFF parameters for small molecules in combination with more conventional force fields for proteins and other components of your system (using ParmEd to combine parameterized structures)
 * [check_dataset_parameter_coverage](https://github.com/openforcefield/openforcefield/tree/master/examples/check_dataset_parameter_coverage) - shows how to use the Open Force Field Toolkit to ingest a dataset of molecules, and generate a report summarizing any chemistry that can not be parameterized.

examples/swap_amber_parameters/README.md

@@ -0,0 +1,8 @@
+## Taking an AMBER system and replacing the ligand parameters with OpenFF parameters
+
+These examples illustrate how the [ParmEd](http://parmed.github.io/ParmEd/html/index.html) utility can be used to take a fully parameterized (and solvated) protein-ligand system and replace the ligand parameters with those from OpenFF. In this case, the system uses an AMBER protein force field, ions, and TIP3P water, and we replace the GAFF ligand parameters with OpenFF 1.0 parameters, writing out the resulting fully parameterized system.
+
+### BRD4:inhibitor complex
+
+
+[`swap_existing_ligand_parameters.ipynb`](swap_existing_ligand_parameters.ipynb) contains an example illustrating taking a fully parameterized BRD4 protein-ligand system, with an AMBER protein force field and GAFF ligand parameters, and replacing the ligand parameters with OpenFF parameters from SMIRNOFF format. The BRD4:inhibitor complex is taken from the [free energy benchmark systems living review](https://www.annualreviews.org/doi/abs/10.1146/annurev-biophys-070816-033654) [GitHub repo](https://github.com/MobleyLab/benchmarksets/tree/master/input_files/BRD4).