* Template generators no longer choose default force fields
* Only call add_molecules() when a template generator is present
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* Support virtual sites and multiple SMIRNOFF force fields
* Put test files where tests can actually find them
* Clean up some changes in template_generators.py
* Clean up virtual site permutation handling in test cases
* Unfinished draft
* Allow specifying multiple force fields
* Support constraints and virtual sites
* Add more tests for constraints
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Run tests on OpenMM 8.5.0 beta since we need ForceField changes
* Need openmm_dev channel
* Use correct channel names (openmm_rc for beta)
* Minor improvement to torsion handling, fix incorrect comment
* Basic test for proteins
* Default to unconstrained variant of force field when given name
* Test molecule is unstable due to vsite/H overlap
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update vsite tests with more varieties of molecules
* Autoformatter
* Update openmmforcefields/generators/template_generators.py
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
* 1-4 exception check (not vsites) now uses non-zero scalings
* Use preset list of known force field names, update documentation
* Reduce test set size after Interchange cache behavior change
* Update openmmforcefields/tests/test_template_generators.py
Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com>
* Water constraints test also checks TIP3P inside openff_unconstrained
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix error message if preset force field file can't be located
* Update CHARMM force field scripts (see openmm/openmm#5181)
* Change caching behavior so molecules must be added
* Regenerate CHARMM force fields
* Test regenerated force fields on OpenMM 8.5.0 beta
* Refactor multi-residue molecule test
* Put back CHARMM files that didn't change other than generation date
* Add test with virtual site frame atoms spanning residue
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Add test file with many amino acids
* Run tests on release version of OpenMM instead of beta
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com>
* Support virtual sites and multiple SMIRNOFF force fields
* Put test files where tests can actually find them
* Clean up some changes in template_generators.py
* Clean up virtual site permutation handling in test cases
* Unfinished draft
* Allow specifying multiple force fields
* Support constraints and virtual sites
* Add more tests for constraints
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Run tests on OpenMM 8.5.0 beta since we need ForceField changes
* Need openmm_dev channel
* Use correct channel names (openmm_rc for beta)
* Minor improvement to torsion handling, fix incorrect comment
* Default to unconstrained variant of force field when given name
* Test molecule is unstable due to vsite/H overlap
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Update vsite tests with more varieties of molecules
* Autoformatter
* Update openmmforcefields/generators/template_generators.py
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
* 1-4 exception check (not vsites) now uses non-zero scalings
* Use preset list of known force field names, update documentation
* Reduce test set size after Interchange cache behavior change
* Update openmmforcefields/tests/test_template_generators.py
Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com>
* Water constraints test also checks TIP3P inside openff_unconstrained
* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
* Fix error message if preset force field file can't be located
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org>
Co-authored-by: Jeff Wagner <jwagnerjpl@gmail.com>
* Allow for any barostat in SystemGenerator
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Fix doc strings
* Add test for MonteCarloMembraneBarostat
* [pre-commit.ci] auto fixes from pre-commit.com hooks
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* Cleanups:
* Remove residue_atoms argument of generate_residue_template() methods: fixes#379
* OpenMMSystemMixin.convert_system_to_ffxml improper_atom_ordering was silently ignored
* Removal of unused kwargs that could cause misspelled parameters to be silently ignored
* Removal of some unused local variables
* DummySystemGenerator: was broken due to early return
* Consolidate custom classproperty implementation
* Docstrings: parameters out of order, errors, formatting
* Fix OpenFF units import for older openff-toolkit version compatible with espaloma
* Fix broken DummySystemGenerator feature
* Partial charge normalization
* Use common logic for checking user-specified partial charges sum to
total formal charge, and raising a warning if so
* GAFFTemplateGenerator no longer silently adjusts user-specified
partial charges if they don't sum to the formal charge: fixes#373
* Cleanups to test cases:
* Consolidate propagate_dynamics() implementations into
TemplateGeneratorBaseCase
* Remove charges_from_system(), charges_are_equal(), compute_energy(),
and compare_energies() from TestGAFFTemplateGenerator since identical
implementations are available in TemplateGeneratorBaseCase
* Bump CI OpenMM versions
* Testing template generator user charge feature:
* Ensure warnings are raised / not raised as appropriate (GAFF, SMIRNOFF)
* SMIRNOFF should accept user charges not matching once we warn about it
* Make template_generator_kwargs explicit
* ruff format
* Remove unused imports
* Formatting, remove unused local assignments
* Remove references to and tests for DummySystemGenerator
* Style update: import classproperty
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
