diff --git a/devtools/conda/meta.yaml b/devtools/conda/meta.yaml index 065f1fb5..6d4c0f7e 100644 --- a/devtools/conda/meta.yaml +++ b/devtools/conda/meta.yaml @@ -24,7 +24,7 @@ requirements: - networkx - rdkit - ambertools - - openforcefield==0.8.3 + - openff-toolkit==0.9.2 about: home: https://github.com/martimunicoy/peleffy diff --git a/devtools/envs/standard.yaml b/devtools/envs/standard.yaml index a247706a..98ec262b 100644 --- a/devtools/envs/standard.yaml +++ b/devtools/envs/standard.yaml @@ -1,7 +1,6 @@ name: standard channels: - conda-forge - - omnia dependencies: - python @@ -11,6 +10,7 @@ dependencies: - pytest-cov - codecov - coverage < 5.0 + - ipython - ambertools - rdkit - - openforcefield ==0.8.3 + - openff-toolkit==0.9.2 diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index ab4e34dd..cd1e561b 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -8,6 +8,16 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 `_: Migrated openforcefield imports to openff.toolkit + + 1.3.1 - PELE Platform support ----------------------------- @@ -19,7 +29,7 @@ New features Bugfixes """""""" -- Minor error when parsing Impact templates. +- `PR #143 `_: Minor error when parsing Impact templates. 1.3.0 - BCE conformations and automatic heteromolecules extraction diff --git a/peleffy/tests/test_molecule.py b/peleffy/tests/test_molecule.py index 2ae2d692..341742d7 100644 --- a/peleffy/tests/test_molecule.py +++ b/peleffy/tests/test_molecule.py @@ -276,7 +276,7 @@ def test_undefined_stereo(self): It checks the behaviour when ignoring the stereochemistry in the Molecule initialization. """ - from openforcefield.utils.toolkits import UndefinedStereochemistryError + from openff.toolkit.utils.toolkits import UndefinedStereochemistryError from peleffy.forcefield import OpenForceField # This should crash due to an undefined stereochemistry error @@ -328,7 +328,7 @@ def test_from_openff(self): It checks the initialization of a peleffy Molecule from an OpenFF molecular representation. """ - from openforcefield.topology import Molecule as OpenFFMolecule + from openff.toolkit.topology import Molecule as OpenFFMolecule openff_molecule = OpenFFMolecule.from_smiles('C(C(=O)[O-])C(=O)[OH]') diff --git a/peleffy/topology/molecule.py b/peleffy/topology/molecule.py index 26b497c7..a11ada18 100644 --- a/peleffy/topology/molecule.py +++ b/peleffy/topology/molecule.py @@ -79,7 +79,7 @@ def __init__(self, path=None, smiles=None, pdb_block=None, from qcportal and the Open Force Field Toolkit) >>> import qcportal as ptl - >>> from openforcefield.topology import Molecule as OFFMolecule + >>> from openff.toolkit.topology import Molecule as OFFMolecule >>> ds = client.get_collection('OptimizationDataset', 'Kinase Inhibitors: WBO Distributions') diff --git a/peleffy/utils/toolkits.py b/peleffy/utils/toolkits.py index f4c1453d..4b0cc6e2 100644 --- a/peleffy/utils/toolkits.py +++ b/peleffy/utils/toolkits.py @@ -782,7 +782,7 @@ def is_available(): True if OpenForceField is installed, False otherwise. """ try: - importlib.import_module('openforcefield') + importlib.import_module('openff.toolkit') return True except ImportError: return False @@ -802,7 +802,7 @@ def from_rdkit(self, molecule): molecule : an openforcefield.topology.Molecule object The OpenForceField's Molecule """ - from openforcefield.topology.molecule import Molecule + from openff.toolkit.topology.molecule import Molecule rdkit_molecule = molecule.rdkit_molecule return Molecule.from_rdkit( @@ -825,7 +825,7 @@ def get_forcefield(self, forcefield_name): object The OpenForceField's forcefield """ - from openforcefield.typing.engines.smirnoff import ForceField + from openff.toolkit.typing.engines.smirnoff import ForceField if isinstance(forcefield_name, str): forcefield = ForceField(forcefield_name) @@ -852,8 +852,8 @@ def get_parameters_from_forcefield(self, forcefield, molecule): openforcefield_parameters : dict The OpenFF parameters stored in a dict keyed by parameter type """ - from openforcefield.typing.engines.smirnoff import ForceField - from openforcefield.topology import Topology + from openff.toolkit.typing.engines.smirnoff import ForceField + from openff.toolkit.topology import Topology off_molecule = molecule.off_molecule topology = Topology.from_molecules([off_molecule]) @@ -892,7 +892,7 @@ def get_parameter_handler_from_forcefield(self, parameter_handler_name, object The ParameterHandler that was requested """ - from openforcefield.typing.engines.smirnoff import ForceField + from openff.toolkit.typing.engines.smirnoff import ForceField if isinstance(forcefield, str): forcefield = ForceField(forcefield)