add cryst statement to pdb parser

vermouth/pdb/pdb.py

@@ -61,6 +61,7 @@ def __init__(self, exclude=('SOL',), ignh=False, modelidx=1):
         self.ignh = ignh
         self.modelidx = modelidx
         self._skipahead = False
+        self.cryst = {}
 
     def dispatch(self, line):
         """
@@ -151,7 +152,6 @@ def _skip(line, lineno=0):
     site   = _skip
 
     # CRYSTALLOGRAPHIC AND COORDINATE TRANSFORMATION SECTION
-    cryst1 = _skip
     origx1 = _skip
     origx2 = _skip
     origx3 = _skip
@@ -265,6 +265,38 @@ def _atom(self, line, lineno=0):
     atom = _atom
     hetatm = _atom
 
+    def cryst1(self, line, lineno=0):
+        """
+        Parse the CRYST1 record. Crystal structure information are stored with
+        the parser object and may be extracted later.
+        """
+        fields = [
+            ('', str, 6),
+            ('a', float, 9),
+            ('b', float, 9),
+            ('c', float, 9),
+            ('alpha', float, 7),
+            ('beta', float, 7),
+            ('gamma', float, 7),
+            ('space_group', str, 11),
+            ('z_value', int, 4),
+            ]
+        start = 0
+        field_slices = []
+        for name, type_, width in fields:
+            if name == "space_group":
+                start+=1
+            if name:
+                field_slices.append((name, type_, slice(start, start + width)))
+            start += width
+
+        for name, type_, slice_ in field_slices:
+            value = line[slice_].strip()
+            if value:
+                self.cryst[name] = type_(value)
+            else:
+                LOGGER.warning(f"CRYST1 directive incomplete. Missing entry for {name}.")
+
     def model(self, line, lineno=0):
         """
         Parse a MODEL record. If the model is not the same as :attr:`modelidx`,

vermouth/tests/pdb/test_read_pdb.py

@@ -155,7 +155,6 @@ def test_single_model(pdbstr, ignh, nnodesnedges):
         assert len(mol.nodes) == nnodes
         assert len(mol.edges) == nedges
 
-
 @pytest.mark.parametrize('ignh', [True, False])
 @pytest.mark.parametrize('modelidx', range(1, 16))
 def test_integrative(ignh, modelidx):
@@ -233,3 +232,34 @@ def test_atom_attributes():
                     assert np.allclose(n_attrs[n_idx][attr], mol.nodes[n_idx][attr])
                 else:
                     assert n_attrs[n_idx][attr] == mol.nodes[n_idx][attr]
+
+
+@pytest.mark.parametrize('pdbstr, cryst_dict', (
+    # complete directive
+    ('''CRYST1   77.987   77.987   77.987  90.00  90.00  90.00 P 1           1
+    MODEL        1
+    ATOM      1  EO  PEO     0      74.550  37.470  22.790  1.00  0.00
+    ATOM      2  EO  PEO     1      77.020  38.150  25.000  1.00  0.00
+    ATOM      3  EO  PEO     2      76.390  37.180  28.130  1.00  0.00
+    ATOM      4  EO  PEO     3      75.430  37.920  31.450  1.00  0.00
+    ''',
+    {"a": 77.987, "b": 77.987, "c": 77.987,
+     "alpha": 90.0, "beta": 90.0, "gamma": 90,
+    "space_group": "P 1", "z_value": 1}
+    ),
+    # incomplete directive
+    ('''CRYST1   77.987   77.987   77.987
+    MODEL        1
+    ATOM      1  EO  PEO     0      74.550  37.470  22.790  1.00  0.00
+    ATOM      2  EO  PEO     1      77.020  38.150  25.000  1.00  0.00
+    ATOM      3  EO  PEO     2      76.390  37.180  28.130  1.00  0.00
+    ATOM      4  EO  PEO     3      75.430  37.920  31.450  1.00  0.00
+    ''',
+    {"a": 77.987, "b": 77.987, "c": 77.987,}
+    )))
+def test_cryst1(caplog, pdbstr, cryst_dict):
+    parser = PDBParser()
+    mols = list(parser.parse(pdbstr.splitlines()))
+    assert parser.cryst == cryst_dict
+    if len(cryst_dict) < 8:
+        assert any(rec.levelname == 'WARNING' for rec in caplog.records)