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Merge pull request #7 from OpenFreeEnergy/start_GromacsMDProtocol
GromacsMDSetupUnit
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name: test | ||
channels: | ||
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- jaimergp/label/unsupported-cudatoolkit-shim | ||
- conda-forge | ||
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- defaults | ||
dependencies: | ||
# Base depends | ||
- python | ||
- pip | ||
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- openff-toolkit-base >=0.16 | ||
- openff-units | ||
- openff-models | ||
- ambertools =23 | ||
# Testing | ||
- pytest | ||
- pytest-xdist | ||
- pytest-cov | ||
- pydantic >1 | ||
- codecov | ||
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# Pip-only installs | ||
#- pip: | ||
# - codecov | ||
- numpy | ||
- networkx | ||
- rdkit | ||
- openfe>=1.0.0rc0 | ||
- click | ||
- openmm | ||
- openmmtools | ||
- plugcli | ||
- gufe |
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name: test | ||
channels: | ||
- conda-forge | ||
dependencies: | ||
- openfe | ||
- compilers | ||
- mpi4py | ||
- gromacs | ||
- pytest | ||
- pytest-xdist | ||
- pytest-cov |
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"""Gromacs-based protocols for Open Free Energy""" | ||
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# Add imports here | ||
from ._version import __version__ # noqa: F401 | ||
from .openfe_gromacs import * # noqa: F401,F403 | ||
from gufe import ( | ||
AlchemicalNetwork, | ||
ChemicalSystem, | ||
Component, | ||
LigandAtomMapping, | ||
NonTransformation, | ||
ProteinComponent, | ||
SmallMoleculeComponent, | ||
SolventComponent, | ||
Transformation, | ||
) | ||
from gufe.protocols import ( | ||
Protocol, | ||
ProtocolDAG, | ||
ProtocolDAGResult, | ||
ProtocolResult, | ||
ProtocolUnit, | ||
ProtocolUnitFailure, | ||
ProtocolUnitResult, | ||
execute_DAG, | ||
) |
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# This code is part of OpenFE and is licensed under the MIT license. | ||
# For details, see https://github.com/OpenFreeEnergy/openfe-gromacs |
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# This code is part of OpenFE and is licensed under the MIT license. | ||
# For details, see https://github.com/OpenFreeEnergy/openfe-gromacs | ||
""" | ||
Run MD simulation using OpenMM and OpenMMTools. | ||
""" | ||
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from .md_methods import ( | ||
GromacsMDProtocol, | ||
GromacsMDProtocolResult, | ||
GromacsMDProtocolSettings, | ||
GromacsMDSetupUnit, | ||
) | ||
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__all__ = [ | ||
"GromacsMDProtocol", | ||
"GromacsMDProtocolSettings", | ||
"GromacsMDProtocolResult", | ||
"GromacsMDProtocolUnit", | ||
] |
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