Merge pull request #537 from marrink-lab/box_attr

add box attribute to molecule and propagate from pdb parser

vermouth/molecule.py

@@ -360,6 +360,8 @@ def __init__(self, *args, **kwargs):
         # {loglevel: {entry: [fmt_args]}}
         self.log_entries = defaultdict(lambda: defaultdict(list))
         self.max_node = None
+        # box of the system the molecule is in
+        self.box = None
 
     def __eq__(self, other):
         return (

vermouth/pdb/pdb.py

@@ -341,6 +341,10 @@ def _finish_molecule(self, line="", lineno=0):
         # since there's a very good chance it's CONECT records have not been
         # parsed yet, and the molecule won't have any edges.
         if self.active_molecule:
+            if {"a", "b", "c"}.issubset(set(self.cryst.keys())):
+                self.active_molecule.box = np.array([self.cryst['a']/10.,
+                                                     self.cryst['b']/10.,
+                                                     self.cryst['b']/10.])
             self.molecules.append(self.active_molecule)
         self.active_molecule = Molecule()
 

vermouth/tests/pdb/test_read_pdb.py

@@ -260,6 +260,7 @@ def test_atom_attributes():
 def test_cryst1(caplog, pdbstr, cryst_dict):
     parser = PDBParser()
     mols = list(parser.parse(pdbstr.splitlines()))
+    assert np.all(np.isclose(mols[0].box, np.array([7.7987, 7.7987, 7.7987])))
     assert parser.cryst == cryst_dict
     if len(cryst_dict) < 8:
         assert any(rec.levelname == 'WARNING' for rec in caplog.records)