Update molecule mapping

CI/functional_tests/test_water_study.py

@@ -0,0 +1,107 @@
+"""
+MDSuite: A Zincwarecode package.
+
+License
+-------
+This program and the accompanying materials are made available under the terms
+of the Eclipse Public License v2.0 which accompanies this distribution, and is
+available at https://www.eclipse.org/legal/epl-v20.html
+
+SPDX-License-Identifier: EPL-2.0
+
+Copyright Contributors to the Zincwarecode Project.
+
+Contact Information
+-------------------
+email: [email protected]
+github: https://github.com/zincware
+web: https://zincwarecode.com/
+
+Citation
+--------
+If you use this module please cite us with:
+
+Summary
+-------
+Functional test for the analysis of a GROMACS water simulation.
+"""
+from typing import List
+
+import pytest
+from zinchub import DataHub
+
+import mdsuite as mds
+import mdsuite.file_io.chemfiles_read
+from mdsuite.utils import Units
+
+
+@pytest.fixture(scope="session")
+def traj_files(tmp_path_factory) -> List[str]:
+    """Download trajectory file into a temporary directory and keep it for all tests"""
+    temporary_path = tmp_path_factory.getbasetemp()
+
+    water = DataHub(url="https://github.com/zincware/DataHub/tree/main/Water_14_Gromacs")
+    water.get_file(temporary_path)
+    file_paths = [(temporary_path / f).as_posix() for f in water.file_raw]
+    return file_paths
+
+
+@pytest.fixture()
+def mdsuite_project(traj_files, tmp_path) -> mdsuite.Project:
+    """
+    Create the MDSuite project and add data to be used for the rest of the tests.
+
+    Parameters
+    ----------
+    traj_files : list
+            Files include:
+                * Water Simulation
+    tmp_path : Path
+            Temporary path that may be changed into.
+
+    Returns
+    -------
+    project: mdsuite.Project
+            An MDSuite project to be tested.
+    """
+    gmx_units = Units(
+        time=1e-12,
+        length=1e-10,
+        energy=1.6022e-19,
+        NkTV2p=1.6021765e6,
+        boltzmann=8.617343e-5,
+        temperature=1,
+        pressure=100000,
+    )
+    project = mds.Project(storage_path=tmp_path.as_posix())
+
+    file_reader = mdsuite.file_io.chemfiles_read.ChemfilesRead(
+        traj_file_path=traj_files[2], topol_file_path=traj_files[0]
+    )
+
+    project.add_experiment(
+        name="water_sim",
+        timestep=0.002,
+        temperature=300.0,
+        units=gmx_units,
+        simulation_data=file_reader,
+    )
+    project.run.CoordinateWrapper()
+    return project
+
+
+def test_water_analysis(mdsuite_project):
+    """Run a functional test by performing a study on an MD simulation of water"""
+
+    water = mdsuite_project.experiments["water_sim"]
+
+    water.run.MolecularMap(
+        molecules={"water": {"smiles": "[H]O[H]", "amount": 14, "cutoff": 1.7}}
+    )
+    mdsuite_project.run.AngularDistributionFunction(plot=False)
+    mdsuite_project.run.RadialDistributionFunction(plot=False)
+    mdsuite_project.run.AngularDistributionFunction(plot=False, molecules=True)
+    mdsuite_project.run.RadialDistributionFunction(plot=False, molecules=True)
+    mdsuite_project.run.EinsteinDiffusionCoefficients(plot=False)
+    mdsuite_project.run.EinsteinDiffusionCoefficients(plot=False, molecules=True)
+    mdsuite_project.run.GreenKuboDiffusionCoefficients(plot=False)

CI/integration_tests/transformations/test_molecular_mapping_results.py

@@ -0,0 +1,206 @@
+"""
+MDSuite: A Zincwarecode package.
+
+License
+-------
+This program and the accompanying materials are made available under the terms
+of the Eclipse Public License v2.0 which accompanies this distribution, and is
+available at https://www.eclipse.org/legal/epl-v20.html
+
+SPDX-License-Identifier: EPL-2.0
+
+Copyright Contributors to the Zincwarecode Project.
+
+Contact Information
+-------------------
+email: [email protected]
+github: https://github.com/zincware
+web: https://zincwarecode.com/
+
+Citation
+--------
+If you use this module please cite us with:
+
+Summary
+-------
+Test the outcome of molecular mapping.
+"""
+from typing import List
+
+import pytest
+from zinchub import DataHub
+
+import mdsuite
+import mdsuite.file_io.chemfiles_read
+import mdsuite.transformations
+from mdsuite.utils import Units
+
+
+@pytest.fixture(scope="session")
+def traj_files(tmp_path_factory) -> List[str]:
+    """Download trajectory file into a temporary directory and keep it for all tests"""
+    temporary_path = tmp_path_factory.getbasetemp()
+
+    water = DataHub(url="https://github.com/zincware/DataHub/tree/main/Water_14_Gromacs")
+    water.get_file(temporary_path)
+    file_paths = [(temporary_path / f).as_posix() for f in water.file_raw]
+    return file_paths
+
+
+@pytest.fixture()
+def mdsuite_project(traj_files, tmp_path) -> mdsuite.Project:
+    """
+    Create the MDSuite project and add data to be used for the rest of the tests.
+
+    Parameters
+    ----------
+    traj_files : list
+            Files include:
+                * Water Simulation
+    tmp_path : Path
+            Temporary path that may be changed into.
+
+    Returns
+    -------
+    project: mdsuite.Project
+            An MDSuite project to be tested.
+    """
+    gmx_units = Units(
+        time=1e-12,
+        length=1e-10,
+        energy=1.6022e-19,
+        NkTV2p=1.6021765e6,
+        boltzmann=8.617343e-5,
+        temperature=1,
+        pressure=100000,
+    )
+    project = mdsuite.Project(storage_path=tmp_path.as_posix())
+
+    file_reader_1 = mdsuite.file_io.chemfiles_read.ChemfilesRead(
+        traj_file_path=traj_files[2], topol_file_path=traj_files[0]
+    )
+    file_reader_2 = mdsuite.file_io.chemfiles_read.ChemfilesRead(
+        traj_file_path=traj_files[2], topol_file_path=traj_files[1]
+    )
+    project.add_experiment(
+        name="simple_water",
+        timestep=0.002,
+        temperature=300.0,
+        units=gmx_units,
+        simulation_data=file_reader_1,
+    )
+    project.add_experiment(
+        name="ligand_water",
+        timestep=0.002,
+        temperature=300.0,
+        units=gmx_units,
+        simulation_data=file_reader_2,
+    )
+
+    project.run.CoordinateWrapper()
+
+    return project
+
+
+def test_water_molecule_smiles(mdsuite_project):
+    """
+    Test that water molecules are built correctly using a SMILES string. Also check
+    that the molecule information is stored correctly in the experiment.
+
+    Parameters
+    ----------
+    mdsuite_project : Callable
+            Callable that returns an MDSuite project created in a temporary
+            directory.
+
+    Returns
+    -------
+    Tests that the molecule groups detected are done so correctly and that the
+    constructed trajectory is also correct.
+    """
+    reference_molecules = {
+        "water": {
+            "n_particles": 14,
+            "indices": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13],
+            "mass": 18.015,
+            "groups": {
+                "0": {"H": [0, 1], "O": [0]},
+                "1": {"H": [2, 3], "O": [1]},
+                "2": {"H": [4, 5], "O": [2]},
+                "3": {"H": [6, 7], "O": [3]},
+                "4": {"H": [8, 9], "O": [4]},
+                "5": {"H": [10, 11], "O": [5]},
+                "6": {"H": [12, 13], "O": [6]},
+                "7": {"H": [14, 15], "O": [7]},
+                "8": {"H": [16, 17], "O": [8]},
+                "9": {"H": [18, 19], "O": [9]},
+                "10": {"H": [20, 21], "O": [10]},
+                "11": {"H": [22, 23], "O": [11]},
+                "12": {"H": [24, 25], "O": [12]},
+                "13": {"H": [26, 27], "O": [13]},
+            },
+        }
+    }
+    mdsuite_project.experiments["simple_water"].run.MolecularMap(
+        molecules={"water": {"smiles": "[H]O[H]", "amount": 14, "cutoff": 1.7}}
+    )
+    molecules = mdsuite_project.experiments["simple_water"].molecules
+    assert molecules == reference_molecules
+
+    assert "water" not in mdsuite_project.experiments["simple_water"].species
+
+
+def test_water_molecule_reference_dict(mdsuite_project):
+    """
+    Test that water molecules are built correctly using a reference dict.
+
+    Parameters
+    ----------
+    mdsuite_project : Callable
+            Callable that returns an MDSuite project created in a temporary
+            directory.
+
+    Returns
+    -------
+    Tests that the molecule groups detected are done so correctly and that the
+    constructed trajectory is also correct.
+    """
+    mdsuite_project.experiments["ligand_water"].species["OW"].mass = [15.999]
+    mdsuite_project.experiments["ligand_water"].species["HW1"].mass = [1.00784]
+    mdsuite_project.experiments["ligand_water"].species["HW2"].mass = [1.00784]
+    reference_molecules = {
+        "water": {
+            "n_particles": 14,
+            "indices": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13],
+            "mass": 18.014680000000002,
+            "groups": {
+                "0": {"HW1": [0], "OW": [0], "HW2": [0]},
+                "1": {"HW1": [1], "OW": [1], "HW2": [1]},
+                "2": {"HW1": [2], "OW": [2], "HW2": [2]},
+                "3": {"HW1": [3], "OW": [3], "HW2": [3]},
+                "4": {"HW1": [4], "OW": [4], "HW2": [4]},
+                "5": {"HW1": [5], "OW": [5], "HW2": [5]},
+                "6": {"HW1": [6], "OW": [6], "HW2": [6]},
+                "7": {"HW1": [7], "OW": [7], "HW2": [7]},
+                "8": {"HW1": [8], "OW": [8], "HW2": [8]},
+                "9": {"HW1": [9], "OW": [9], "HW2": [9]},
+                "10": {"HW1": [10], "OW": [10], "HW2": [10]},
+                "11": {"HW1": [11], "OW": [11], "HW2": [11]},
+                "12": {"HW1": [12], "OW": [12], "HW2": [12]},
+                "13": {"HW1": [13], "OW": [13], "HW2": [13]},
+            },
+        }
+    }
+    mdsuite_project.experiments["ligand_water"].run.MolecularMap(
+        molecules={
+            "water": {
+                "reference": {"OW": 1, "HW1": 1, "HW2": 1},
+                "amount": 14,
+                "cutoff": 1.7,
+            }
+        }
+    )
+    molecules = mdsuite_project.experiments["ligand_water"].molecules
+    assert molecules == reference_molecules
+
+    assert "water" not in mdsuite_project.experiments["ligand_water"].species