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tsoc
openmm
Commits
d85ccb06
"platforms/reference/tests/TestReferenceSettle.cpp" did not exist on "df4b64cb0058d216076e08fb19aee7892ad03673"
Commit
d85ccb06
authored
Aug 15, 2017
by
John Chodera
Browse files
Fix some sphinx errors
parent
ad0ee95f
Changes
2
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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):
...
@@ -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
...
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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):
...
@@ -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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