diff --git a/src/alchemtest/amber/__init__.py b/src/alchemtest/amber/__init__.py
index 63cc447..1c772f5 100644
--- a/src/alchemtest/amber/__init__.py
+++ b/src/alchemtest/amber/__init__.py
@@ -4,6 +4,7 @@
from .access import load_bace_improper
from .access import load_bace_example
+from .access import load_tyk2_example
from .access import load_simplesolvated
from .access import load_invalidfiles
from .access import load_testfiles
diff --git a/src/alchemtest/amber/access.py b/src/alchemtest/amber/access.py
index 36122ef..8e3c086 100644
--- a/src/alchemtest/amber/access.py
+++ b/src/alchemtest/amber/access.py
@@ -58,6 +58,27 @@ def load_bace_example():
return Bunch(data=data,
DESCR=fdescr)
+def load_tyk2_example():
+ """Load Amber TYK2 example perturbation.
+
+ Returns
+ -------
+ data: Bunch
+ Dictionary-like object, the interesting attributes are:
+
+ - 'data' : the data files by system and alchemical leg
+
+ """
+ module_path = Path(__file__).parent
+ data = {'complex': list(map(str, module_path.glob('tyk2_ejm_47~ejm_31/complex/*/ti-*.out.bz2'))),
+ 'solvated': list(map(str, module_path.glob('tyk2_ejm_47~ejm_31/solvated/*/ti-*.out.bz2')))
+ }
+
+ with open(module_path / 'tyk2_ejm_47~ejm_31' / 'descr.rst') as rst_file:
+ fdescr = rst_file.read()
+
+ return Bunch(data=data,
+ DESCR=fdescr)
def load_simplesolvated():
"""Load the Amber solvated dataset.
diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.00922/ti-0.00922.out.bz2 b/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.00922/ti-0.00922.out.bz2
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diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst b/src/alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst
new file mode 100644
index 0000000..234b809
--- /dev/null
+++ b/src/alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst
@@ -0,0 +1,43 @@
+Amber: Small molecule thermodynamic integration free energy difference in water
+===============================================================================
+
+TYK2 complex and solvated small molecule perturbation, alchemical perturbation of ligand 1 into ligand
+2. This example uses ligands ejm_47 to ejm_31 from [Wang2015a]_.
+
+
+Notes
+-----
+Data Set Characteristics:
+ :Number of Legs: 1 (1 step concerted)
+ :Number of Windows: 12 for each leg
+ :Length of Windows: 5ns
+ :System Size: 24229 atoms (complex), 9932 atoms (solvated)
+ :Temperature: 300 K
+ :Pressure: 1 bar
+ :Alchemical Pathway: ligand 1 --> ligand 2,
+ smoothstep softcore (SSC) potential [Lee2020a]_
+ used in both complex and solvated legs
+ :Experimental Free Energy difference: 0.16 kcal/mol
+ :Missing Values: None
+ :Energy unit: kcal/mol
+ :Time unit: ps
+ :Date: March 2023
+ :License: `CC0 `_
+ Public Domain Dedication
+
+This dataset was generated using the `Amber `_
+molecular dynamics engine.
+
+
+.. [Wang2015a] L. Wang, Y. Wu, Y. Deng, B. Kim, L. Pierce, G. Krilov, D. Lupyan, S. Robinson, M. K. Dahlgren, J. Greenwood, D. L. Romero, C. Masse, J. L. Knight, T. Steinbrecher, T. Beuming, W. Damm, E. Harder, W. Sherman, M. Brewer, R. Wester, M. Murcko, L. Frye, R. Farid, T. Lin, D. L. Mobley, W. L. Jorgensen, B. J. Berne, R. A. Friesner,
+ and R. Abel. Accurate and reliable prediction of
+ relative ligand binding potency in prospective drug
+ discovery by way of a modern free-energy calculation
+ protocol and force field. Journal of the American
+ Chemical Society,
+ 137(7):2695–2703, 2015. PMID: 25625324. DOI:
+ `10.1021/ja512751q `_.
+
+.. [Lee2020a] T.-S. Lee, Z. Lin, B. K. Allen, C. Lin, B. K. Radak, Y. Tao, H.-C. Tsai, W. Sherman and D. M. York. Improved Alchemical Free Energy Calculations with Optimized Smoothstep Softcore Potentials. Journal of Chemical Theory and Computation,
+ 16(9):5512–5525, 2020. PMID: 32672455. DOI:
+ `10.1021/acs.jctc.0c00237 `_.
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diff --git a/src/alchemtest/gmx/__init__.py b/src/alchemtest/gmx/__init__.py
index 10a3869..68c868d 100644
--- a/src/alchemtest/gmx/__init__.py
+++ b/src/alchemtest/gmx/__init__.py
@@ -3,7 +3,7 @@
"""
from .access import load_benzene
-from .access import (load_benzene, load_ABFE,
+from .access import (load_benzene, load_ethanol, load_ABFE,
load_expanded_ensemble_case_1,
load_expanded_ensemble_case_2,
load_expanded_ensemble_case_3,
diff --git a/src/alchemtest/gmx/access.py b/src/alchemtest/gmx/access.py
index 7ddb19f..52f7356 100644
--- a/src/alchemtest/gmx/access.py
+++ b/src/alchemtest/gmx/access.py
@@ -31,6 +31,30 @@ def load_benzene():
return Bunch(data=data,
DESCR=fdescr)
+def load_ethanol():
+ """Load the Gromacs ethanol dataset.
+
+ Returns
+ -------
+ data : Bunch
+ Dictionary-like object, the interesting attributes are:
+
+ - 'data' : the data files by alchemical leg
+ - 'DESCR': the full description of the dataset
+
+ """
+
+ module_path = dirname(__file__)
+
+ data = {'Coulomb': sorted(glob(join(module_path, 'ethanol', 'Coulomb', 'dhdl.*.xvg.bz2'))),
+ 'VDW': sorted(glob(join(module_path, 'ethanol', 'VDW', 'dhdl.*.xvg.bz2')))}
+
+ with open(join(module_path, 'ethanol', 'descr.rst')) as rst_file:
+ fdescr = rst_file.read()
+
+ return Bunch(data=data,
+ DESCR=fdescr)
+
def load_ABFE():
"""Load the Gromacs ABFE dataset.
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diff --git a/src/alchemtest/gmx/ethanol/descr.rst b/src/alchemtest/gmx/ethanol/descr.rst
new file mode 100644
index 0000000..ead257d
--- /dev/null
+++ b/src/alchemtest/gmx/ethanol/descr.rst
@@ -0,0 +1,32 @@
+Gromacs: Ethanol in water
+=========================
+
+Ethanol in water, alchemically turned into ethanol in vacuum separated from water
+
+Notes
+-----
+Data Set Characteristics:
+ :Number of Legs: 2 (Coulomb, VDW)
+ :Number of Windows: 14 for Coulomb, 13 for VDW
+ :Length of Windows: 6ns
+ :System Size: 2694 atoms
+ :Temperature: 300 K
+ :Pressure: 1 bar
+ :Alchemical Pathway: vdw + coul --> vdw --> vacuum
+ :Experimental Hydration Free Energy: -5.00 +- 0.6 kcal/mol
+ :Missing Values: None
+ :Energy unit: kJ/mol
+ :Time unit: ps
+ :Date: April 2023
+ :License: `CC0
+ `_
+ Public Domain Dedication
+
+This dataset was generated using input files from `GROMACS 4.6 example: Direct ethanol solvation free energy `_, with
+the `Gromacs `_ molecular dynamics engine.
+
+Experimental value sourced from [Mobley2013]_.
+
+.. [Mobley2013] Mobley, David L. (2013). Experimental and Calculated Small
+ Molecule Hydration Free Energies. UC Irvine: Department of Pharmaceutical
+ Sciences, UCI. Retrieved from: http://escholarship.org/uc/item/6sd403pz
diff --git a/src/alchemtest/tests/test_amber.py b/src/alchemtest/tests/test_amber.py
index 39287a1..17c3ec9 100644
--- a/src/alchemtest/tests/test_amber.py
+++ b/src/alchemtest/tests/test_amber.py
@@ -4,7 +4,7 @@
from alchemtest import Bunch
from alchemtest.amber import (load_bace_improper, load_bace_example,
load_simplesolvated, load_invalidfiles,
- load_testfiles, )
+ load_testfiles, load_tyk2_example)
@@ -67,6 +67,26 @@ def dataset(self, request):
return super(TestBACEexample, self).dataset(request)
+# test tyk2 example
+def _load_tyk2_example():
+ dset = load_tyk2_example()
+ return Bunch(data=dset.data,
+ DESCR="TYK2 example:")
+
+class TestTYK2example(BaseDatasetTest):
+ # use pytest.param to add the id for nicer pytest -v output
+ @pytest.fixture(scope="class",
+ params = [
+ pytest.param(
+ (_load_tyk2_example,
+ ('complex', 'solvated'),
+ (12, 12)),
+ id="tyk2"),
+ ])
+ def dataset(self, request):
+ return super(TestTYK2example, self).dataset(request)
+
+
# The invalidfiles dataset does not conform to the API. load_invalidfiles()
# returns a listv with just one element as data (and not a dict) so we create a
# fake dataset:
diff --git a/src/alchemtest/tests/test_gmx.py b/src/alchemtest/tests/test_gmx.py
index 9b2798d..0b97b8a 100644
--- a/src/alchemtest/tests/test_gmx.py
+++ b/src/alchemtest/tests/test_gmx.py
@@ -1,7 +1,7 @@
'''Tests for all the gromacs dataset'''
import pytest
-from alchemtest.gmx import (load_benzene, load_ABFE,
+from alchemtest.gmx import (load_benzene, load_ABFE, load_ethanol,
load_expanded_ensemble_case_1,
load_expanded_ensemble_case_2,
load_expanded_ensemble_case_3,
@@ -17,6 +17,7 @@ class TestGROMACS(BaseDatasetTest):
@pytest.fixture(scope="class",
params = [(load_benzene, ('Coulomb', 'VDW'), (5, 16)),
(load_ABFE, ('complex', 'ligand'), (30, 20)),
+ (load_ethanol, ('Coulomb', 'VDW'), (14, 13)),
(load_expanded_ensemble_case_1, ('AllStates', ), (1,)),
(load_expanded_ensemble_case_2, ('AllStates', ), (2,)),
(load_expanded_ensemble_case_3, ('AllStates', ), (32,)),