Add generic aromatic bond

src/biotite/structure/bonds.pyx

@@ -60,6 +60,7 @@ class BondType(IntEnum):
         - `AROMATIC_SINGLE` - Aromatic bond with a single formal bond
         - `AROMATIC_DOUBLE` - Aromatic bond with a double formal bond
         - `AROMATIC_TRIPLE` - Aromatic bond with a triple formal bond
+        - `AROMATIC` - Aromatic bond without specification of the formal bond
         - `COORDINATION` - Coordination complex involving a metal atom
     """
     ANY = 0
@@ -71,6 +72,7 @@ class BondType(IntEnum):
     AROMATIC_DOUBLE = 6
     AROMATIC_TRIPLE = 7
     COORDINATION = 8
+    AROMATIC = 9
 
 
     def without_aromaticity(self):
@@ -97,6 +99,8 @@ class BondType(IntEnum):
             return BondType.DOUBLE
         elif self == BondType.AROMATIC_TRIPLE:
             return BondType.TRIPLE
+        elif self == BondType.AROMATIC:
+            return BondType.ANY
         else:
             return self
 
@@ -517,7 +521,8 @@ class BondList(Copyable):
         for aromatic_type, non_aromatic_type in [
             (BondType.AROMATIC_SINGLE, BondType.SINGLE),
             (BondType.AROMATIC_DOUBLE, BondType.DOUBLE),
-            (BondType.AROMATIC_TRIPLE, BondType.TRIPLE)
+            (BondType.AROMATIC_TRIPLE, BondType.TRIPLE),
+            (BondType.AROMATIC, BondType.ANY),
         ]:
             bond_types[bond_types == aromatic_type] = non_aromatic_type
 

src/biotite/structure/io/mol/ctab.py

@@ -24,19 +24,13 @@
     1: BondType.SINGLE,
     2: BondType.DOUBLE,
     3: BondType.TRIPLE,
+    4: BondType.AROMATIC,
     5: BondType.ANY,
-    6: BondType.SINGLE,
-    7: BondType.DOUBLE,
+    6: BondType.AROMATIC_SINGLE,
+    7: BondType.AROMATIC_DOUBLE,
     8: BondType.ANY,
 }
-BOND_TYPE_MAPPING_REV = {
-    BondType.SINGLE: 1,
-    BondType.DOUBLE: 2,
-    BondType.TRIPLE: 3,
-    BondType.AROMATIC_SINGLE: 1,
-    BondType.AROMATIC_DOUBLE: 2,
-    BondType.ANY: 8,
-}
+BOND_TYPE_MAPPING_REV = {v: k for k, v in BOND_TYPE_MAPPING.items()}
 
 CHARGE_MAPPING = {0: 0, 1: 3, 2: 2, 3: 1, 5: -1, 6: -2, 7: -3}
 CHARGE_MAPPING_REV = {val: key for key, val in CHARGE_MAPPING.items()}

src/biotite/structure/io/pdbx/convert.py

@@ -81,6 +81,7 @@
     BondType.AROMATIC_TRIPLE: "trip",
     # These are masked later, it is merely added here to avoid a KeyError
     BondType.ANY: "",
+    BondType.AROMATIC: "",
     BondType.COORDINATION: "",
 }
 # Map 'chem_comp_bond' bond orders and aromaticity to 'BondType'...
@@ -92,6 +93,7 @@
     ("SING", "Y"): BondType.AROMATIC_SINGLE,
     ("DOUB", "Y"): BondType.AROMATIC_DOUBLE,
     ("TRIP", "Y"): BondType.AROMATIC_TRIPLE,
+    ("AROM", "Y"): BondType.AROMATIC,
 }
 # ...and vice versa
 COMP_BOND_TYPE_TO_ORDER = {

tests/structure/io/test_mol.py

@@ -10,6 +10,7 @@
 import numpy as np
 import pytest
 import biotite.structure as struc
+import biotite.structure.info as info
 import biotite.structure.io.mol as mol
 import biotite.structure.io.pdbx as pdbx
 from biotite.structure.bonds import BondType
@@ -83,7 +84,7 @@ def test_header_conversion():
         [False, True],
     ),
 )
-def test_structure_conversion(
+def test_structure_conversion_from_file(
     FileClass,  # noqa: N803
     path,
     version,
@@ -116,7 +117,6 @@ def test_structure_conversion(
 
     temp.seek(0)
     mol_file = FileClass.read(temp)
-    print(mol_file)
     test_atoms = mol.get_structure(mol_file)
     if omit_charge:
         assert np.all(test_atoms.charge == 0)
@@ -126,6 +126,58 @@ def test_structure_conversion(
     assert test_atoms == ref_atoms
 
 
+@pytest.mark.parametrize(
+    "FileClass, component_name, version, omit_charge, use_charge_property",
+    itertools.product(
+        [mol.MOLFile, mol.SDFile],
+        [
+            "ALA",  # Alanine
+            "BNZ",  # Benzene (has aromatic bonds)
+            "3P8",  # Methylammonium ion (has charge)
+            "MCH",  # Trichloromethane (has element with multiple letters)
+        ],
+        ["V2000", "V3000"],
+        [False, True],
+        [False, True],
+    ),
+)
+def test_structure_conversion_to_file(
+    FileClass,  # noqa: N803
+    component_name,
+    version,
+    omit_charge,
+    use_charge_property,
+):
+    """
+    Writing a component to a file and reading it again should give the same
+    structure.
+    """
+    ref_atoms = info.residue(component_name)
+
+    mol_file = FileClass()
+    mol.set_structure(mol_file, ref_atoms, version=version)
+    temp = TemporaryFile("w+")
+    mol_file.write(temp)
+
+    if version == "V2000":
+        if use_charge_property:
+            # Enforce usage of 'M  CHG' entries
+            _delete_charge_columns(temp)
+        else:
+            # Enforce usage of charge column in atom block
+            _delete_charge_property(temp)
+
+    temp.seek(0)
+    mol_file = FileClass.read(temp)
+    test_atoms = mol.get_structure(mol_file)
+    temp.close()
+
+    assert np.all(test_atoms.element == ref_atoms.element)
+    assert np.all(test_atoms.charge == ref_atoms.charge)
+    assert np.allclose(test_atoms.coord, ref_atoms.coord)
+    assert test_atoms.bonds == ref_atoms.bonds
+
+
 @pytest.mark.parametrize(
     "path",
     [