feat: Add support for reading unit cell dimensions from MOL2 CRYSIN records

package/MDAnalysis/coordinates/MOL2.py

@@ -241,6 +241,10 @@ def _read_frame(self, frame):
 
         sections, coords = self.parse_block(block)
 
+        if "crysin" in sections:
+            dims = sections["crysin"][0].split()[:6]
+            self.ts.dimensions = np.array(dims, dtype=np.float32)
+
         for sect in ["molecule", "substructure"]:
             try:
                 self.ts.data[sect] = sections[sect]

testsuite/MDAnalysisTests/coordinates/test_mol2.py

@@ -21,6 +21,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 import pytest
+import numpy as np
 
 import os
 from numpy.testing import (
@@ -39,6 +40,7 @@
     mol2_comments_header,
     mol2_ligand,
     mol2_sodium_ion,
+    mol2_crysin,
 )
 from MDAnalysis import Universe
 import MDAnalysis as mda
@@ -232,3 +234,11 @@ def test_mol2_universe_write(tmpdir):
         assert_almost_equal(u.atoms.positions, u2.atoms.positions)
         # MDA does not current implement @<TRIPOS>CRYSIN reading
         assert u2.dimensions is None
+
+
+def test_mol2_crysin_dimensions():
+    # test that crysin records are read as dimensions
+    u = mda.Universe(mol2_crysin)
+
+    expected = np.array([40.0, 50.0, 60.0, 90.0, 90.0, 90.0], dtype=np.float32)
+    assert_array_almost_equal(u.dimensions, expected, decimal=3)

testsuite/MDAnalysisTests/data/mol2/test_crysin.mol2

@@ -0,0 +1,10 @@
+@<TRIPOS>MOLECULE
+test_structure
+ 1 0 0 0 0
+SMALL
+USER_CHARGES
+@<TRIPOS>ATOM
+      1 C          0.0000      0.0000      0.0000 C.3     1  ALA        0.0000
+@<TRIPOS>CRYSIN
+   40.0000   50.0000   60.0000   90.0000   90.0000   90.0000    1    1
+@<TRIPOS>END

testsuite/MDAnalysisTests/datafiles.py

@@ -241,6 +241,7 @@
     "mol2_comments_header",
     "mol2_ligand",
     "mol2_sodium_ion",
+    "mol2_crysin",
     "capping_input",
     "capping_output",
     "capping_ace",
@@ -735,6 +736,7 @@
 mol2_zinc = (_data_ref / "mol2/zinc_856218.mol2").as_posix()
 # MOL2 file without bonds
 mol2_sodium_ion = (_data_ref / "mol2/sodium_ion.mol2").as_posix()
+mol2_crysin = (_data_ref / "mol2/test_crysin.mol2").as_posix()
 
 capping_input = (_data_ref / "capping/aaqaa.gro").as_posix()
 capping_output = (_data_ref / "capping/maestro_aaqaa_capped.pdb").as_posix()