Merge branch 'main' into cassandra-gmso

.github/workflows/CI.yaml

@@ -20,7 +20,7 @@ jobs:
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11"]
-        pydantic-version: ["1", "2"]
+        pydantic-version: ["2"]
 
     defaults:
       run:

codecov.yml

@@ -2,3 +2,4 @@ ignore:
   - "gmso/examples"
   - "gmso/tests"
   - "gmso/formats/networkx.py"
+  - "gmso/external/convert_foyer_xml.py"

docs/installation.rst

@@ -50,8 +50,8 @@ Once all dependencies have been installed and the ``conda`` environment has been
 Supported Python Versions
 -------------------------
 
-Python 3.7 is the recommend version for users. It is the only version on which
-development and testing consistently takes place.  Older (3.6) and newer (3.8+)
+Python 3.8-3.11 is the recommend version for users. It is the only version on which
+development and testing consistently takes place.  Older (3.6-3.7) and newer (3.12+)
 versions of Python 3 are likely to work but no guarantee is made and, in
 addition, some dependencies may not be available for other versions.  No effort
 is made to support Python 2 because it is considered obsolete as of early 2020.

gmso/core/forcefield.py

@@ -8,10 +8,19 @@
 
 from lxml import etree
 
+try:
+    from pydantic.v1 import ValidationError
+except:
+    from pydantic import ValidationError
+
 from gmso.core.element import element_by_symbol
-from gmso.exceptions import GMSOError, MissingPotentialError
+from gmso.exceptions import (
+    ForceFieldParseError,
+    GMSOError,
+    MissingPotentialError,
+)
 from gmso.utils._constants import FF_TOKENS_SEPARATOR
-from gmso.utils.decorators import deprecate_kwargs
+from gmso.utils.decorators import deprecate_function, deprecate_kwargs
 from gmso.utils.ff_utils import (
     parse_ff_atomtypes,
     parse_ff_connection_types,
@@ -45,10 +54,8 @@ class ForceField(object):
 
     Parameters
     ----------
-    name : str
-        Name of the forcefield, default 'ForceField'
-    version : str
-        a cannonical semantic version of the forcefield, default 1.0.0
+    xml_loc : str
+        Path to the forcefield xml. The forcefield xml can be either in Foyer or GMSO style.
     strict: bool, default=True
         If true, perform a strict validation of the forcefield XML file
     greedy: bool, default=True
@@ -104,6 +111,7 @@ def __init__(
                 "ffutils",
             ]:
                 ff = ForceField.xml_from_forcefield_utilities(xml_loc)
+
             else:
                 raise (
                     GMSOError(
@@ -565,10 +573,14 @@ def __eq__(self, other):
 
     @classmethod
     def xml_from_forcefield_utilities(cls, filename):
-        from forcefield_utilities.xml_loader import GMSOFFs
-
-        loader = GMSOFFs()
-        ff = loader.load(filename).to_gmso_ff()
+        from forcefield_utilities.xml_loader import FoyerFFs, GMSOFFs
+
+        try:
+            loader = GMSOFFs()
+            ff = loader.load(filename).to_gmso_ff()
+        except (ForceFieldParseError, FileNotFoundError, ValidationError):
+            loader = FoyerFFs()
+            ff = loader.load(filename).to_gmso_ff()
         return ff
 
     def to_xml(self, filename, overwrite=False, backend="gmso"):
@@ -723,6 +735,9 @@ def _xml_from_gmso(self, filename, overwrite=False):
         )
 
     @classmethod
+    @deprecate_function(
+        "The internal `from_xml` will be deprecated soon. Please load the XML with the `xml_from_forcefield_utilities`."
+    )
     def from_xml(cls, xmls_or_etrees, strict=True, greedy=True):
         """Create a gmso.Forcefield object from XML File(s).
 

gmso/core/topology.py

@@ -647,6 +647,61 @@ def get_scaling_factors(self, *, molecule_id=None):
             ]
         )
 
+    def remove_site(self, site):
+        """Remove a site from the topology.
+
+        Parameters
+        ----------
+        site : gmso.core.Site
+            The site to be removed.
+
+        Notes
+        -----
+        When a site is removed, any connections that site belonged
+        to are also removed.
+
+        See Also
+        --------
+        gmso.core.topology.Topology.iter_connections_by_site
+            The method that shows all connections belonging to a specific site
+        """
+        if site not in self._sites:
+            raise ValueError(
+                f"Site {site} is not currently part of this topology."
+            )
+        site_connections = [
+            conn for conn in self.iter_connections_by_site(site)
+        ]
+        for conn in site_connections:
+            self.remove_connection(conn)
+        self._sites.remove(site)
+
+    def remove_connection(self, connection):
+        """Remove a connection from the topology.
+
+        Parameters
+        ----------
+        connection : gmso.abc.abstract_conneciton.Connection
+            The connection to be removed from the topology
+
+        Notes
+        -----
+        The sites that belong to this connection are
+        not removed from the topology.
+        """
+        if connection not in self.connections:
+            raise ValueError(
+                f"Connection {connection} is not currently part of this topology."
+            )
+        if isinstance(connection, gmso.core.bond.Bond):
+            self._bonds.remove(connection)
+        elif isinstance(connection, gmso.core.angle.Angle):
+            self._angles.remove(connection)
+        elif isinstance(connection, gmso.core.dihedral.Dihedral):
+            self._dihedrals.remove(connection)
+        elif isinstance(connection, gmso.core.improper.Improper):
+            self._impropers.remove(connection)
+
     def set_scaling_factors(self, lj, electrostatics, *, molecule_id=None):
         """Set both lj and electrostatics scaling factors."""
         self.set_lj_scale(
@@ -831,7 +886,6 @@ def add_connection(self, connection, update_types=False):
             Improper: self._impropers,
         }
         connections_sets[type(connection)].add(connection)
-
         if update_types:
             self.update_topology()
 
@@ -1367,6 +1421,44 @@ def iter_sites_by_molecule(self, molecule_tag):
         else:
             return self.iter_sites("molecule", molecule_tag)
 
+    def iter_connections_by_site(self, site, connections=None):
+        """Iterate through this topology's connections which contain
+        this specific site.
+
+        Parameters
+        ----------
+        site : gmso.core.Site
+            Site to limit connections search to.
+        connections : set or list or tuple, optional, default=None
+            The connection types to include in the search.
+            If None, iterates through all of a site's connections.
+            Options include "bonds", "angles", "dihedrals", "impropers"
+
+        Yields
+        ------
+        gmso.abc.abstract_conneciton.Connection
+            Connection where site is in Connection.connection_members
+
+        """
+        if site not in self._sites:
+            raise ValueError(
+                f"Site {site} is not currently part of this topology."
+            )
+        if connections is None:
+            connections = ["bonds", "angles", "dihedrals", "impropers"]
+        else:
+            connections = set([option.lower() for option in connections])
+            for option in connections:
+                if option not in ["bonds", "angles", "dihedrals", "impropers"]:
+                    raise ValueError(
+                        "Valid connection types are limited to: "
+                        '"bonds", "angles", "dihedrals", "impropers"'
+                    )
+        for conn_str in connections:
+            for conn in getattr(self, conn_str):
+                if site in conn.connection_members:
+                    yield conn
+
     def create_subtop(self, label_type, label):
         """Create a new Topology object from a molecule or graup of the current Topology.
 

gmso/external/__init__.py

@@ -1,5 +1,4 @@
 """Support for various in-memory representations of chemical systems."""
-from .convert_foyer_xml import from_foyer_xml
 from .convert_hoomd import (
     to_gsd_snapshot,
     to_hoomd_forcefield,

gmso/external/convert_foyer_xml.py

@@ -4,8 +4,12 @@
 from lxml import etree
 
 from gmso.exceptions import ForceFieldParseError
+from gmso.utils.decorators import deprecate_function
 
 
+@deprecate_function(
+    "The `from_foyer_xml` method will be deprecated soon. Please use the package `forcefield-utilities.FoyerFFs`."
+)
 def from_foyer_xml(
     foyer_xml, gmso_xml=None, overwrite=False, validate_foyer=False
 ):

gmso/tests/base_test.py

@@ -1,4 +1,3 @@
-import forcefield_utilities as ffutils
 import foyer
 import mbuild as mb
 import numpy as np
@@ -17,7 +16,6 @@
 from gmso.core.pairpotential_type import PairPotentialType
 from gmso.core.topology import Topology
 from gmso.external import from_mbuild, from_parmed
-from gmso.external.convert_foyer_xml import from_foyer_xml
 from gmso.parameterization import apply
 from gmso.tests.utils import get_path
 from gmso.utils.io import get_fn
@@ -74,11 +72,7 @@ def benzene_ua_box(self):
     @pytest.fixture
     def typed_benzene_ua_system(self, benzene_ua_box):
         top = benzene_ua_box
-        trappe_benzene = (
-            ffutils.FoyerFFs()
-            .load(get_path("benzene_trappe-ua.xml"))
-            .to_gmso_ff()
-        )
+        trappe_benzene = ForceField(get_path("benzene_trappe-ua.xml"))
         top = apply(top=top, forcefields=trappe_benzene, remove_untyped=True)
         return top
 
@@ -104,7 +98,7 @@ def benzene_aa_box(self):
     @pytest.fixture
     def typed_benzene_aa_system(self, benzene_aa_box):
         top = benzene_aa_box
-        oplsaa = ffutils.FoyerFFs().load("oplsaa").to_gmso_ff()
+        oplsaa = ForceField("oplsaa")
         top = apply(top=top, forcefields=oplsaa, remove_untyped=True)
         return top
 
@@ -281,41 +275,25 @@ def typed_tip3p_rigid_system(self, water_system):
     def foyer_fullerene(self):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn("fullerene.xml"), overwrite=True)
-        gmso_ff = ForceField("fullerene_gmso.xml")
-
-        return gmso_ff
+        return ForceField(get_fn("fullerene.xml"))
 
     @pytest.fixture
     def foyer_periodic(self):
-        # TODO: this errors out with backend="ffutils"
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn("oplsaa-periodic.xml"), overwrite=True)
-        gmso_ff = ForceField("oplsaa-periodic_gmso.xml", backend="gmso")
-
-        return gmso_ff
+        return ForceField(get_fn("oplsaa-periodic.xml"))
 
     @pytest.fixture
     def foyer_urey_bradley(self):
-        # TODO: this errors out with backend="ffutils"
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(get_fn("charmm36_cooh.xml"), overwrite=True)
-        gmso_ff = ForceField("charmm36_cooh_gmso.xml", backend="gmso")
-
-        return gmso_ff
+        return ForceField(get_fn("charmm36_cooh.xml"))
 
     @pytest.fixture
     def foyer_rb_torsion(self):
         from foyer.tests.utils import get_fn
 
-        from_foyer_xml(
-            get_fn("refs-multi.xml"), overwrite=True, validate_foyer=True
-        )
-        gmso_ff = ForceField("refs-multi_gmso.xml")
-
-        return gmso_ff
+        return ForceField(get_fn("refs-multi.xml"))
 
     @pytest.fixture
     def methane(self):