Update to unit cell matrices

paulsbond · Nov 28, 2024 · 9ab6f1d · 9ab6f1d
1 parent 4dce7ed
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Showing 6 changed files with 15 additions and 9 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](https://semver.org).
 
-## [5.0.0] - Unreleased
+## [5.0.1] - 2024-11-28
+
+## Changed
+
+- Gemmi fractionalization_matrix to frac.mat and orthogonalization_matrix to orth.mat.
+
+## [5.0.0] - 2024-11-08
 
 ### Added
 

diff --git a/modelcraft/__init__.py b/modelcraft/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "5.0.0"
+__version__ = "5.0.1"
 
 from .cell import max_distortion as max_cell_distortion
 from .cell import remove_scale

diff --git a/modelcraft/cell.py b/modelcraft/cell.py
@@ -17,8 +17,8 @@ def remove_scale(structure: gemmi.Structure) -> None:
 
 def max_distortion(old_cell: gemmi.UnitCell, new_cell: gemmi.UnitCell) -> float:
     "Return the maximum distortion between two cells as a fraction"
-    frac1 = old_cell.fractionalization_matrix
-    orth2 = new_cell.orthogonalization_matrix
+    frac1 = old_cell.frac.mat
+    orth2 = new_cell.orth.mat
     identity = gemmi.Mat33()
     matrix = np.array(identity) - np.array(orth2.multiply(frac1))
     eigenvalues, _ = scipy.linalg.eig(matrix)

diff --git a/modelcraft/tests/ccp4/test_cell.py b/modelcraft/tests/ccp4/test_cell.py
@@ -12,9 +12,9 @@ def test_1ana():
     urllib.request.urlretrieve(url, "1ana.cif.gz")
     structure = read_structure("1ana.cif.gz")
     assert structure.cell.parameters == (41.1, 41.1, 26.7, 90, 90, 90)
-    assert structure.cell.fractionalization_matrix.tolist()[0][0] == 0
+    assert structure.cell.frac.mat.tolist()[0][0] == 0
     remove_scale(structure)
-    assert structure.cell.fractionalization_matrix.tolist()[0][0] != 0
+    assert structure.cell.frac.mat.tolist()[0][0] != 0
     new_parameters = (41, 41, 27, 90, 90, 90)
     new_cell = gemmi.UnitCell(*new_parameters)
     assert max_distortion(structure.cell, new_cell) < 0.05

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-gemmi >=0.5.4
+gemmi >=0.5.5
 numpy
 pandas
 requests

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="modelcraft",
-    version="5.0.0",
+    version="5.0.1",
     author="Paul Bond",
     author_email="[email protected]",
     description="Automated model building pipeline for X-ray crystallography",
@@ -26,7 +26,7 @@
     ],
     python_requires="~=3.7",
     install_requires=[
-        "gemmi >=0.5.4",
+        "gemmi >=0.5.5",
         "numpy",
         "pandas",
         "requests",