mirror of
https://github.com/OpenFreeEnergy/openfe.git
synced 2026-06-04 14:14:22 +08:00
Merge branch 'main' into maint/remove_element_change_warning
This commit is contained in:
Irfan Alibay
GitHub
@@ -3,16 +3,16 @@ Checklist for releasing a new version of openfe.
|
||||
-->
|
||||
|
||||
Make the PR:
|
||||
* [ ] Create a new release-prep branch corresponding to the version name, e.g. `release-prep-v1.2.0`. Note: please follow [semantic versioning](https://semver.org/).
|
||||
* [ ] Create a new release prep branch corresponding to the version name, e.g. `release/v1.2.0`. Note: please follow [semantic versioning](https://semver.org/).
|
||||
* [ ] Check that all user-relevant updates are included in the `news/` rever `.rst` files. You can backfill any additional items by making a new .rst, e.g. `backfill.rst`
|
||||
* [ ] Run [rever](https://regro.github.io/rever-docs/index.html#), e.g. `rever 1.2.0`. This will auto-commit `docs/CHANGELOG.md` and remove the `.rst` files from `news/`.
|
||||
* [ ] Verify that`docs/CHANGELOG.rst` looks correct.
|
||||
* [ ] Verify that`docs/CHANGELOG.rst` looks correct and that it renders as expected in the docs preview.
|
||||
* [ ] If needed, create a release of the [example notebooks repository](https://github.com/OpenFreeEnergy/ExampleNotebooks) and update the pinned release version in the `openfe/docs/conf.py`.
|
||||
* [ ] Make the PR and verify that CI/CD passes.
|
||||
* [ ] (feedstock packaging tests)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-feedstock.yaml]
|
||||
* [ ] (example notebooks)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-examplenotebooks.yaml]
|
||||
* [ ] (GPU tests)[https://github.com/OpenFreeEnergy/openfe/actions/workflows/aws-gpu-integration-tests.yaml]
|
||||
* [ ] [feedstock packaging tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-feedstock.yaml)
|
||||
* [ ] [example notebooks](https://github.com/OpenFreeEnergy/openfe/actions/workflows/release-prep-examplenotebooks.yaml)
|
||||
* [ ] [GPU tests](https://github.com/OpenFreeEnergy/openfe/actions/workflows/aws-gpu-integration-tests.yaml)
|
||||
* [ ] Merge the PR into `main`.
|
||||
* [ ] Make a PR into the [example notebooks repository](https://github.com/OpenFreeEnergy/ExampleNotebooks) to update the version used in `showcase/openfe_showcase.ipynb` and `.binder/environment.yml`
|
||||
|
||||
After Merging the PR [follow this guide](https://github.com/OpenFreeEnergy/openfe/wiki/How-to-create-a-new-release)
|
||||
|
||||
|
||||
@@ -4,6 +4,58 @@ Changelog
|
||||
|
||||
.. current developments
|
||||
|
||||
v1.11.1
|
||||
====================
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* Fixed slow response time of CLI commands (`PR #1972 <https://github.com/OpenFreeEnergy/openfe/pull/1972>`_).
|
||||
|
||||
|
||||
|
||||
|
||||
v1.11.0
|
||||
====================
|
||||
|
||||
* **openfe v1.11.0** introduces support for protein-membrane systems both with the Python API and the CLI. See our tutorial `RBFE calculations of a Protein-Membrane System <https://docs.openfree.energy/en/latest/tutorials/rbfe_membrane_protein.html>`_ for details.
|
||||
|
||||
The `ability to resume execution of incomplete transformations <https://docs.openfree.energy/en/v1.10.0/guide/execution/quickrun_execution.html>`_ that was introduced in ``openfe v1.10.0`` is now available for the plain MD and SepTop protocols.
|
||||
|
||||
See below for the full changelog for this release:
|
||||
|
||||
**Added:**
|
||||
|
||||
* Added support for systems with membranes to the following protocols:
|
||||
PlainMDProtocol, RelativeHybridTopologyProtocol, SepTopProtocol, and AbsoluteBindingProtocol (`PR #1561 <https://github.com/OpenFreeEnergy/openfe/pull/1561>`_).
|
||||
* Added support for membrane systems to ``openfe plan-rbfe-network``.
|
||||
Use ``--protein-membrane`` instead of the ``--protein`` argument, and see the tutorial on preparing membrane systems (`PR #1896 <https://github.com/OpenFreeEnergy/openfe/pull/1896>`_).
|
||||
* Added API support for resuming the PlainMDProtocol (`PR #1884 <https://github.com/OpenFreeEnergy/openfe/pull/1884>`_).
|
||||
* Added API support for resuming the SepTopProtocol. (`PR #1949 <https://github.com/OpenFreeEnergy/openfe/pull/1949>`_).
|
||||
* The ``validate`` method for the SepTopProtocol has been implemented.
|
||||
This means that settings and system validation can mostly be done prior to Protocol execuation by calling ``SepTopProtocol.validate(stateA, stateB, mapping=None)`` (`PR #1946 <https://github.com/OpenFreeEnergy/openfe/pull/1946>`_).
|
||||
|
||||
**Changed:**
|
||||
|
||||
* The SepTopProtocol now has a dedicated Analysis unit.
|
||||
At the top level API, this does not change behavior, but if you are directly interfacing with th ProtocolUnits, you will have to account for this change.
|
||||
The SepTopProtocolResult now solely uses the Analysis units (`PR #1937 <https://github.com/OpenFreeEnergy/openfe/pull/1937>`_).
|
||||
* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support (`PR #1933 <https://github.com/OpenFreeEnergy/openfe/pull/1933>`_).
|
||||
* The default value for the Hybrid TopologyProtocol setting ``turn_off_core_unique_exceptions`` has been changed to ``True``.
|
||||
This means 1-4 interactions involving the unique alchemical atoms and core regions will now be interpolated on/off accordingly by default (`PR #1856 <https://github.com/OpenFreeEnergy/openfe/pull/1856>`_).
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* Perses atom mapper and scorer functionality is deprecated, now slated to be removed in ``openfe v1.12``.
|
||||
This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* Fix erroneous logging information message which would mention setting up the alchemical system when running simulation or analysis units with the hybrid topology, AHFE or ABFE Protocols (`PR #1915 <https://github.com/OpenFreeEnergy/openfe/pull/1915>`_).
|
||||
* System equality checks on resuming no longer expect complete equality in the force parameters.
|
||||
This fixes a scenario where small changes in precision due to running on different machines would prevent users from restarting their simulations (`PR #1914 <https://github.com/OpenFreeEnergy/openfe/pull/1914>`_).
|
||||
|
||||
|
||||
|
||||
v1.10.0
|
||||
====================
|
||||
|
||||
@@ -19,7 +71,7 @@ See the `quickrun documentation <https://docs.openfree.energy/en/v1.10.0/guide/e
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0``.
|
||||
* Perses atom mapper and scorer functionality is deprecated, slated to be removed in ``openfe v2.0``.
|
||||
This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
|
||||
|
||||
**Fixed:**
|
||||
@@ -90,7 +142,7 @@ v1.8.0
|
||||
|
||||
**Added:**
|
||||
|
||||
* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms.
|
||||
* The ``HybridTopologyFactory`` supports building hybrid OpenMM systems which contain ``CMAPTorsionForces`` on non-alchemical atoms.
|
||||
This should allow for simulations using Amber ff19SB (`PR #1695 <https://github.com/OpenFreeEnergy/openfe/pull/1695>`_).
|
||||
* Added experimental features ``openfe gather-septop`` and ``openfe gather-abfe``, which are analogous to ``openfe gather`` and allow for gathering results generated by the Separated Topologies and Absolute Binding Free Energy protocols, respectively. These commands are experimental and are liable to be changed in a future release.
|
||||
* Emit a clarifying log message when a user gets a warning from JAX (`PR #1585 <https://github.com/OpenFreeEnergy/openfe/pull/1585>`_, fixes `Issue #1499 <https://github.com/OpenFreeEnergy/openfe/issues/1499>`_).
|
||||
|
||||
@@ -193,7 +193,7 @@ try:
|
||||
else:
|
||||
repo = git.Repo.clone_from(
|
||||
"https://github.com/OpenFreeEnergy/ExampleNotebooks.git",
|
||||
branch="main", # TODO: update this after making ExampleNotebooks release
|
||||
branch="2026.04.28",
|
||||
to_path=example_notebooks_path,
|
||||
)
|
||||
except Exception as e:
|
||||
|
||||
@@ -6,8 +6,7 @@ See `Supported Hardware`_ for more details.
|
||||
|
||||
We try to follow `SPEC0 <https://scientific-python.org/specs/spec-0000/>`_ as far as minimum supported dependencies, with the following caveats:
|
||||
|
||||
- OpenMM 8.0, 8.1.2, 8.2.0 - **we do not yet support OpenMM v8.3.0**
|
||||
- ``OpenEye Toolkits`` is not yet compatible with Python 3.13, so **openfe** cannot use openeye functionality with Python 3.13.
|
||||
- OpenMM 8.0, 8.1.2, 8.2, and 8.4 - **OpenMM v8.3.0 is not supported**
|
||||
|
||||
When you install **openfe** through any of the methods described below, you will install both the core library and the command line interface (CLI).
|
||||
|
||||
@@ -417,7 +416,7 @@ functionality. This is called a "developer" or "editable" installation.
|
||||
|
||||
Getting a developer installation for **openfe** first installing the
|
||||
requirements, and then creating the editable installation. We recommend
|
||||
doing that with ``mamba`` using the following procedure:
|
||||
doing that with ``micromamba`` using the following procedure:
|
||||
|
||||
First, clone the **openfe** repository, and switch into its root directory::
|
||||
|
||||
@@ -427,11 +426,11 @@ First, clone the **openfe** repository, and switch into its root directory::
|
||||
Next create a ``conda`` environment containing the requirements from the
|
||||
specification in that directory::
|
||||
|
||||
$ mamba create -f environment.yml
|
||||
$ micromamba create -f environment.yml
|
||||
|
||||
Then activate the **openfe** environment with::
|
||||
Then activate the openfe environment with::
|
||||
|
||||
$ mamba activate openfe
|
||||
$ micromamba activate openfe_env
|
||||
|
||||
Finally, create the editable installation::
|
||||
|
||||
|
||||
@@ -19,7 +19,7 @@ dependencies:
|
||||
- openff-toolkit-base >=0.16.2
|
||||
- openff-units==0.3.1 # https://github.com/OpenFreeEnergy/openfe/pull/1374
|
||||
- openmm ~=8.4.0 # omit 8.3.0 and 8.3.1 due to https://github.com/openmm/openmm/pull/5069
|
||||
- openmmforcefields >=0.15.1 # min needed for https://github.com/OpenFreeEnergy/openfe/pull/414
|
||||
- openmmforcefields >=0.15.1 # min needed for https://github.com/openmm/openmmforcefields/pull/414
|
||||
- openmmtools >=0.26 # fix to support membrane barostat: https://github.com/choderalab/openmmtools/pull/798
|
||||
- packaging
|
||||
- pandas
|
||||
|
||||
25
news/afe-uuid.rst
Normal file
25
news/afe-uuid.rst
Normal file
@@ -0,0 +1,25 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* AFE Protocols (AbsoluteBindingProtocol and AbsoluteSolvationProtocol)
|
||||
now assign a single uuid for all ProtocolUnits in a repeat rather than
|
||||
separating the uuid by legs of the transformation. PR #1948
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,27 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* The SepTopProtocol now has a dedicated Analysis unit.
|
||||
At the top level API, this does not change behaviour, but
|
||||
if you are directly interfacing with the ProtocolUnits, you
|
||||
will have to account for this change. The SepTopProtocolResult now
|
||||
solely uses the Analysis units. PR #1937
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,24 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* Perses atom mapper and scorer functionality is deprecated, now slated to be removed in ``openfe v1.12``.
|
||||
This includes ``PersesAtomMapper`` and ``default_perses_scorer`` (`PR #1857 <https://github.com/OpenFreeEnergy/openfe/pull/1857>`_).
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,25 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* Fix erroneous logging information message which would mention
|
||||
setting up the alchemical system when running simulation or
|
||||
analysis units with the hybrid topology, AHFE or ABFE Protocols (PR #1915).
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,23 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* The default value for the Hybrid TopologyProtocol setting ``turn_off_core_unique_exceptions`` has been changed to ``True`. This means 1-4 interactions involving the unique alchemical atoms and core regions will now be interpolated on/off accordingly by default PR #1856.
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,26 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* System equality checks on resuming no longer expect complete equality
|
||||
in the force parameters. This fixes a scenario where small changes
|
||||
in precision due to running on different machines would prevent users from
|
||||
restarting their simulations (Issue #1913, PR #1914).
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,24 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* Added support for systems with membranes to the following protocols:
|
||||
PlainMDProtocol, RelativeHybridTopologyProtocol, SepTopProtocol, and AbsoluteBindingProtocol.
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,24 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* Added support for membrane systems to ``openfe plan-rbfe-network``.
|
||||
Use ``--protein-membrane`` instead of the ``--protein`` argument, and see the tutorial on preparing membrane systems (`PR #1896 <https://github.com/OpenFreeEnergy/openfe/pull/1896>`_).
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,24 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* * Added API support for resuming the PlainMDProtocol.
|
||||
PR #1884.
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,24 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* Added API support for resuming the SepTopProtocol.
|
||||
PR #1949.
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,23 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Changed:**
|
||||
|
||||
* Updated the chemical systems user guide and the defining protocols user guide to reflect recent protocol updates, including adding membrane support.
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -1,26 +0,0 @@
|
||||
**Added:**
|
||||
|
||||
* The `validate` method for the SepTopProtocol has been implemented.
|
||||
This means that settings and system validation can mostly be done prior
|
||||
to Protocol execuation by calling
|
||||
`SepTopProtocol.validate(stateA, stateB, mapping=None)`.
|
||||
|
||||
**Changed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Deprecated:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Removed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Fixed:**
|
||||
|
||||
* <news item>
|
||||
|
||||
**Security:**
|
||||
|
||||
* <news item>
|
||||
@@ -502,10 +502,9 @@ class AbsoluteBindingProtocol(gufe.Protocol):
|
||||
|
||||
protocol_units: dict[str, list[gufe.ProtocolUnit]] = {"solvent": [], "complex": []}
|
||||
|
||||
for phase in ["solvent", "complex"]:
|
||||
for i in range(self.settings.protocol_repeats):
|
||||
repeat_id = int(uuid.uuid4())
|
||||
|
||||
for i in range(self.settings.protocol_repeats):
|
||||
repeat_id = int(uuid.uuid4())
|
||||
for phase in ["solvent", "complex"]:
|
||||
setup = unit_classes[phase]["setup"](
|
||||
protocol=self,
|
||||
stateA=stateA,
|
||||
|
||||
@@ -466,10 +466,9 @@ class AbsoluteSolvationProtocol(gufe.Protocol):
|
||||
|
||||
protocol_units: dict[str, list[gufe.ProtocolUnit]] = {"solvent": [], "vacuum": []}
|
||||
|
||||
for phase in ["solvent", "vacuum"]:
|
||||
for i in range(self.settings.protocol_repeats):
|
||||
repeat_id = int(uuid.uuid4())
|
||||
|
||||
for i in range(self.settings.protocol_repeats):
|
||||
repeat_id = int(uuid.uuid4())
|
||||
for phase in ["solvent", "vacuum"]:
|
||||
setup = unit_classes[phase]["setup"](
|
||||
protocol=self,
|
||||
stateA=stateA,
|
||||
|
||||
@@ -158,8 +158,8 @@ def test_create_independent_repeat_ids(benzene_modifications, T4_protein_compone
|
||||
for u in dag.protocol_units:
|
||||
repeat_ids.add(u.inputs["repeat_id"])
|
||||
|
||||
# squashed by repeat_id, that's 2 sets of 6
|
||||
assert len(repeat_ids) == 12
|
||||
# squashed by repeat_id, that's 1 uuid per repeat
|
||||
assert len(repeat_ids) == 6
|
||||
|
||||
|
||||
def test_mda_universe_error():
|
||||
|
||||
@@ -142,8 +142,8 @@ def test_create_independent_repeat_ids(benzene_system):
|
||||
for u in dag.protocol_units:
|
||||
repeat_ids.add(u.inputs["repeat_id"])
|
||||
|
||||
# squashed by repeat_id, that's 2 sets of 6
|
||||
assert len(repeat_ids) == 12
|
||||
# squashed by repeat_id, that's 1 uuid by repeat
|
||||
assert len(repeat_ids) == 6
|
||||
|
||||
|
||||
def _assert_num_forces(system, forcetype, number):
|
||||
|
||||
@@ -6,7 +6,6 @@ from typing import List, Literal
|
||||
import click
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
from openff.units import unit
|
||||
|
||||
from openfecli import OFECommandPlugin
|
||||
from openfecli.clicktypes import HyphenAwareChoice
|
||||
@@ -108,6 +107,8 @@ def _get_legs_from_result_jsons(
|
||||
"""
|
||||
from collections import defaultdict
|
||||
|
||||
from openff.units import unit
|
||||
|
||||
dgs = defaultdict(lambda: defaultdict(list))
|
||||
|
||||
for result_fn in result_fns:
|
||||
|
||||
@@ -6,8 +6,6 @@ from typing import List, Literal
|
||||
import click
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
from cinnabar import FEMap, Measurement
|
||||
from openff.units import unit
|
||||
|
||||
from openfecli import OFECommandPlugin
|
||||
from openfecli.clicktypes import HyphenAwareChoice
|
||||
@@ -84,6 +82,8 @@ def _get_legs_from_result_jsons(
|
||||
"""
|
||||
from collections import defaultdict
|
||||
|
||||
from openff.units import unit
|
||||
|
||||
ddgs = defaultdict(lambda: defaultdict(list))
|
||||
|
||||
for result_fn in result_fns:
|
||||
@@ -253,6 +253,8 @@ def _generate_dg_mle(
|
||||
pd.DataFrame
|
||||
A pandas DataFrame with the dG results for each ligand pair.
|
||||
"""
|
||||
from cinnabar import FEMap, Measurement
|
||||
from openff.units import unit
|
||||
|
||||
DDGs = _get_ddgs(results_dict)
|
||||
|
||||
|
||||
@@ -4,11 +4,7 @@ import sys
|
||||
import click
|
||||
import pytest
|
||||
|
||||
from openfe.data import _downloader
|
||||
from openfe.data._registry import zenodo_data_registry as api_test_data_registry
|
||||
from openfecli import OFECommandPlugin
|
||||
from openfecli.data._registry import POOCH_CACHE
|
||||
from openfecli.data._registry import zenodo_data_registry as cli_test_data_registry
|
||||
from openfecli.utils import write
|
||||
|
||||
|
||||
@@ -34,7 +30,13 @@ def test(long, download_only):
|
||||
"""
|
||||
|
||||
if download_only:
|
||||
from openfe.data import _downloader
|
||||
from openfe.data._registry import zenodo_data_registry as api_test_data_registry
|
||||
from openfecli.data._registry import POOCH_CACHE
|
||||
from openfecli.data._registry import zenodo_data_registry as cli_test_data_registry
|
||||
|
||||
click.echo(f"Checking for test data in cache location:\n{POOCH_CACHE}")
|
||||
|
||||
_downloader.retrieve_registry_data(
|
||||
cli_test_data_registry + api_test_data_registry, POOCH_CACHE
|
||||
)
|
||||
|
||||
@@ -6,8 +6,6 @@ from typing import Iterable
|
||||
import click
|
||||
from plugcli.params import Option
|
||||
|
||||
from openfe import ProteinComponent, ProteinMembraneComponent
|
||||
|
||||
_PDB_EXT = [".pdb"]
|
||||
_PDBX_EXT = [".cif", ".pdbx"]
|
||||
|
||||
@@ -16,7 +14,7 @@ def _contains_any_substring(input: str, substrings: Iterable[str]) -> bool:
|
||||
return any([substring in input for substring in substrings])
|
||||
|
||||
|
||||
def _load_protein_from_file(input_file, protein_class: ProteinComponent | ProteinMembraneComponent):
|
||||
def _load_protein_from_file(input_file, protein_class):
|
||||
valid_ext = _PDB_EXT + _PDBX_EXT
|
||||
info_str = (
|
||||
f"Unable to load a {protein_class.__name__} from {click.format_filename(input_file)}: "
|
||||
@@ -34,10 +32,14 @@ def _load_protein_from_file(input_file, protein_class: ProteinComponent | Protei
|
||||
|
||||
# TODO: these functions are shims to work with plugcli. We should consider migrating to just click.
|
||||
def _get_protein(user_input, context):
|
||||
from openfe import ProteinComponent
|
||||
|
||||
return _load_protein_from_file(user_input, ProteinComponent)
|
||||
|
||||
|
||||
def _get_protein_membrane(user_input, context):
|
||||
from openfe import ProteinMembraneComponent
|
||||
|
||||
return _load_protein_from_file(user_input, ProteinMembraneComponent)
|
||||
|
||||
|
||||
|
||||
@@ -2,7 +2,6 @@
|
||||
# For details, see https://github.com/OpenFreeEnergy/openfe
|
||||
from __future__ import annotations
|
||||
|
||||
import json
|
||||
import pathlib
|
||||
|
||||
from openfe import AlchemicalNetwork, LigandNetwork
|
||||
|
||||
Reference in New Issue
Block a user