Bonds and Angles handle wildcards for bonds and sites. (#928)

* Add bond/angle wildcard handling

* change dihedral sample value so that c5 is 0 and rb torsion conversion is allowed

* Add tests for reversed version of wildcard ordering

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Change get_forcefield methods and parameterizations to apply wildcard parameters

* Add classes and types to gmso xsd schema, proprely get mbuild bond_orders

* [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci

* Add doc strings for connections bonds functions, remove bonds setter, and dynamically set bonds based on connection_members when initialized with set_dependent_value_default

* rename some of the utility functions used in identifying connections via masking, remove unused functions

* pin openmm to less than 8.4

* Use equivalents for _get_improper_type strings

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Chris Jones <[email protected]>

Author: 3 people

environment-dev.yml

@@ -18,7 +18,7 @@ dependencies:
   - pytest
   - garnett>=0.7.1
   - openff-toolkit-base>0.16.7
-  - openmm
+  - openmm<8.4.0
   - gsd>=2.9
   - freud>=3.2
   - parmed>=3.4.3

gmso/__init__.py

@@ -138,4 +138,4 @@ def print_level(self, level: str):
 
 # Example usage in __init__.py
 gmso_logger = GMSOLogger()
-gmso_logger.library_logger.setLevel(logging.INFO)
+gmso_logger.library_logger.setLevel(logging.WARNING)

gmso/abc/abstract_connection.py

@@ -1,3 +1,4 @@
+import itertools
 from typing import Optional, Sequence
 
 from pydantic import ConfigDict, Field, model_validator
@@ -111,3 +112,16 @@ def __repr__(self):
 
     def __str__(self):
         return f"<{self.__class__.__name__} {self.name}, id: {id(self)}> "
+
+    def get_connection_identifiers(self):
+        borderDict = {1: "-", 2: "=", 3: "#", 0: "~", None: "~", 1.5: ":"}
+        choices = [
+            (site.atom_type.name, site.atom_type.atomclass, "*")
+            for site in self.connection_members
+        ]
+        if not getattr(self, "bonds", None):
+            bond_identifiers = [borderDict[self.bond_order]]
+        else:
+            bond_identifiers = [borderDict[b.bond_order] for b in self.bonds]
+        choices += [(val, "~") for val in bond_identifiers]
+        return itertools.product(*choices)

gmso/core/angle.py

@@ -2,11 +2,12 @@
 
 from typing import Callable, ClassVar, Optional, Tuple
 
-from pydantic import ConfigDict, Field
+from pydantic import ConfigDict, Field, model_validator
 
 from gmso.abc.abstract_connection import Connection
 from gmso.core.angle_type import AngleType
 from gmso.core.atom import Atom
+from gmso.core.bond import Bond
 
 
 class Angle(Connection):
@@ -22,16 +23,30 @@ class Angle(Connection):
     __eq__, __repr__, _validate methods
 
     Additional _validate methods are presented.
+
+    self.connectivity is the associated indices that defines the way connection_members are bonded to match self.bonds.
     """
 
     __members_creator__: ClassVar[Callable] = Atom.model_validate
 
+    connectivity: ClassVar[Tuple[Tuple[int]]] = ((0, 1), (1, 2))
+
     connection_members_: Tuple[Atom, Atom, Atom] = Field(
         ...,
         description="The 3 atoms involved in the angle.",
         alias="connection_members",
     )
 
+    bonds_: Tuple[Bond, Bond] = Field(
+        default=None,
+        description="""
+        List of connection bonds.
+        Ordered to align with connection_members, such that self.bonds_[0] is
+        the bond between (self.connection_members[0], self.connection_members[1]).
+        """,
+        alias="bonds",
+    )
+
     angle_type_: Optional[AngleType] = Field(
         default=None,
         description="AngleType of this angle.",
@@ -48,6 +63,7 @@ class Angle(Connection):
         """,
         alias="restraint",
     )
+
     model_config = ConfigDict(
         alias_to_fields=dict(
             **Connection.model_config["alias_to_fields"],
@@ -73,6 +89,16 @@ def restraint(self):
         """Return the restraint of this angle."""
         return self.__dict__.get("restraint_")
 
+    @property
+    def bonds(self):
+        """Return a tuple of gmso.core.Bond objects that correspond to this angle."""
+        return self.__dict__.get("bonds_")
+
+    @property
+    def bonds_orders(self):
+        """Return the bond_order strings of this angle."""
+        return "".join([str(b.bond_order) for b in self.bonds])
+
     def equivalent_members(self):
         """Return a set of the equivalent connection member tuples.
 
@@ -99,3 +125,15 @@ def __setattr__(self, key, value):
             super(Angle, self).__setattr__("angle_type", value)
         else:
             super(Angle, self).__setattr__(key, value)
+
+    @model_validator(mode="before")
+    @classmethod
+    def set_dependent_value_default(cls, data):
+        """Automatically set bonds for this angle if connection_members is defined."""
+        if "bonds" not in data and "connection_members" in data:
+            atoms = data["connection_members"]
+            data["bonds"] = (
+                Bond(connection_members=(atoms[0], atoms[1])),
+                Bond(connection_members=(atoms[1], atoms[2])),
+            )
+        return data

gmso/core/bond.py

@@ -26,6 +26,8 @@ class Bond(Connection):
 
     __members_creator__: ClassVar[Callable] = Atom.model_validate
 
+    connectivity: ClassVar[Tuple[Tuple[int]]] = ((0, 1),)
+
     connection_members_: Tuple[Atom, Atom] = Field(
         ...,
         description="The 2 atoms involved in the bond.",
@@ -46,12 +48,20 @@ class Bond(Connection):
         """,
         alias="restraint",
     )
+
+    bond_order_: Optional[float] = Field(
+        default=None,
+        description="Bond order of this bond.",
+        alias="bond_order",
+    )
+
     model_config = ConfigDict(
         alias_to_fields=dict(
             **Connection.model_config["alias_to_fields"],
             **{
                 "bond_type": "bond_type_",
                 "restraint": "restraint_",
+                "bond_order": "bond_order_",
             },
         )
     )
@@ -71,6 +81,16 @@ def restraint(self):
         """Return the restraint of this bond."""
         return self.__dict__.get("restraint_")
 
+    @property
+    def bond_order(self):
+        """Return the bond_order of this bond."""
+        return self.__dict__.get("bond_order_")
+
+    @bond_order.setter
+    def bond_order(self, order):
+        """Set the bond_order of this bond."""
+        self._bond_order = order
+
     def equivalent_members(self):
         """Get a set of the equivalent connection member tuples.
 

gmso/core/dihedral.py

@@ -1,9 +1,10 @@
 from typing import Callable, ClassVar, Optional, Tuple
 
-from pydantic import ConfigDict, Field
+from pydantic import ConfigDict, Field, model_validator
 
 from gmso.abc.abstract_connection import Connection
 from gmso.core.atom import Atom
+from gmso.core.bond import Bond
 from gmso.core.dihedral_type import DihedralType
 
 
@@ -28,12 +29,24 @@ class Dihedral(Connection):
 
     __members_creator__: ClassVar[Callable] = Atom.model_validate
 
+    connectivity: ClassVar[Tuple[Tuple[int]]] = ((0, 1), (1, 2), (2, 3))
+
     connection_members_: Tuple[Atom, Atom, Atom, Atom] = Field(
         ...,
         description="The 4 atoms involved in the dihedral.",
         alias="connection_members",
     )
 
+    bonds_: Tuple[Bond, Bond, Bond] = Field(
+        default=None,
+        description="""
+        List of connection bonds.
+        Ordered to align with connection_members, such that self.bonds_[0] is
+        the bond between (self.connection_members[0], self.connection_members[1]).
+        """,
+        alias="bonds",
+    )
+
     dihedral_type_: Optional[DihedralType] = Field(
         default=None,
         description="DihedralType of this dihedral.",
@@ -50,6 +63,7 @@ class Dihedral(Connection):
         """,
         alias="restraint",
     )
+
     model_config = ConfigDict(
         alias_to_fields=dict(
             **Connection.model_config["alias_to_fields"],
@@ -74,6 +88,19 @@ def restraint(self):
         """Return the restraint of this dihedral."""
         return self.__dict__.get("restraint_")
 
+    @property
+    def bonds(self):
+        """Return the bonds that makeup this dihedral.
+
+        Connectivity is ((0,1), (1,2), (2,3))
+        """
+        return self.__dict__.get("bonds_")
+
+    @property
+    def bonds_orders(self):
+        """Return the bond_order strings of this dihedral."""
+        return "".join([b.bond_order for b in self.bonds])
+
     def equivalent_members(self):
         """Get a set of the equivalent connection member tuples
 
@@ -99,3 +126,16 @@ def __setattr__(self, key, value):
             super(Dihedral, self).__setattr__("dihedral_type_", value)
         else:
             super(Dihedral, self).__setattr__(key, value)
+
+    @model_validator(mode="before")
+    @classmethod
+    def set_dependent_value_default(cls, data):
+        """Automatically set bonds for this dihedral if connection_members is defined."""
+        if "bonds" not in data and "connection_members" in data:
+            atoms = data["connection_members"]
+            data["bonds"] = (
+                Bond(connection_members=(atoms[0], atoms[1])),
+                Bond(connection_members=(atoms[1], atoms[2])),
+                Bond(connection_members=(atoms[2], atoms[3])),
+            )
+        return data