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tsoc
openmm
Commits
d85ccb06
"...reference/src/SimTKReference/ReferenceCustomBondIxn.h" did not exist on "76e2849ccf0aea4dd118a77e8d7d7e66b1107ab0"
Commit
d85ccb06
authored
Aug 15, 2017
by
John Chodera
Browse files
Fix some sphinx errors
parent
ad0ee95f
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21 additions
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18 deletions
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-18
wrappers/python/simtk/openmm/app/charmmpsffile.py
wrappers/python/simtk/openmm/app/charmmpsffile.py
+14
-13
wrappers/python/simtk/openmm/app/forcefield.py
wrappers/python/simtk/openmm/app/forcefield.py
+7
-5
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wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @
d85ccb06
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@@ -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
...
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wrappers/python/simtk/openmm/app/forcefield.py
View file @
d85ccb06
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@@ -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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