"platforms/reference/tests/TestReferenceSettle.cpp" did not exist on "df4b64cb0058d216076e08fb19aee7892ad03673"
Commit d85ccb06 authored by John Chodera's avatar John Chodera
Browse files

Fix some sphinx errors

parent ad0ee95f
...@@ -117,6 +117,7 @@ class CharmmPsfFile(object): ...@@ -117,6 +117,7 @@ class CharmmPsfFile(object):
This structure has numerous attributes that are lists of the elements of This structure has numerous attributes that are lists of the elements of
this structure, including atoms, bonds, torsions, etc. The attributes are this structure, including atoms, bonds, torsions, etc. The attributes are
- residue_list - residue_list
- atom_list - atom_list
- bond_list - bond_list
...@@ -713,7 +714,7 @@ class CharmmPsfFile(object): ...@@ -713,7 +714,7 @@ class CharmmPsfFile(object):
solvent. solvent.
implicitSolventSaltConc : float=0.0*u.moles/u.liter implicitSolventSaltConc : float=0.0*u.moles/u.liter
Salt concentration for GB simulations. Converted to Debye length Salt concentration for GB simulations. Converted to Debye length
`kappa' ``kappa``
temperature : float=298.15*u.kelvin temperature : float=298.15*u.kelvin
Temperature used in the salt concentration-to-kappa conversion for Temperature used in the salt concentration-to-kappa conversion for
GB salt concentration term GB salt concentration term
......
...@@ -445,16 +445,18 @@ class ForceField(object): ...@@ -445,16 +445,18 @@ class ForceField(object):
generator : function generator : function
A function that will be called when a residue is encountered that does not match an existing forcefield template. A function that will be called when a residue is encountered that does not match an existing forcefield template.
When a residue without a template is encountered, the `generator` function is called with: When a residue without a template is encountered, the ``generator`` function is called with:
:: ::
success = generator(forcefield, residue) success = generator(forcefield, residue)
```
where `forcefield` is the calling `ForceField` object and `residue` is a simtk.openmm.app.topology.Residue object. where ``forcefield`` is the calling ``ForceField`` object and ``residue`` is a simtk.openmm.app.topology.Residue object.
``generator`` must conform to the following API:
`generator` must conform to the following API:
:: ::
generator API
Parameters Parameters
---------- ----------
forcefield : simtk.openmm.app.ForceField forcefield : simtk.openmm.app.ForceField
......
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