47 support reading of lists in custom xyz files

TCutility/molecule.py

@@ -13,6 +13,9 @@ def parse_str(s: str):
     if not isinstance(s, str):
         return s
 
+    if ',' in s:
+        return [parse_str(part.strip()) for part in s.split(',')]
+
     # to parse the string we use try/except method
     try:
         return int(s)
@@ -86,15 +89,15 @@ def load(path) -> plams.Molecule:
     '''
     def parse_flags(args):
         ret = result.Result()
-        ret.tags = []
+        ret.tags = set()
         for arg in args:
             # flags are given as key=value pairs
             # tags are given as loose keys
             if '=' in arg:
                 key, value = arg.split('=')
                 ret[key.strip()] = parse_str(value.strip())
             else:
-                ret.tags.append(parse_str(arg.strip()))
+                ret.tags.add(parse_str(arg.strip()))
         return ret
 
     with open(path) as f:

TCutility/results/result.py

@@ -53,6 +53,9 @@ def __hash__(self):
         '''
         raise KeyError(f'Tried to hash {self.get_parent_tree()}, but it is empty')
 
+    def __reduce__(self):
+        return 'TCutility.results.result.Result'
+
     def __bool__(self):
         '''Make sure that keys starting and ending in "__" are skipped'''
         return len([key for key in self.keys() if not (key.startswith('__') and key.endswith('__'))]) > 0

test/fixtures/xyz/pyr.xyz

@@ -0,0 +1,18 @@
+12
+
+C       0.00000000       1.14206764       0.90887116
+C       0.00000000       1.19134753      -0.47779047
+C       0.00000000       0.00000000      -1.18863009
+C       0.00000000      -1.19134753      -0.47779047
+C       0.00000000      -1.14206764       0.90887116
+N       0.00000000       0.00000000       1.58935329
+H       0.00000000       2.05493274       1.49740370
+H       0.00000000       2.14479192      -0.99199860
+H       0.00000000       0.00000000      -2.27369478
+H       0.00000000      -2.14479192      -0.99199860
+H       0.00000000      -2.05493274       1.49740370
+Xx       0.12739120      -0.00077609       2.50049043
+
+conn = 6, 12
+test_list = 3.14, pi
+active_atoms = 8

test/test_molecules.py

@@ -6,39 +6,63 @@
 
 
 def test_atom_flags() -> None:
-    xyzfile = j('test', 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
     mol = molecule.load(xyzfile)
     atom = mol[2]
     assert atom.flags.origin == 'substrate'
 
 
 def test_atom_tags() -> None:
-    xyzfile = j('test', 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
     mol = molecule.load(xyzfile)
     atom = mol[3]
     assert 'R1' in atom.flags.tags
 
 
 def test_mol_reading() -> None:
-    xyzfile = j('test', 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
     tcmol = molecule.load(xyzfile)
     plamsmol = plams.Molecule(xyzfile)
     assert all(tcatom.symbol == plamsatom.symbol and tcatom.coords == plamsatom.coords for tcatom, plamsatom in zip(tcmol.atoms, plamsmol.atoms))
 
 
 def test_mol_flags() -> None:
-    xyzfile = j('test', 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
     mol = molecule.load(xyzfile)
     assert mol.flags.task == 'TransitionStateSearch'
 
 
 def test_mol_tags() -> None:
-    xyzfile = j('test', 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
     mol = molecule.load(xyzfile)
     assert 'vibrations' in mol.flags.tags
 
 
 def test_comment() -> None:
-    xyzfile = j('test', 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'transitionstate_radical_addition.xyz')
     mol = molecule.load(xyzfile)
     assert mol.comment == 'molecule used for testing the molecule module'
+
+
+def test_list_value() -> None:
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'pyr.xyz')
+    mol = molecule.load(xyzfile)
+    assert mol.flags.conn == [6, 12]
+
+
+def test_list_value2() -> None:
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'pyr.xyz')
+    mol = molecule.load(xyzfile)
+    assert mol.flags.test_list == [3.14, 'pi']
+
+
+def test_mol_copy() -> None:
+    xyzfile = j(os.path.split(__file__)[0], 'fixtures', 'xyz', 'pyr.xyz')
+    mol = molecule.load(xyzfile)
+    mol.copy()
+
+
+if __name__ == '__main__':
+    import pytest
+
+    pytest.main()