testing update

meteor/sfcalc.py

@@ -5,7 +5,7 @@
 from .rsmap import Map
 
 
-def sf_calc(structure: gemmi.Structure, *, high_resolution_limit: float) -> Map:
+def structure_to_calculated_map(structure: gemmi.Structure, *, high_resolution_limit: float) -> Map:
     density_map = gemmi.DensityCalculatorX()
     density_map.d_min = high_resolution_limit
     density_map.grid.setup_from(structure)
@@ -24,4 +24,4 @@ def pdb_to_calculated_map(pdb_file: Path, *, high_resolution_limit: float) -> Ma
         msg = f"could not find file: {pdb_file}"
         raise OSError(msg)
     structure = gemmi.read_structure(str(pdb_file))
-    return sf_calc(structure, high_resolution_limit=high_resolution_limit)
+    return structure_to_calculated_map(structure, high_resolution_limit=high_resolution_limit)

test/conftest.py

@@ -4,5 +4,10 @@
 
 
 @pytest.fixture(scope="session")
-def test_data_dir() -> Path:
+def data_dir() -> Path:
     return Path(__file__).parent.resolve() / "data"
+
+
+@pytest.fixture(scope="session")
+def example_pdb_file(data_dir: Path) -> Path:
+    return data_dir / "rsEGFP2_dark_no-chromophore.pdb"

test/unit/test_sfcalc.py

@@ -1,4 +1,44 @@
 from pathlib import Path
 
+import gemmi
+import numpy as np
+import pytest
+from numpy import testing as npt
 
-def test_sf_calc(test_data_dir: Path): ...
+from meteor import sfcalc
+from meteor.rsmap import Map
+from meteor.testing import single_carbon_structure
+
+RESOLUTION = 1.0
+UNIT_CELL = gemmi.UnitCell(a=10.0, b=10.0, c=10.0, alpha=90, beta=90, gamma=90)
+SPACE_GROUP = gemmi.find_spacegroup_by_name("P1")
+CARBON1_POSITION = (5.0, 5.0, 5.0)
+
+
+@pytest.fixture
+def structure() -> gemmi.Structure:
+    return single_carbon_structure(CARBON1_POSITION, SPACE_GROUP, UNIT_CELL)
+
+
+def test_sf_calc(structure: gemmi.Structure) -> None:
+    calc_map: Map = sfcalc.structure_to_calculated_map(structure, high_resolution_limit=RESOLUTION)
+    assert calc_map.resolution_limits[1] == RESOLUTION
+    assert calc_map.spacegroup == SPACE_GROUP
+    assert calc_map.cell == UNIT_CELL
+    assert not calc_map.has_uncertainties
+    assert np.any(calc_map.amplitudes != 0.0)
+    assert np.any(calc_map.phases != 0.0)
+
+
+def test_pdb_to_calculated_map(example_pdb_file: Path) -> None:
+    calc_map: Map = sfcalc.pdb_to_calculated_map(example_pdb_file, high_resolution_limit=RESOLUTION)
+    npt.assert_allclose(calc_map.resolution_limits[1], RESOLUTION, atol=1e-5)
+
+    # CRYST1   51.990   62.910   72.030  90.00  90.00  90.00 P 21 21 21
+    assert calc_map.spacegroup == gemmi.find_spacegroup_by_name("P 21 21 21")
+    assert calc_map.cell == gemmi.UnitCell(
+        a=51.990, b=62.910, c=72.030, alpha=90, beta=90, gamma=90
+    )
+
+    assert np.any(calc_map.amplitudes != 0.0)
+    assert np.any(calc_map.phases != 0.0)