"...reference/src/SimTKReference/ReferenceCustomBondIxn.h" did not exist on "76e2849ccf0aea4dd118a77e8d7d7e66b1107ab0"
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):
This structure has numerous attributes that are lists of the elements of
this structure, including atoms, bonds, torsions, etc. The attributes are
- residue_list
- atom_list
- bond_list
......@@ -713,7 +714,7 @@ class CharmmPsfFile(object):
solvent.
implicitSolventSaltConc : float=0.0*u.moles/u.liter
Salt concentration for GB simulations. Converted to Debye length
`kappa'
``kappa``
temperature : float=298.15*u.kelvin
Temperature used in the salt concentration-to-kappa conversion for
GB salt concentration term
......
......@@ -445,16 +445,18 @@ class ForceField(object):
generator : function
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)
```
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
----------
forcefield : simtk.openmm.app.ForceField
......
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