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openforcefield · Jan 22, 2025 · e43307a · e43307a
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Showing 9 changed files with 30 additions and 66 deletions.
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst
@@ -73,10 +73,10 @@
    {%- endfor %}
 
    {% if types %}
-   .. rubric:: {{ _('Classes') }}
+   .. rubric:: {{ _('Other Objects') }}
 
    .. autosummary::
-      :caption: Classes
+      :caption: Other Objects
       :toctree:
       :nosignatures:
    {% for item in types %}

diff --git a/docs/make.bat b/docs/make.bat
diff --git a/openff/pablo/__init__.py b/openff/pablo/__init__.py
@@ -4,7 +4,7 @@
 
 from importlib.metadata import version
 
-from . import ccd, exceptions, residue
+from . import ccd, chem, exceptions, residue
 from ._pdb import topology_from_pdb
 from .ccd import CCD_RESIDUE_DEFINITION_CACHE
 
@@ -14,6 +14,7 @@
     "exceptions",
     "ccd",
     "residue",
+    "chem",
 ]
 
 __version__ = version("openff.pablo")
diff --git a/openff/pablo/_pdb_data.py b/openff/pablo/_pdb_data.py
@@ -11,6 +11,11 @@
 from .exceptions import UnknownOrAmbiguousSerialInConectError
 from .residue import AtomDefinition, ResidueDefinition
 
+__all__ = [
+    "ResidueMatch",
+    "PdbData",
+]
+
 
 @dataclass(frozen=True)
 class ResidueMatch:

diff --git a/openff/pablo/_utils.py b/openff/pablo/_utils.py
@@ -1,13 +1,12 @@
 from collections import defaultdict
-from collections.abc import Iterable, Iterator
+from collections.abc import Callable, Iterable, Iterator, Mapping
 from typing import (
     DefaultDict,
     TypeAlias,
     TypeVar,
     TypeVarTuple,
     no_type_check,
 )
-from collections.abc import Callable, Mapping
 
 from openff.toolkit.topology._mm_molecule import _SimpleMolecule
 from openff.toolkit.topology.molecule import MoleculeLike
@@ -16,11 +15,16 @@
 from pint import Quantity
 
 __all__ = [
+    "default_dict",
     "unwrap",
+    "sort_tuple",
     "flatten",
+    "with_neighbours",
     "float_or_unknown",
     "dec_hex",
+    "int_or_none",
     "cryst_to_box_vectors",
+    "assign_stereochemistry_from_3d",
     "__UNSET__",
 ]
 

diff --git a/openff/pablo/ccd/patches.py b/openff/pablo/ccd/patches.py
@@ -24,6 +24,7 @@
     "add_protonation_variants",
     "add_synonyms",
     "disambiguate_alt_ids",
+    "add_disulfide_crosslink",
 ]
 
 

diff --git a/openff/pablo/chem.py b/openff/pablo/chem.py
@@ -1,5 +1,14 @@
+"""
+Chemical information for re-use across residue databases.
+"""
+
 from openff.pablo.residue import BondDefinition
 
+__all__ = [
+    "DISULFIDE_BOND",
+    "PEPTIDE_BOND",
+]
+
 DISULFIDE_BOND = BondDefinition(
     atom1="SG",
     atom2="SG",

diff --git a/openff/pablo/residue.py b/openff/pablo/residue.py
@@ -154,7 +154,7 @@ class ResidueDefinition:
       ``linking_bond.atom2`` are absent in the latter residue. Leaving atoms
       are those that have the ``AtomDefinition.leaving`` attribute set to
       ``True``. A leaving atom is associated with atom `a` if it is bonded to
-      `a`, or it is bonded to an atom associated with `a`.
+      `a`, or it is bonded to a leaving atom associated with `a`.
     - There is at least one leaving atom associated with each linking atom
 
     The charge of linking atoms is not modified; any change in valence is
@@ -183,8 +183,8 @@ class ResidueDefinition:
     - All leaving atoms associated with each residues' ``crosslink.atom1``
       attribute are absent in that residue. Leaving atoms are those that have
       the ``AtomDefinition.leaving`` attribute set to ``True``. A leaving atom
-      is associated with atom `a` if it is bonded to `a`, or it is bonded to an
-      atom associated with `a`.
+      is associated with atom `a` if it is bonded to `a`, or it is bonded to a
+      leaving atom associated with `a`.
     - There is at least one leaving atom associated with each cross-linking atom
 
     The charge of linking atoms is not modified; any change in valence is
@@ -242,7 +242,7 @@ def from_molecule(
         description: str | None = None,
     ) -> Self:
         """
-        Create a ``ResidueDefinition`` from an :py:cls:`openff.toolkit.Molecule`
+        Create a ``ResidueDefinition`` from an :py:class:`openff.toolkit.Molecule`
 
         Parameters
         ----------
@@ -349,7 +349,7 @@ def from_capped_molecule(
         description: str | None = None,
     ) -> Self:
         """
-        Create a linking ``ResidueDefinition`` from an :py:cls:`openff.toolkit.Molecule`
+        Create a linking ``ResidueDefinition`` from an :py:class:`openff.toolkit.Molecule`
 
         Parameters
         ----------