Fix leaking of wrapped coordinates when writing PDB file

Author: tovrstra

CHANGELOG.md

@@ -7,9 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Fixed
+
+- Fix leaking of wrapped coordinates when writing PDB file.
+
+
 ## [0.2.1] - 2024-10-08
 
-## Fixed
+### Fixed
 
 - Fix bug in `PairwiseForceField` class: use `rmax` only, never `rcut`.
 - Fix version import.
@@ -18,7 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [0.2.0] - 2024-10-07
 
-## Changed
+### Changed
 
 - Add mandatory `rcut` option to `build_random_cell`.
 

src/tinyff/trajectory.py

@@ -97,7 +97,7 @@ def _dump_low(self, fh: TextIO, atpos: ArrayLike, cell_lengths: ArrayLike):
         atpos = parse_atpos(atpos, len(self.atnums))
         cell_lengths = parse_cell_lengths(cell_lengths)
         # Wrap atoms in cell for nicer visual
-        atpos -= np.floor(atpos / cell_lengths) * cell_lengths
+        atpos = atpos - np.floor(atpos / cell_lengths) * cell_lengths
         # Actual writing
         a, b, c = cell_lengths * self.to_angstrom
         print(f"CRYST1{a:9.3f}{b:9.3f}{c:9.3f}  90.00  90.00  90.00 P 1           1", file=fh)

tests/test_trajectory.py

@@ -79,6 +79,16 @@ def test_pdb_writer_stride(tmpdir):
         assert fh.read().count("CRYST1") == 3
 
 
+def test_pdb_writer_no_modify(tmpdir):
+    cell_length = 3.0
+    atpos0 = np.array([[0.0, 2.0, 0.5], [1.0, 3.3, 2.44], [-1.0, 2.8, 1.7]])
+    atpos1 = atpos0.copy()
+    path_pdb = os.path.join(tmpdir, "test.pdb")
+    pdb_writer = PDBWriter(path_pdb, to_angstrom=10.0, atnums=[18] * len(atpos0))
+    pdb_writer.dump(atpos0, cell_length)
+    assert atpos0 == pytest.approx(atpos1)
+
+
 PDB_REF_SINGLE = """\
 CRYST1   10.000   10.000   10.000  90.00  90.00  90.00 P 1           1
 HETATM    1 Ar   ATM     1       3.000   4.000   5.000  1.00  1.00          Ar