Merge pull request #57 from SimoneMartino98/main

@SimoneMartino98 added normalization options to compute_rdf function

src/dynsight/_internal/analysis/rdf.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Literal
 
 if TYPE_CHECKING:
     import MDAnalysis
@@ -17,6 +17,7 @@ def compute_rdf(
     s2: str = "all",
     exclusion_block: list[int] | None = None,
     nbins: int = 200,
+    norm: Literal["rdf", "density", "none"] = "rdf",
     start: int | None = None,
     stop: int | None = None,
     step: int = 1,
@@ -52,6 +53,12 @@ def compute_rdf(
         nbins:
             The number of bins used to divide the distance range for
             histogramming the RDF.
+        norm :
+            Type of normalization to apply:
+
+            - **'rdf'**: Standard RDF normalization (default).
+            - **'density'**: Normalize with respect to system density.
+            - **'none'**: No normalization applied.
         start:
             Initial molecular dynamics step.
         stop:
@@ -106,6 +113,7 @@ def compute_rdf(
         nbins=nbins,
         range=distances_range,
         exclusion_block=exclusion_block,
+        norm=norm,
     )
 
     rdf.run(verbose=True, start=start, stop=stop, step=step)

tests/analysis/rdf/case_data.py

@@ -0,0 +1,12 @@
+from dataclasses import dataclass
+from typing import Literal
+
+
+@dataclass(frozen=True, slots=True)
+class RDFCaseData:
+    topology_filename: str
+    trajectory_filename: str
+    expected_bins: str
+    expected_rdf: str
+    norm: Literal["rdf", "density", "none"]
+    name: str

tests/analysis/rdf/conftest.py

@@ -0,0 +1,38 @@
+import pytest
+
+from .case_data import RDFCaseData
+
+
+@pytest.fixture(
+    scope="session",
+    params=(
+        lambda name: RDFCaseData(
+            topology_filename="test_coex.gro",
+            trajectory_filename="test_coex.xtc",
+            expected_bins="test_bins_rdf.npy",
+            expected_rdf="test_rdf_rdf.npy",
+            norm="rdf",
+            name=name,
+        ),
+        lambda name: RDFCaseData(
+            topology_filename="test_coex.gro",
+            trajectory_filename="test_coex.xtc",
+            expected_bins="test_bins_density.npy",
+            expected_rdf="test_rdf_density.npy",
+            norm="density",
+            name=name,
+        ),
+        lambda name: RDFCaseData(
+            topology_filename="test_coex.gro",
+            trajectory_filename="test_coex.xtc",
+            expected_bins="test_bins_none.npy",
+            expected_rdf="test_rdf_none.npy",
+            norm="none",
+            name=name,
+        ),
+    ),
+)
+def case_data(request: pytest.FixtureRequest) -> RDFCaseData:
+    return request.param(
+        f"{request.fixturename}{request.param_index}",  # type: ignore [attr-defined]
+    )

tests/analysis/rdf/test_rdf.py

@@ -0,0 +1,44 @@
+"""Pytest for dynsight.analysis.compute_rdf."""
+
+from pathlib import Path
+
+import MDAnalysis
+import numpy as np
+import pytest
+
+from dynsight.analysis import compute_rdf
+from tests.analysis.rdf.case_data import RDFCaseData
+
+
+def test_compute_rdf(case_data: RDFCaseData) -> None:
+    original_dir = Path(__file__).resolve().parent
+    topology_file = (
+        original_dir / "../../systems/coex" / case_data.topology_filename
+    )
+    trajectory_file = (
+        original_dir / "../../systems/coex" / case_data.trajectory_filename
+    )
+    expected_bins = original_dir / "test_rdf" / case_data.expected_bins
+    expected_rdf = original_dir / "test_rdf" / case_data.expected_rdf
+
+    u = MDAnalysis.Universe(topology_file, trajectory_file)
+
+    selection = "type O"
+
+    test_bins, test_rdf = compute_rdf(
+        universe=u,
+        s1=selection,
+        s2=selection,
+        distances_range=[0.0, 5.0],
+        norm=case_data.norm,
+    )
+
+    if not expected_bins.exists() or not expected_rdf.exists():
+        np.save(expected_bins, test_bins)
+        np.save(expected_rdf, test_rdf)
+        pytest.fail("RDF test files were not present. They have been created.")
+
+    exp_bins = np.load(expected_bins)
+    exp_rdf = np.load(expected_rdf)
+    assert np.array_equal(exp_rdf, test_rdf)
+    assert np.array_equal(exp_bins, test_bins)