Commit 4f48402f authored by John Chodera's avatar John Chodera
Browse files

Fix typo, and add documentation for 'ordering'

parent bf57b12e
......@@ -2331,6 +2331,22 @@ second atom has class OS and the third has class P:
<Proper class1="" class2="OS" class3="P" class4="" periodicity1="3" phase1="0.0" k1="1.046"/>
The :code:`<PeriodicTorsionForce>` tag also supports an optional
:code:`ordering` attribute to provide better compatibility with the way
impropers are assigned in different simulation packages:
* :code:`ordering="default"` specifies the default behavior if the attribute
is omitted.
* :code:`ordering="amber"` produces behavior that replicates the behavior of
AmberTools LEaP
* :code:`ordering="charmm"` produces behavior more consistent with CHARMM
* :code:`ordering="smirnoff"` allows multiple impropers to be added using
exact matching to replicate the beheavior of `SMIRNOFF <https://open-forcefield-toolkit.readthedocs.io/en/latest/smirnoff.html>`_
impropers
Different :code:`<PeriodicTorsionForce>` tags can specify different :code:`ordering`
values to be used for the sub-elements appearing within their tags.
<RBTorsionForce>
================
......
......@@ -970,7 +970,7 @@ class TestForceField(unittest.TestCase):
for index in range(force.getNumTorsions()):
i,j,k,l,_,_,_ = force.getTorsionParameters(index)
created_torsions.add((i,j,k,l))
expected_torsions = set((0,3,1,2), (0,1,2,3), (0,2,3,1))
expected_torsions = set([(0,3,1,2), (0,1,2,3), (0,2,3,1)])
self.assertEqual(expected_torsions, created_torsions)
def test_Disulfides(self):
......
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