From 1a3e96c1d29d3bc5b954ada36cf6bfe7528df81a Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Fri, 27 Sep 2024 15:22:34 -0500 Subject: [PATCH] DOC: Document that charges on the topology are ignored --- openff/interchange/components/interchange.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/openff/interchange/components/interchange.py b/openff/interchange/components/interchange.py index 4b3fd94e..98906750 100644 --- a/openff/interchange/components/interchange.py +++ b/openff/interchange/components/interchange.py @@ -109,7 +109,8 @@ 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. @@ -121,6 +122,10 @@ 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