Implement BondList and connection functionalities in Rust

Cargo.toml

@@ -7,6 +7,8 @@ edition = "2018"
 numpy = "0.27"
 ndarray = "0.17"
 num-traits = "0.2"
+smallvec = "1"
+itertools = "0.14"
 
 [dependencies.pyo3]
 version = "0.27"

src/biotite/application/autodock/app.py

@@ -11,7 +11,7 @@
 import numpy as np
 from biotite.application.application import AppState, requires_state
 from biotite.application.localapp import LocalApp, cleanup_tempfile
-from biotite.structure.bonds import find_connected
+from biotite.structure.connect import find_connected
 from biotite.structure.error import BadStructureError
 from biotite.structure.io.pdbqt import PDBQTFile
 from biotite.structure.residues import get_residue_masks, get_residue_starts_for

src/biotite/structure/__init__.py

@@ -116,6 +116,7 @@
 from .chains import *
 from .charges import *
 from .compare import *
+from .connect import *
 from .density import *
 from .dotbracket import *
 from .error import *

src/biotite/structure/basepairs.py

@@ -292,9 +292,9 @@ class Edge(IntEnum):
     This enum type represents the interacting edge for a given base.
     """
 
-    INVALID = (0,)
-    WATSON_CRICK = (1,)
-    HOOGSTEEN = (2,)
+    INVALID = 0
+    WATSON_CRICK = 1
+    HOOGSTEEN = 2
     SUGAR = 3
 
 
@@ -305,8 +305,8 @@ class GlycosidicBond(IntEnum):
     """
 
     INVALID = 0
-    CIS = (1,)
-    TRANS = (2,)
+    CIS = 1
+    TRANS = 2
 
 
 def base_pairs_edge(atom_array, base_pairs):

src/biotite/structure/bonds.py

@@ -0,0 +1,67 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = [
+    "BondList",
+    "BondType",
+]
+
+from enum import IntEnum
+from biotite.rust.structure import BondList, bond_type_members
+
+
+def _without_aromaticity(self):
+    """
+    Get the non-aromatic counterpart of this bond type.
+
+    If this bond type is already non-aromatic, it is returned unchanged.
+
+    Returns
+    -------
+    BondType
+        The non-aromatic counterpart of this bond type.
+
+    Examples
+    --------
+    >>> BondType.AROMATIC_DOUBLE.without_aromaticity()
+    <BondType.DOUBLE: 2>
+    >>> BondType.SINGLE.without_aromaticity()
+    <BondType.SINGLE: 1>
+    """
+    match self:
+        case BondType.AROMATIC_SINGLE:
+            return BondType.SINGLE
+        case BondType.AROMATIC_DOUBLE:
+            return BondType.DOUBLE
+        case BondType.AROMATIC_TRIPLE:
+            return BondType.TRIPLE
+        case BondType.AROMATIC:
+            return BondType.ANY
+        case _:
+            return self
+
+
+# Create BondType IntEnum dynamically from Rust enum members
+BondType = IntEnum(
+    "BondType",
+    {name: value for name, value in bond_type_members().items()},
+    module=__name__,
+)
+BondType.__doc__ = """
+This enum type represents the type of a chemical bond.
+
+- ``ANY`` - Used if the actual type is unknown
+- ``SINGLE`` - Single bond
+- ``DOUBLE`` - Double bond
+- ``TRIPLE`` - Triple bond
+- ``QUADRUPLE`` - A quadruple bond
+- ``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
+- ``COORDINATION`` - Coordination complex involving a metal atom
+- ``AROMATIC`` - Aromatic bond without specification of the formal bond
+"""
+BondType.without_aromaticity = _without_aromaticity