added tests for triclinic box wrapping modes

Author: stefdoerr

moleculekit/molecule.py

@@ -3623,7 +3623,7 @@ def test_append_inverse_collisions(self):
         assert new_n_waters == (n_waters - 6)  # No waters were killed
         assert (n_lipids - new_n_lipids) == 1 * popc_n_atoms  # 1 lipid removed
 
-    def test_wrapping(self):
+    def test_orthogonal_wrapping(self):
         from moleculekit.home import home
 
         homedir = home(dataDir="test-wrapping")

moleculekit/test-data/molecule-readers/dodecahedral_box/output_compact_wrapped.xtc

@@ -0,0 +1 @@
+../moleculekit/test-data/molecule-readers/dodecahedral_box

moleculekit/test-data/molecule-readers/dodecahedral_box/output_rectangular_wrapped.xtc

@@ -0,0 +1,25 @@
+from moleculekit.molecule import Molecule
+import numpy as np
+import os
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
+
+def _test_triclinic_wrapping():
+    refdir = os.path.join(curr_dir, "dodecahedral_box")
+    mol = Molecule(os.path.join(refdir, "3ptb_dodecahedron.psf"))
+
+    mol.read(os.path.join(refdir, "output.xtc"))
+    mol.wrap(wrapsel="protein", unitcell="triclinic")
+    refcoords = Molecule(os.path.join(refdir, "output_triclinic_wrapped.xtc"))
+    assert np.max(np.abs(mol.coords - refcoords.coords)) < 1e-2
+
+    mol.read(os.path.join(refdir, "output.xtc"))
+    mol.wrap(wrapsel="protein", unitcell="compact")
+    refcoords = Molecule(os.path.join(refdir, "output_compact_wrapped.xtc"))
+    assert np.max(np.abs(mol.coords - refcoords.coords)) < 1e-2
+
+    mol.read(os.path.join(refdir, "output.xtc"))
+    mol.wrap(wrapsel="protein", unitcell="rectangular")
+    refcoords = Molecule(os.path.join(refdir, "output_rectangular_wrapped.xtc"))
+    assert np.max(np.abs(mol.coords - refcoords.coords)) < 1e-2