Add gaussian quadrature test (#87)

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Add an Amber gaussian quadrature test

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correct a mistake in rst file

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Add a testset for multi-lambda simulations with gromacs

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add test for new dataset

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new test

* Delete src/alchemtest/gmx/ethanol directory

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new test

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test

---------

Co-authored-by: Zhiyi Wu <[email protected]>

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

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.

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 <https://creativecommons.org/publicdomain/zero/1.0/>`_
+              Public Domain Dedication
+
+This dataset was generated using the `Amber <http://www.ambermd.org/>`_
+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 <https://doi.org/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 <https://doi.org/10.1021/acs.jctc.0c00237>`_.

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,

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.
 

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
+	      <https://creativecommons.org/publicdomain/zero/1.0/>`_
+	      Public Domain Dedication       
+
+This dataset was generated using input files from `GROMACS 4.6 example: Direct ethanol solvation free energy <http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy>`_, with
+the `Gromacs <http://www.gromacs.org/>`_ 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

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:

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,)),