Moved "Open Questions" from the SMIRNOFF spec page and put them in #120

openforcefield · Apr 5, 2019 · 4d26d0c · 4d26d0c
1 parent f998e2c
commit 4d26d0c
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 14 deletions.
diff --git a/The-SMIRNOFF-force-field-format.md b/The-SMIRNOFF-force-field-format.md
@@ -675,12 +675,5 @@ This is a backwards-incompatible overhaul of the SMIRNOFF 0.1 draft specificatio
 
 Initial draft specification.
 
-## Open Questions
 
 
-### How should we use multiple conformations in charging?
-
-Should we follow the RESP approach, where the charges or averaged?
-Or the ELF approach, where we use some kind of energy function to evaluate which single conformer is used to compute which conformer is to be used for quantum chemical calculations?
-What scheme should we use to generate the conformers in a deterministic manner?
-
diff --git a/docs/examples.rst b/docs/examples.rst
@@ -8,12 +8,10 @@ These examples are described in more detail below.
 
 .. mdinclude:: ../examples/SMIRNOFF_comparison/README.md
 
-.. mdinclude:: ../examples/forcefield_modification/README.md
-
-.. mdinclude:: ../examples/mixedFF_structure/README.md
-
-.. mdinclude:: ../examples/partial_bondorder/README.md
+.. mdinclude:: ../examples/conversion_amber_gromacs/README.md
 
-.. mdinclude:: ../examples/host_guest_simulation/README.md
+.. mdinclude:: ../examples/forcefield_modification/README.md
 
 .. mdinclude:: ../examples/label_molecule/README.md
+
+.. mdinclude:: ../examples/mixedFF_complex/README.md
diff --git a/openforcefield/topology/molecule.py b/openforcefield/topology/molecule.py
@@ -1248,7 +1248,7 @@ class Bond(Serializable):
 
     Attributes
     ----------
-    atom1, atom2 : Atom
+    atom1, atom2 : openforcefield.topology.Atom
         Atoms involved in the bond
     bondtype : int
         Discrete bond type representation for the Open Forcefield aromaticity model