Merge pull request #1064 from openforcefield/doc-topology-charges

Document that topology charges are ignored

docs/using/edges.md

@@ -11,6 +11,10 @@ Currently, the `Interchange.topology` attribute is defined by the OpenFF Toolkit
 
 For example, `Interchange.topology.get_positions()` will never include positions of virtual sites. To get the positions of a system with virtual sites included, use `Interchange.get_positions()`. The default behavior of `Interchange.positions` is also to return positions without virtual sites, but this may change in the future.
 
+### Existing charges are ignored by default
+
+`Molecule` and `Topology` objects can store partial charges, but these are ignored by default in methods like `Interchange.from_smirnoff`. This is because partial charges in SMIRNOFF force fields are defined by sections in the force field. To override this behavior, use the `charge_from_molecules` argument. Be aware that charges, and as a result most physics, differ from what's perscribed by the contents of the force field.
+
 ## Quirks of `from_openmm`
 
 ### Modified masses are ignored

openff/interchange/components/interchange.py

@@ -110,7 +110,8 @@ def from_smirnoff(
             positions are taken from the molecules in topology, if present on all molecules.
         charge_from_molecules : `List[openff.toolkit.molecule.Molecule]`, optional
             If specified, partial charges will be taken from the given molecules
-            instead of being determined by the force field.
+            instead of being determined by the force field. In either case, charges
+            on the input topology are ignored.
         partial_bond_orders_from_molecules : List[openff.toolkit.molecule.Molecule], optional
             If specified, partial bond orders will be taken from the given molecules
             instead of being determined by the force field.
@@ -122,6 +123,10 @@ def from_smirnoff(
         If the `Molecule` objects in the `topology` argument each contain conformers, the returned `Interchange` object
         will have its positions set via concatenating the 0th conformer of each `Molecule`.
 
+        If the `Molecule` objects in the `topology` argument have stored partial charges, these are ignored and charges
+        are assigned according to the contents of the force field. To override the force field and use preset charges,
+        use the `charge_from_molecules` argument.
+
         Examples
         --------
         Generate an Interchange object from a single-molecule (OpenFF) topology and